------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for openbabel-3.1.1.178: CAIRO=on: PNG support via cairo library GUI=on: GUI (Graphical User Interface) support ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PKG_CONFIG=pkgconf XDG_DATA_HOME=/construction/science/openbabel XDG_CONFIG_HOME=/construction/science/openbabel XDG_CACHE_HOME=/construction/science/openbabel/.cache HOME=/construction/science/openbabel TMPDIR="/tmp" PATH=/construction/science/openbabel/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/openbabel/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 WX_CONFIG=/usr/local/bin/wxgtk3u-3.0-config LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/science/openbabel XDG_CONFIG_HOME=/construction/science/openbabel XDG_CACHE_HOME=/construction/science/openbabel/.cache HOME=/construction/science/openbabel TMPDIR="/tmp" PATH=/construction/science/openbabel/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/openbabel/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 WX_CONFIG=/usr/local/bin/wxgtk3u-3.0-config LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/science/openbabel/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- VERSION=3.1.1 CAIRO="" NO_CAIRO="@comment " GUI="" NO_GUI="@comment " CMAKE_BUILD_TYPE="release" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/openbabel" EXAMPLESDIR="share/examples/openbabel" DATADIR="share/openbabel" WWWDIR="www/openbabel" ETCDIR="etc/openbabel" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- CAIRO="" NO_CAIRO="@comment " GUI="" NO_GUI="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/openbabel DOCSDIR=/usr/local/share/doc/openbabel EXAMPLESDIR=/usr/local/share/examples/openbabel WWWDIR=/usr/local/www/openbabel ETCDIR=/usr/local/etc/openbabel SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/rapidjson-1.1.0.709.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/libuv-1.46.0.pkg Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/rhash-1.4.3.pkg Installing /packages/All/pkg-1.19.2.pkg Installing /packages/All/liblz4-1.9.4,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/zstd-1.5.5.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libarchive-3.6.2,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/ncurses-6.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/cmake-core-3.26.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gmp-6.2.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/mpfr-4.2.0_1,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/mpc-1.3.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.40_4,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gcc12-12.2.0_6.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from gcc12-12.2.0_6: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc12 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/blas-3.11.0_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/lapack-3.11.0_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/eigen-3.4.0_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/pkgconf-1.8.1,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/ccache-3.7.12_4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) create symlink for gcc12 create symlink for gcc12 (world) create symlink for g++12 create symlink for g++12 (world) create symlink for cpp12 create symlink for cpp12 (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. Installing /packages/All/icu-73.2,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/boost-libs-1.82.0_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from boost-libs-1.82.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/maeparser-1.3.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/coordgenlibs-3.0.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/brotli-1.0.9,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/png-1.6.39.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/freetype2-2.12.1_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from freetype2-2.12.1_2: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). Installing /packages/All/fontconfig-2.14.2,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Running fc-cache to build fontconfig cache... Installing /packages/All/libffi-3.4.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/pcre2-10.42.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/readline-8.2.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libxml2-2.10.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libiconv-1.17.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/mpdecimal-2.5.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/python39-3.9.17.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 Installing /packages/All/glib-2.76.4,2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Generating GIO modules cache Compiling glib schemas No schema files found: doing nothing. Installing /packages/All/libXau-1.0.9.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/xorgproto-2022.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXdmcp-1.1.3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libxcb-1.15_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libX11-1.8.6,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXext-1.3.4,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libglvnd-1.6.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/pixman-0.42.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXrender-0.9.10_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/cairo-1.17.4_2,3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/graphite2-1.3.14.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/harfbuzz-7.3.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libgpg-error-1.47.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libgcrypt-1.10.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libunistring-1.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libidn2-2.3.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libpsl-0.21.2_3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default Installing /packages/All/libedit-3.1.20221030,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/sqlite3-3.42.0,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/nettle-3.9.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libtasn1-4.19.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/p11-kit-0.24.1_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gnutls-3.7.9.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libproxy-0.4.17_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gsettings-desktop-schemas-42.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Compiling glib schemas Installing /packages/All/glib-networking-2.76.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Generating GIO modules cache Installing /packages/All/libsoup-2.74.3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from libsoup-2.74.3: -- libsoup can use NTLM authentication if it is compiled with the SMB option. To use it, you must install a port that provides NTLM, like net/samba412 or net/samba413. Installing /packages/All/libdeflate-1.18.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/jbigkit-2.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/jpeg-turbo-2.1.5.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/tiff-4.4.0_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libmspack-0.11alpha.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/perl5-5.32.1_3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/hunspell-1.7.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/enchant2-2.2.15_3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/fribidi-1.0.13.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/giflib-5.2.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/webp-1.3.0_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libsecret-0.20.5_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/shared-mime-info-2.2_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Building the Shared MIME-Info database cache Installing /packages/All/gdk-pixbuf2-2.42.10.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Generating gdk-pixbuf modules cache Installing /packages/All/libnotify-0.8.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/hyphen-2.8.8.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/lcms2-2.15_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/openjpeg-2.5.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/harfbuzz-icu-7.3.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/woff2-1.0.2_4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libepoll-shim-0.0.20230411.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/wayland-1.22.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from wayland-1.22.0: -- Wayland requires XDG_RUNTIME_DIR to be defined to a path that will contain "wayland-%d" unix(4) sockets. This is usually handled by consolekit2 (via ck-launch-session) or pam_xdg (via login). Installing /packages/All/xkeyboard-config-2.34_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libxkbcommon-1.5.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from libxkbcommon-1.5.0: -- If arrow keys don't work under X11 switch to legacy rules e.g., For sh/bash/ksh/zsh run and (optionally) add into ~/.profile: export XKB_DEFAULT_RULES=xorg For csh/tcsh run and (optionally) add into ~/.login: setenv XKB_DEFAULT_RULES xorg Installing /packages/All/libwpe-1.12.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libepoxy-1.5.9.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/wpebackend-fdo-1.12.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libICE-1.1.0_1,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libSM-1.2.3,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/dbus-1.14.6,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/libXfixes-6.0.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXi-1.8,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXtst-1.2.3_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/at-spi2-core-2.48.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libdaemon-0.14_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/dbus-glib-0.112.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gdbm-1.23.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libevent-2.1.12.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gnome_subr-1.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/avahi-app-0.8_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/libpaper-1.1.28.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/cups-2.4.6.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. Installing /packages/All/libdatrie-0.2.13_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libthai-0.1.29.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from libthai-0.1.29: -- ===> NOTICE: The libthai port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing Installing /packages/All/libfontenc-1.1.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/mkfontscale-1.2.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/font-bh-ttf-1.0.3_4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Running fc-cache to build fontconfig cache... Installing /packages/All/font-misc-meltho-1.0.3_4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/font-misc-ethiopic-1.0.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/encodings-1.0.5,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/dejavu-2.37_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Running fc-cache to build fontconfig cache... ===== Message from dejavu-2.37_1: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Installing /packages/All/xorg-fonts-truetype-7.7_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXft-2.3.7.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/pango-1.50.14.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/hicolor-icon-theme-0.17.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gtk-update-icon-cache-3.24.31.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/adwaita-icon-theme-40.1.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Generating GTK icon cache for /usr/local/share/icons/Adwaita Installing /packages/All/librsvg2-rust-2.56.3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Generating gdk-pixbuf modules cache Installing /packages/All/libXcomposite-0.4.6,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXcursor-1.2.0.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXdamage-1.1.6.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXinerama-1.1.4_2,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXrandr-1.5.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gtk3-3.24.34_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Generating GTK icon cache for /usr/local/share/icons/hicolor Compiling glib schemas Installing /packages/All/libxslt-1.1.37.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default Installing /packages/All/libunwind-20211201_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gstreamer1-1.22.5.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gobject-introspection-1.76.1,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/json-glib-1.6.6.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/geoclue-2.5.7.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/orc-0.4.34_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libnice-0.1.21_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/iso-codes-4.7.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gstreamer1-plugins-1.22.5.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gstreamer1-plugins-bad-1.22.5.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/pygobject3-common-3.42.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/py39-cairo-1.21.0,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/py39-gobject3-3.42.2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/graphene-1.10.8.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libGLU-9.0.2_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gstreamer1-plugins-gl-1.22.5.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXt-1.2.1,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/webkit2-gtk3-2.34.6_7.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXxf86vm-1.1.4_3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/wx30-gtk3-3.0.5.1_2.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required UNFLAVORED devel/binutils -> use devel/binutils@native UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default SUCCEEDED 00:01:25 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> openbabel-3.1.1.178 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> openbabel-3.1.1.178 depends on file: /usr/local/sbin/pkg - found => openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/openbabel/openbabel/tar.gz/3-1-1-178-g2b211d6ac?dummy=/openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.tar.gz fetch: https://codeload.github.com/openbabel/openbabel/tar.gz/3-1-1-178-g2b211d6ac?dummy=/openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.tar.gz: size unknown fetch: https://codeload.github.com/openbabel/openbabel/tar.gz/3-1-1-178-g2b211d6ac?dummy=/openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.tar.gz: size of remote file is not known openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 0 B 0 Bps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 1024 kB 1223 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 3712 kB 2623 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 6624 kB 2963 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 9856 kB 3242 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 12 MB 3453 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 16 MB 3510 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 19 MB 3628 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 23 MB 3894 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 27 MB 4058 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 31 MB 3900 kBps openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.t 35 MB 3385 kBps 10s ===> Fetching all distfiles required by openbabel-3.1.1.178 for building SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> openbabel-3.1.1.178 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by openbabel-3.1.1.178 for building => SHA256 Checksum OK for openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> openbabel-3.1.1.178 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by openbabel-3.1.1.178 for building ===> Extracting for openbabel-3.1.1.178 ===> openbabel-3.1.1.178 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by openbabel-3.1.1.178 for building => SHA256 Checksum OK for openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.tar.gz. Extracted Memory Use: 242.63M SUCCEEDED 00:00:06 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for openbabel-3.1.1.178 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> openbabel-3.1.1.178 depends on package: rapidjson>0 - found ===> openbabel-3.1.1.178 depends on file: /usr/local/bin/cmake - found ===> openbabel-3.1.1.178 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> openbabel-3.1.1.178 depends on package: pkgconf>=1.3.0_1 - found ===> openbabel-3.1.1.178 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> openbabel-3.1.1.178 depends on shared library: libmaeparser.so - found (/usr/local/lib/libmaeparser.so) ===> openbabel-3.1.1.178 depends on shared library: libcoordgen.so - found (/usr/local/lib/libcoordgen.so) ===> openbabel-3.1.1.178 depends on shared library: libboost_thread.so - found (/usr/local/lib/libboost_thread.so) ===> openbabel-3.1.1.178 depends on shared library: libcairo.so - found (/usr/local/lib/libcairo.so) ===> openbabel-3.1.1.178 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> openbabel-3.1.1.178 depends on shared library: libwx_baseu-3.0.so - found (/usr/local/lib/libwx_baseu-3.0.so) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> openbabel-3.1.1.178 depends on package: rapidjson>0 - found ===> openbabel-3.1.1.178 depends on file: /usr/local/bin/cmake - found ===> openbabel-3.1.1.178 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> openbabel-3.1.1.178 depends on package: pkgconf>=1.3.0_1 - found ===> openbabel-3.1.1.178 depends on file: /usr/local/bin/ccache - found ===> openbabel-3.1.1.178 depends on shared library: libmaeparser.so - found (/usr/local/lib/libmaeparser.so) ===> openbabel-3.1.1.178 depends on shared library: libcoordgen.so - found (/usr/local/lib/libcoordgen.so) ===> openbabel-3.1.1.178 depends on shared library: libboost_thread.so - found (/usr/local/lib/libboost_thread.so) ===> openbabel-3.1.1.178 depends on shared library: libcairo.so - found (/usr/local/lib/libcairo.so) ===> openbabel-3.1.1.178 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> openbabel-3.1.1.178 depends on shared library: libwx_baseu-3.0.so - found (/usr/local/lib/libwx_baseu-3.0.so) ===> Configuring for openbabel-3.1.1.178 /usr/bin/env WRKSRC=/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac REWARNFILE=/construction/science/openbabel/reinplace_warnings.txt /bin/sh /xports/Mk/Scripts/sed_checked.sh -e '/pkgconfig/s,${LIB_INSTALL_DIR},libdata,' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/CMakeLists.txt ===> Performing out-of-source build /bin/mkdir -p /construction/science/openbabel/.build -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:14 (cmake_policy): The OLD behavior for policy CMP0042 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Using included inchi library. -- Found LibXml2: /usr/local/lib/libxml2.so (found version "2.10.4") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Found wxWidgets: -L/usr/local/lib;-pthread;;;-lwx_baseu-3.0;-lwx_gtk3u_core-3.0;-lwx_gtk3u_adv-3.0 (found version "3.0.5") -- Looking for conio.h -- Looking for conio.h - not found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for rpc/xdr.h -- Looking for rpc/xdr.h - not found -- Looking for regex.h -- Looking for regex.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for rint -- Looking for rint - not found -- Looking for snprintf -- Looking for snprintf - found -- Looking for sranddev -- Looking for sranddev - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strncasecmp -- Looking for strncasecmp - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of clock_t -- Check size of clock_t - done -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success Using built-in specs. COLLECT_GCC=/usr/libexec/gcc80/cc COLLECT_LTO_WRAPPER=/usr/libexec/gcc80/lto-wrapper Target: x86_64-pc-dragonflybsd Configured with: DragonFly/x86_64 system compiler (c c++ LTO) Thread model: posix gcc version 8.3 [DragonFly] Release/2019-02-22 CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:318 (find_package) CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:318 (find_package) CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:318 (find_package) -- Found Boost: /usr/local/include (found version "1.82.0") found components: program_options iostreams regex -- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0") CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:434 (find_package) CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:434 (find_package) CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:434 (find_package) CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:434 (find_package) -- Found Boost: /usr/local/include (found version "1.82.0") found components: filesystem iostreams unit_test_framework regex -- maeparser include dir set as '/usr/local/include' -- maeparser libraries set as '/usr/local/lib/libmaeparser.so' -- Maestro formats will be supported. Using MaeParser libraries at /usr/local/lib/libmaeparser.so. -- coordgen include dir set as /usr/local/include -- coordgen libraries set as '/usr/local/lib/libcoordgen.so' -- Coordinate generation with Coordgen will be supported. Using Coordgen libraries at /usr/local/lib/libcoordgen.so. -- Found PkgConfig: /usr/local/bin/pkgconf (found version "1.8.1") -- Found RapidJSON: /usr/local/include (found suitable version "1.1.0", minimum required is "1.1.0") -- JSON formats will be supported. Using RapidJSON 1.1.0 at /usr/local/include -- Checking for module 'cairo' -- Found cairo, version 1.17.4 -- Found Cairo: /usr/local/lib/libcairo.so -- Cairo found. PNG output will be supported. -- Found Perl: /usr/local/bin/perl (found version "5.32.1") CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) src/CMakeLists.txt:6 (find_package) -- Found Boost: /usr/local/include (found suitable version "1.82.0", minimum required is "1.45.0") found components: system -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Found Threads: TRUE CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) tools/CMakeLists.txt:6 (find_package) CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) tools/CMakeLists.txt:6 (find_package) CMake Warning at /usr/local/share/cmake/Modules/FindBoost.cmake:1390 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindBoost.cmake:1514 (_Boost_COMPONENT_DEPENDENCIES) /usr/local/share/cmake/Modules/FindBoost.cmake:2125 (_Boost_MISSING_DEPENDENCIES) tools/CMakeLists.txt:6 (find_package) -- Found Boost: /usr/local/include (found version "1.82.0") found components: program_options iostreams regex -- Looking for getopt -- Looking for getopt - found -- Attempting to build the GUI -- wxWidgets found => GUI will be built CMake Deprecation Warning at scripts/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (8.0s) -- Generating done (1.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_DEBUG FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /construction/science/openbabel/.build SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for openbabel-3.1.1.178 /usr/local/bin/cmake -S/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac -B/construction/science/openbabel/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/openbabel/.build/CMakeFiles /construction/science/openbabel/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- data/CMakeFiles/data_headers.dir/all --- --- src/formats/libinchi/CMakeFiles/inchi.dir/all --- --- data/CMakeFiles/data_headers.dir/all --- /usr/bin/make -f data/CMakeFiles/data_headers.dir/build.make data/CMakeFiles/data_headers.dir/depend --- src/formats/libinchi/CMakeFiles/inchi.dir/all --- /usr/bin/make -f src/formats/libinchi/CMakeFiles/inchi.dir/build.make src/formats/libinchi/CMakeFiles/inchi.dir/depend --- data/CMakeFiles/data_headers.dir/all --- --- data/CMakeFiles/data_headers.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data /construction/science/openbabel/.build /construction/science/openbabel/.build/data /construction/science/openbabel/.build/data/CMakeFiles/data_headers.dir/DependInfo.cmake --- src/formats/libinchi/CMakeFiles/inchi.dir/all --- --- src/formats/libinchi/CMakeFiles/inchi.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/libinchi /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats/libinchi /construction/science/openbabel/.build/src/formats/libinchi/CMakeFiles/inchi.dir/DependInfo.cmake --- data/CMakeFiles/data_headers.dir/all --- /usr/bin/make -f data/CMakeFiles/data_headers.dir/build.make data/CMakeFiles/data_headers.dir/build --- src/formats/libinchi/CMakeFiles/inchi.dir/all --- /usr/bin/make -f src/formats/libinchi/CMakeFiles/inchi.dir/build.make src/formats/libinchi/CMakeFiles/inchi.dir/build --- data/CMakeFiles/data_headers.dir/all --- --- data/atomizationenergies.h --- --- data/atomtyp.h --- --- data/bondtyp.h --- --- data/phmodeldata.h --- --- data/resdata.h --- --- data/ringtyp.h --- --- data/spacegroups.h --- --- data/torlib.h --- --- data/types.h --- --- data/atomizationenergies.h --- [ 0%] Generating atomizationenergies.h --- data/atomtyp.h --- [ 0%] Generating atomtyp.h --- src/formats/libinchi/CMakeFiles/inchi.dir/all --- --- src/formats/libinchi/CMakeFiles/inchi.dir/ichi_bns.c.o --- --- src/formats/libinchi/CMakeFiles/inchi.dir/ichi_io.c.o --- --- src/formats/libinchi/CMakeFiles/inchi.dir/ichican2.c.o --- --- src/formats/libinchi/CMakeFiles/inchi.dir/ichicano.c.o --- --- data/CMakeFiles/data_headers.dir/all --- --- data/atomizationenergies.h --- cd /construction/science/openbabel/.build/data && /usr/local/bin/perl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bin2hex.pl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/atomization-energies.txt AtomicHeatOfFormationData AtomicHeatOfFormationData > atomizationenergies.h --- data/atomtyp.h --- cd /construction/science/openbabel/.build/data && /usr/local/bin/perl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bin2hex.pl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/atomtyp.txt AtomTypeData AtomTypeData > atomtyp.h --- data/phmodeldata.h --- [ 1%] Generating phmodeldata.h cd /construction/science/openbabel/.build/data && /usr/local/bin/perl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bin2hex.pl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/phmodel.txt PhModelData PhModelData > phmodeldata.h --- data/resdata.h --- [ 1%] Generating resdata.h --- data/types.h --- [ 1%] Generating types.h --- data/torlib.h --- [ 1%] Generating torlib.h --- data/resdata.h --- cd /construction/science/openbabel/.build/data && /usr/local/bin/perl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bin2hex.pl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/resdata.txt ResidueData ResidueData > resdata.h --- data/types.h --- cd /construction/science/openbabel/.build/data && /usr/local/bin/perl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bin2hex.pl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/types.txt TypesData TypesData > types.h --- data/torlib.h --- cd /construction/science/openbabel/.build/data && /usr/local/bin/perl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bin2hex.pl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/torlib.txt TorsionDefaults TorsionDefaults > torlib.h --- data/bondtyp.h --- [ 1%] Generating bondtyp.h cd /construction/science/openbabel/.build/data && /usr/local/bin/perl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bin2hex.pl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bondtyp.txt BondTypeData BondTypeData > bondtyp.h --- src/formats/libinchi/CMakeFiles/inchi.dir/all --- [ 2%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichicano.c.o --- data/CMakeFiles/data_headers.dir/all --- --- data/spacegroups.h --- [ 2%] Generating spacegroups.h --- src/formats/libinchi/CMakeFiles/inchi.dir/all --- --- src/formats/libinchi/CMakeFiles/inchi.dir/ichi_bns.c.o --- [ 2%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_bns.c.o --- src/formats/libinchi/CMakeFiles/inchi.dir/ichican2.c.o --- [ 2%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichican2.c.o --- src/formats/libinchi/CMakeFiles/inchi.dir/ichicano.c.o --- cd /construction/science/openbabel/.build/src/formats/libinchi && /usr/local/libexec/ccache/cc -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D_USRDLL -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DNDEBUG -fPIC -w -MD -MT src/formats/libinchi/CMakeFiles/inchi.dir/ichicano.c.o -MF CMakeFiles/inchi.dir/ichicano.c.o.d -o CMakeFiles/inchi.dir/ichicano.c.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/libinchi/ichicano.c --- src/formats/libinchi/CMakeFiles/inchi.dir/ichi_io.c.o --- [ 2%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_io.c.o --- data/CMakeFiles/data_headers.dir/all --- cd /construction/science/openbabel/.build/data && /usr/local/bin/perl /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data/bin2hex.pl 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src/formats/libinchi/CMakeFiles/inchi.dir/ichilnct.c.o -MF CMakeFiles/inchi.dir/ichilnct.c.o.d -o CMakeFiles/inchi.dir/ichilnct.c.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/libinchi/ichilnct.c --- src/formats/libinchi/CMakeFiles/inchi.dir/ichimak2.c.o --- cd /construction/science/openbabel/.build/src/formats/libinchi && /usr/local/libexec/ccache/cc -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D_USRDLL -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -isystem 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-D_USRDLL -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DNDEBUG -fPIC -w -MD -MT src/formats/libinchi/CMakeFiles/inchi.dir/ichimap1.c.o -MF CMakeFiles/inchi.dir/ichimap1.c.o.d -o CMakeFiles/inchi.dir/ichimap1.c.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/libinchi/ichimap1.c --- src/formats/libinchi/CMakeFiles/inchi.dir/ichimap2.c.o --- [ 3%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichimap2.c.o cd 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/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/descriptor.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/descriptor.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/descriptor.cpp.o -MF CMakeFiles/openbabel.dir/descriptor.cpp.o.d -o CMakeFiles/openbabel.dir/descriptor.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptor.cpp --- src/CMakeFiles/openbabel.dir/elements.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/elements.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/elements.cpp.o -MF CMakeFiles/openbabel.dir/elements.cpp.o.d -o CMakeFiles/openbabel.dir/elements.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/elements.cpp --- src/CMakeFiles/openbabel.dir/fingerprint.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/fingerprint.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/fingerprint.cpp.o -MF CMakeFiles/openbabel.dir/fingerprint.cpp.o.d -o CMakeFiles/openbabel.dir/fingerprint.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/fingerprint.cpp --- src/CMakeFiles/openbabel.dir/bond.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp: In constructor 'OpenBabel::OBBond::OBBond()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:63:18: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] OBBond::OBBond() /*: d(new OBBondPrivate)*/ ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:63:18: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] OBBond::OBBond() /*: d(new OBBondPrivate)*/ ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp: In member function 'void OpenBabel::OBBond::SetLength(OpenBabel::OBAtom*, double)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:124:33: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(v3.length_2())) { // too small to normalize, move the atoms apart ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:124:33: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(v3.length_2())) { // too small to normalize, move the atoms apart ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bond.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- src/CMakeFiles/openbabel.dir/forcefield.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/forcefield.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/forcefield.cpp.o -MF CMakeFiles/openbabel.dir/forcefield.cpp.o.d -o CMakeFiles/openbabel.dir/forcefield.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp --- src/CMakeFiles/openbabel.dir/bondtyper.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bondtyper.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bondtyper.h:22, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/bondtyper.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/CMakeFiles/openbabel.dir/format.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/format.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/format.cpp.o -MF CMakeFiles/openbabel.dir/format.cpp.o.d -o CMakeFiles/openbabel.dir/format.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/format.cpp --- src/formats/libinchi/CMakeFiles/inchi.dir/all --- --- lib/libinchi.so.0.4.1 --- [ 9%] Linking C shared library ../../../lib/libinchi.so cd 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CMakeFiles/inchi.dir/ichirvr1.c.o CMakeFiles/inchi.dir/ichirvr2.c.o CMakeFiles/inchi.dir/ichirvr3.c.o CMakeFiles/inchi.dir/ichirvr4.c.o CMakeFiles/inchi.dir/ichirvr5.c.o CMakeFiles/inchi.dir/ichirvr6.c.o CMakeFiles/inchi.dir/ichirvr7.c.o CMakeFiles/inchi.dir/ichisort.c.o CMakeFiles/inchi.dir/ichister.c.o CMakeFiles/inchi.dir/ichitaut.c.o CMakeFiles/inchi.dir/ikey_base26.c.o CMakeFiles/inchi.dir/ikey_dll.c.o CMakeFiles/inchi.dir/inchi_dll.c.o CMakeFiles/inchi.dir/inchi_dll_a.c.o CMakeFiles/inchi.dir/inchi_dll_a2.c.o CMakeFiles/inchi.dir/inchi_dll_main.c.o CMakeFiles/inchi.dir/runichi.c.o CMakeFiles/inchi.dir/sha2.c.o CMakeFiles/inchi.dir/strutil.c.o CMakeFiles/inchi.dir/util.c.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm cd /construction/science/openbabel/.build/src/formats/libinchi && /usr/local/bin/cmake -E cmake_symlink_library ../../../lib/libinchi.so.0.4.1 ../../../lib/libinchi.so.0 ../../../lib/libinchi.so [ 10%] Built target inchi --- src/CMakeFiles/openbabel.dir/all --- --- src/CMakeFiles/openbabel.dir/generic.cpp.o --- [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/generic.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/generic.cpp.o -MF CMakeFiles/openbabel.dir/generic.cpp.o.d -o CMakeFiles/openbabel.dir/generic.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/generic.cpp --- src/CMakeFiles/openbabel.dir/data_utilities.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/data_utilities.cpp:30: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/graphsym.cpp.o --- [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/graphsym.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/graphsym.cpp.o -MF CMakeFiles/openbabel.dir/graphsym.cpp.o.d -o CMakeFiles/openbabel.dir/graphsym.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/graphsym.cpp --- src/CMakeFiles/openbabel.dir/descriptor.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptor.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/grid.cpp.o --- [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/grid.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/grid.cpp.o -MF CMakeFiles/openbabel.dir/grid.cpp.o.d -o CMakeFiles/openbabel.dir/grid.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/grid.cpp --- src/CMakeFiles/openbabel.dir/griddata.cpp.o --- [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/griddata.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/griddata.cpp.o -MF CMakeFiles/openbabel.dir/griddata.cpp.o.d -o CMakeFiles/openbabel.dir/griddata.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp --- src/CMakeFiles/openbabel.dir/isomorphism.cpp.o --- [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/isomorphism.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/isomorphism.cpp.o -MF CMakeFiles/openbabel.dir/isomorphism.cpp.o.d -o CMakeFiles/openbabel.dir/isomorphism.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/isomorphism.cpp --- src/CMakeFiles/openbabel.dir/kekulize.cpp.o --- [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/kekulize.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/kekulize.cpp.o -MF CMakeFiles/openbabel.dir/kekulize.cpp.o.d -o CMakeFiles/openbabel.dir/kekulize.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/kekulize.cpp --- src/CMakeFiles/openbabel.dir/chains.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/chains.cpp:34: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/locale.cpp.o --- [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/locale.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/locale.cpp.o -MF CMakeFiles/openbabel.dir/locale.cpp.o.d -o CMakeFiles/openbabel.dir/locale.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/locale.cpp --- src/CMakeFiles/openbabel.dir/atom.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp: In member function 'bool OpenBabel::OBAtom::IsInRingSize(int) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:826:71: warning: 'size_t OpenBabel::OBRing::PathSize() const' is deprecated: Use Size() instead [-Wdeprecated-declarations] if ((*i)->IsInRing(GetIdx()) && static_cast((*i)->PathSize()) == size) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:66:15: note: declared here size_t PathSize() const { return(_path.size()); } ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp: In member function 'double OpenBabel::OBAtom::GetAngle(OpenBabel::OBAtom*, OpenBabel::OBAtom*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:1143:39: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(v1.length(), 1.0e-3) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:1143:39: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(v1.length(), 1.0e-3) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:1144:40: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] || IsNearZero(v2.length(), 1.0e-3)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:1144:40: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] || IsNearZero(v2.length(), 1.0e-3)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/atom.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- src/CMakeFiles/openbabel.dir/matrix.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/matrix.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/matrix.cpp.o -MF CMakeFiles/openbabel.dir/matrix.cpp.o.d -o CMakeFiles/openbabel.dir/matrix.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/matrix.cpp --- src/CMakeFiles/openbabel.dir/mcdlutil.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/mcdlutil.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/mcdlutil.cpp.o -MF CMakeFiles/openbabel.dir/mcdlutil.cpp.o.d -o CMakeFiles/openbabel.dir/mcdlutil.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mcdlutil.cpp --- src/CMakeFiles/openbabel.dir/alias.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/alias.h:20, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/alias.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/alias.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/CMakeFiles/openbabel.dir/griddata.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/griddata.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h: In constructor 'OpenBabel::OBFloatGrid::OBFloatGrid()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:115:51: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] OBFloatGrid() : _ival(nullptr), _halfSpace(0.0) {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:115:51: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] OBFloatGrid() : _ival(nullptr), _halfSpace(0.0) {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h: In destructor 'virtual OpenBabel::OBFloatGrid::~OBFloatGrid()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:11: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:11: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:28: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:28: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp: In member function 'void OpenBabel::OBGridData::GetOriginVector(double*) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp:194:26: warning: 'void OpenBabel::OBFloatGrid::GetMin(double*)' is deprecated: Use GetMin() instead [-Wdeprecated-declarations] d->floatGrid.GetMin(o); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:132:10: note: declared here void GetMin(double *a) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp: In member function 'void OpenBabel::OBGridData::SetLimits(const double*, const double*, const double*, const double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp:235:43: warning: 'void OpenBabel::OBFloatGrid::SetLimits(const double*, const double*, const double*, const double*)' is deprecated: Use vector version instead [-Wdeprecated-declarations] d->floatGrid.SetLimits(origin, x, y, z); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/griddata.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:229:10: note: declared here void SetLimits(const double origin[3], const double x[3], const double y[3], ^~~~~~~~~ --- src/CMakeFiles/openbabel.dir/grid.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/grid.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/grid.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h: In constructor 'OpenBabel::OBFloatGrid::OBFloatGrid()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:115:51: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] OBFloatGrid() : _ival(nullptr), _halfSpace(0.0) {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:115:51: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] OBFloatGrid() : _ival(nullptr), _halfSpace(0.0) {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h: In destructor 'virtual OpenBabel::OBFloatGrid::~OBFloatGrid()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:11: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:11: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:28: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:28: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/grid.cpp: In member function 'void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/grid.cpp:82:5: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] _ival=nullptr; ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/grid.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/grid.cpp:82:5: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] _ival=nullptr; ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/grid.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ --- src/CMakeFiles/openbabel.dir/molchrg.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/molchrg.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/molchrg.cpp.o -MF CMakeFiles/openbabel.dir/molchrg.cpp.o.d -o CMakeFiles/openbabel.dir/molchrg.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/molchrg.cpp --- src/CMakeFiles/openbabel.dir/mol.cpp.o --- --- src/CMakeFiles/openbabel.dir/obconversion.cpp.o --- --- src/CMakeFiles/openbabel.dir/mol.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/mol.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/mol.cpp.o -MF CMakeFiles/openbabel.dir/mol.cpp.o.d -o CMakeFiles/openbabel.dir/mol.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp --- src/CMakeFiles/openbabel.dir/obconversion.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/obconversion.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/obconversion.cpp.o -MF CMakeFiles/openbabel.dir/obconversion.cpp.o.d -o CMakeFiles/openbabel.dir/obconversion.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/obconversion.cpp--- src/CMakeFiles/openbabel.dir/kekulize.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/kekulize.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/oberror.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/oberror.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/oberror.cpp.o -MF CMakeFiles/openbabel.dir/oberror.cpp.o.d -o CMakeFiles/openbabel.dir/oberror.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/oberror.cpp --- src/CMakeFiles/openbabel.dir/obfunctions.cpp.o --- --- src/CMakeFiles/openbabel.dir/isomorphism.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/query.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/isomorphism.cpp:5: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/obfunctions.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/obfunctions.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/obfunctions.cpp.o -MF CMakeFiles/openbabel.dir/obfunctions.cpp.o.d -o CMakeFiles/openbabel.dir/obfunctions.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/obfunctions.cpp --- src/CMakeFiles/openbabel.dir/obiter.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/obiter.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/obiter.cpp.o -MF CMakeFiles/openbabel.dir/obiter.cpp.o.d -o CMakeFiles/openbabel.dir/obiter.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/obiter.cpp --- src/CMakeFiles/openbabel.dir/graphsym.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/graphsym.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/graphsym.cpp:30: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/graphsym.cpp:30: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ --- src/CMakeFiles/openbabel.dir/obutil.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/obutil.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/obutil.cpp.o -MF CMakeFiles/openbabel.dir/obutil.cpp.o.d -o CMakeFiles/openbabel.dir/obutil.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/obutil.cpp --- src/CMakeFiles/openbabel.dir/molchrg.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/molchrg.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/molchrg.cpp: In member function 'bool OpenBabel::OBGastChrg::GasteigerSigmaChi(OpenBabel::OBAtom*, double&, double&, double&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/molchrg.cpp:297:27: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!IsNearZero(val[2])) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/molchrg.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/molchrg.cpp:297:27: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!IsNearZero(val[2])) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/molchrg.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- src/CMakeFiles/openbabel.dir/op.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/op.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/op.cpp.o -MF CMakeFiles/openbabel.dir/op.cpp.o.d -o CMakeFiles/openbabel.dir/op.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/op.cpp --- src/CMakeFiles/openbabel.dir/data.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/data.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/parsmart.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/parsmart.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/parsmart.cpp.o -MF CMakeFiles/openbabel.dir/parsmart.cpp.o.d -o CMakeFiles/openbabel.dir/parsmart.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/parsmart.cpp --- src/CMakeFiles/openbabel.dir/patty.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/patty.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/patty.cpp.o -MF CMakeFiles/openbabel.dir/patty.cpp.o.d -o CMakeFiles/openbabel.dir/patty.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/patty.cpp --- src/CMakeFiles/openbabel.dir/phmodel.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/phmodel.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/phmodel.cpp.o -MF CMakeFiles/openbabel.dir/phmodel.cpp.o.d -o CMakeFiles/openbabel.dir/phmodel.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/phmodel.cpp --- src/CMakeFiles/openbabel.dir/generic.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/generic.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/generic.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/generic.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ --- src/CMakeFiles/openbabel.dir/plugin.cpp.o --- [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/plugin.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/plugin.cpp.o -MF CMakeFiles/openbabel.dir/plugin.cpp.o.d -o CMakeFiles/openbabel.dir/plugin.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/plugin.cpp --- src/CMakeFiles/openbabel.dir/obfunctions.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obfunctions.h:22, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/obfunctions.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/pointgroup.cpp.o --- [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/pointgroup.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/pointgroup.cpp.o -MF CMakeFiles/openbabel.dir/pointgroup.cpp.o.d -o CMakeFiles/openbabel.dir/pointgroup.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/pointgroup.cpp --- src/CMakeFiles/openbabel.dir/patty.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/patty.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/patty.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/CMakeFiles/openbabel.dir/query.cpp.o --- [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/query.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/query.cpp.o -MF CMakeFiles/openbabel.dir/query.cpp.o.d -o CMakeFiles/openbabel.dir/query.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/query.cpp --- src/CMakeFiles/openbabel.dir/rand.cpp.o --- [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/rand.cpp.o --- src/CMakeFiles/openbabel.dir/obutil.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/obutil.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/rand.cpp.o --- cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/rand.cpp.o -MF CMakeFiles/openbabel.dir/rand.cpp.o.d -o CMakeFiles/openbabel.dir/rand.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rand.cpp --- src/CMakeFiles/openbabel.dir/reactionfacade.cpp.o --- [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/reactionfacade.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/reactionfacade.cpp.o -MF CMakeFiles/openbabel.dir/reactionfacade.cpp.o.d -o CMakeFiles/openbabel.dir/reactionfacade.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/reactionfacade.cpp --- src/CMakeFiles/openbabel.dir/canon.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/canon.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/residue.cpp.o --- [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/residue.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/residue.cpp.o -MF CMakeFiles/openbabel.dir/residue.cpp.o.d -o CMakeFiles/openbabel.dir/residue.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/residue.cpp --- src/CMakeFiles/openbabel.dir/ring.cpp.o --- [ 15%] Building CXX object src/CMakeFiles/openbabel.dir/ring.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/ring.cpp.o -MF CMakeFiles/openbabel.dir/ring.cpp.o.d -o CMakeFiles/openbabel.dir/ring.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp --- src/CMakeFiles/openbabel.dir/query.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/query.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/query.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/rotamer.cpp.o --- [ 15%] Building CXX object src/CMakeFiles/openbabel.dir/rotamer.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/rotamer.cpp.o -MF CMakeFiles/openbabel.dir/rotamer.cpp.o.d -o CMakeFiles/openbabel.dir/rotamer.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotamer.cpp --- src/CMakeFiles/openbabel.dir/phmodel.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/phmodel.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/phmodel.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/CMakeFiles/openbabel.dir/rotor.cpp.o --- [ 15%] Building CXX object src/CMakeFiles/openbabel.dir/rotor.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/rotor.cpp.o -MF CMakeFiles/openbabel.dir/rotor.cpp.o.d -o CMakeFiles/openbabel.dir/rotor.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp --- src/CMakeFiles/openbabel.dir/spectrophore.cpp.o --- [ 15%] Building CXX object src/CMakeFiles/openbabel.dir/spectrophore.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/spectrophore.cpp.o -MF CMakeFiles/openbabel.dir/spectrophore.cpp.o.d -o CMakeFiles/openbabel.dir/spectrophore.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/spectrophore.cpp--- src/CMakeFiles/openbabel.dir/forcefield.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:34: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h: In constructor 'OpenBabel::OBFloatGrid::OBFloatGrid()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:115:51: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] OBFloatGrid() : _ival(nullptr), _halfSpace(0.0) {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:115:51: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] OBFloatGrid() : _ival(nullptr), _halfSpace(0.0) {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h: In destructor 'virtual OpenBabel::OBFloatGrid::~OBFloatGrid()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:11: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:11: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:28: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:118:28: warning: 'OpenBabel::OBFloatGrid::_ival' is deprecated [-Wdeprecated-declarations] if (_ival) delete [] _ival; ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/grid.h:105:26: note: declared here OB_DEPRECATED int *_ival; //!< for integer values \deprecated ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'double OpenBabel::OBFFConstraints::GetConstraintEnergy()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:482:31: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:482:60: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:482:60: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:499:65: warning: 'static double OpenBabel::OBForceField::VectorAngleDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] theta = OBForceField::VectorAngleDerivative(da, db, dc); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1540:19: note: declared here static double VectorAngleDerivative(vector3 &a, vector3 &b, vector3 &c); ^~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:499:65: warning: 'static double OpenBabel::OBForceField::VectorAngleDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] theta = OBForceField::VectorAngleDerivative(da, db, dc); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1540:19: note: declared here static double VectorAngleDerivative(vector3 &a, vector3 &b, vector3 &c); ^~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:518:71: warning: 'static double OpenBabel::OBForceField::VectorTorsionDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] theta = OBForceField::VectorTorsionDerivative(da, db, dc, dd); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1573:19: note: declared here static double VectorTorsionDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d); ^~~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:518:71: warning: 'static double OpenBabel::OBForceField::VectorTorsionDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] theta = OBForceField::VectorTorsionDerivative(da, db, dc, dd); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1573:19: note: declared here static double VectorTorsionDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d); ^~~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'int OpenBabel::OBForceField::SystematicRotorSearchInitialize(unsigned int, bool)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1180:25: warning: 'void OpenBabel::OBRotorList::SetFixAtoms(OpenBabel::OBBitVec&)' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations] rl.SetFixAtoms(fixed); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:634:10: note: declared here void SetFixAtoms(OBBitVec &fix) ^~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1193:46: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] combinations *= rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1213:47: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] rotorKeys.AddRotor(rotor->GetResolution().size()); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'int OpenBabel::OBForceField::FastRotorSearch(bool)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1301:25: warning: 'void OpenBabel::OBRotorList::SetFixAtoms(OpenBabel::OBBitVec&)' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations] rl.SetFixAtoms(fixed); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:634:10: note: declared here void SetFixAtoms(OBBitVec &fix) ^~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1372:46: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] for (j = 0; j < rotor->GetResolution().size(); j++) { // For each rotor position ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'void OpenBabel::OBForceField::RandomRotorSearchInitialize(unsigned int, unsigned int, bool)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1444:25: warning: 'void OpenBabel::OBRotorList::SetFixAtoms(OpenBabel::OBBitVec&)' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations] rl.SetFixAtoms(fixed); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:634:10: note: declared here void SetFixAtoms(OBBitVec &fix) ^~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1457:46: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] combinations *= rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1482:66: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] rotorKey[i] = generator.NextInt() % rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1622:25: warning: 'void OpenBabel::OBRotorList::SetFixAtoms(OpenBabel::OBBitVec&)' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations] rl.SetFixAtoms(fixed); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:634:10: note: declared here void SetFixAtoms(OBBitVec &fix) ^~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1635:46: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] combinations *= rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1685:57: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] for (unsigned int j = 0; j < rotor->GetResolution().size(); j++) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1712:57: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] for (unsigned int j = 0; j < rotor->GetResolution().size(); j++) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1719:57: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] for (unsigned int j = 0; j < rotor->GetResolution().size(); j++) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1720:41: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(worstE, bestE, 1.0e-3)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1720:41: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(worstE, bestE, 1.0e-3)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1721:45: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] weight = 1 / rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:1761:59: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] for (unsigned int j = 0; j < rotor->GetResolution().size(); j++) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'OpenBabel::vector3 OpenBabel::OBForceField::LineSearch(OpenBabel::OBAtom*, OpenBabel::vector3&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2364:36: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, e_n1, 1.0e-3)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2364:36: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, e_n1, 1.0e-3)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'double OpenBabel::OBForceField::Newton2NumLineSearch(double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2420:25: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(scale)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2420:25: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(scale)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'double OpenBabel::OBForceField::LineSearch(double*, double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2539:36: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, e_n1, 1.0e-3)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2539:36: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, e_n1, 1.0e-3)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'void OpenBabel::OBForceField::ValidateSteepestDescent(int)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2657:36: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, e_n1, 1.0e-7)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2657:36: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, e_n1, 1.0e-7)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'void OpenBabel::OBForceField::ValidateConjugateGradients(int)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2725:38: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, e_n1, 1.0e-7)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2725:38: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, e_n1, 1.0e-7)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'bool OpenBabel::OBForceField::SteepestDescentTakeNSteps(int)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2838:37: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, _e_n1, _econv) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:2838:37: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, _e_n1, _econv) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In member function 'bool OpenBabel::OBForceField::ConjugateGradientsTakeNSteps(int)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3039:37: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, _e_n1, _econv) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3039:37: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(e_n2, _e_n1, _econv) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorAngleDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3652:27: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length1) || IsNearZero(length2)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3652:27: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length1) || IsNearZero(length2)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3652:50: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length1) || IsNearZero(length2)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3652:50: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length1) || IsNearZero(length2)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3669:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3669:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorAngleDerivative(double*, double*, double*, double*, double*, double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3719:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3719:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3719:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3719:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3735:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3735:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorAngle(double*, double*, double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3789:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3789:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3789:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3789:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3802:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3802:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorOOPDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3837:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3837:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3853:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3853:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3869:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3869:26: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3892:25: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3892:25: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3892:59: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3892:59: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3907:22: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dl) || IsNearZero(fabs(dl - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3907:22: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dl) || IsNearZero(fabs(dl - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3907:53: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dl) || IsNearZero(fabs(dl - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3907:53: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dl) || IsNearZero(fabs(dl - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorOOPDerivative(double*, double*, double*, double*, double*, double*, double*, double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3949:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_ji)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3949:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_ji)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3962:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3962:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3973:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_jl)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3973:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_jl)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3991:25: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3991:25: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3991:59: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:3991:59: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4006:22: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dl) || IsNearZero(fabs(dl - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4006:22: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dl) || IsNearZero(fabs(dl - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4006:53: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dl) || IsNearZero(fabs(dl - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4006:53: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dl) || IsNearZero(fabs(dl - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorOOP(double*, double*, double*, double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4067:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_ji)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4067:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_ji)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4076:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4076:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_jk)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4083:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_jl)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4083:29: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(length_jl)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4097:25: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4097:25: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4097:59: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4097:59: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(theta) || IsNearZero(fabs(theta - M_PI))) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorTorsionDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4130:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4130:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4130:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4130:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4130:64: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4130:64: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorTorsionDerivative(double*, double*, double*, double*, double*, double*, double*, double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4195:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4195:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4195:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4195:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4195:64: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4195:64: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp: In static member function 'static double OpenBabel::OBForceField::VectorTorsion(double*, double*, double*, double*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4285:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4285:24: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4285:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4285:44: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4285:64: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:4285:64: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(l_ij) || IsNearZero(l_jk) || IsNearZero(l_kl) ) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefield.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- src/CMakeFiles/openbabel.dir/tautomer.cpp.o --- [ 15%] Building CXX object src/CMakeFiles/openbabel.dir/tautomer.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/tautomer.cpp.o -MF CMakeFiles/openbabel.dir/tautomer.cpp.o.d -o CMakeFiles/openbabel.dir/tautomer.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/tautomer.cpp --- src/CMakeFiles/openbabel.dir/builder.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp: In static member function 'static OpenBabel::vector3 OpenBabel::OBBuilder::GetNewBondVector(OpenBabel::OBAtom*, double)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:310:22: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond2 == VZero || v1 == VZero) { ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:310:37: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond2 == VZero || v1 == VZero) { ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:359:24: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:361:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:430:26: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:432:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:434:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond3 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:450:26: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:452:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:454:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond3 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:469:26: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:471:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:473:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond3 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:494:26: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:496:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:498:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond3 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:514:26: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:516:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:518:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond3 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:520:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond4 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:533:26: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:535:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:537:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond3 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:539:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond4 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:564:26: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:566:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:568:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond3 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:570:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond4 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:572:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond5 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:660:24: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:718:26: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:720:31: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] else if (bond2 == VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp: In member function 'bool OpenBabel::OBBuilder::Build(OpenBabel::OBMol&, bool)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:1089:22: warning: 'OpenBabel::OBAtom* OpenBabel::OBMol::GetFirstAtom() const' is deprecated [-Wdeprecated-declarations] mol.GetFirstAtom()->GetHyb(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/mol.h:280:18: note: declared here OBAtom *GetFirstAtom() const; ^~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp: In static member function 'static void OpenBabel::OBBuilder::ConnectFrags(OpenBabel::OBMol&, OpenBabel::OBMol&, std::vector, std::vector, std::vector)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:1427:20: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (bond1 == VZero) { ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/builder.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/tokenst.cpp.o --- [ 15%] Building CXX object src/CMakeFiles/openbabel.dir/tokenst.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/tokenst.cpp.o -MF CMakeFiles/openbabel.dir/tokenst.cpp.o.d -o CMakeFiles/openbabel.dir/tokenst.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/tokenst.cpp --- src/CMakeFiles/openbabel.dir/obiter.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/obiter.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/transform.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/openbabel.dir/transform.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/transform.cpp.o -MF CMakeFiles/openbabel.dir/transform.cpp.o.d -o CMakeFiles/openbabel.dir/transform.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/transform.cpp --- src/CMakeFiles/openbabel.dir/reactionfacade.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/reactionfacade.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/typer.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/openbabel.dir/typer.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/typer.cpp.o -MF CMakeFiles/openbabel.dir/typer.cpp.o.d -o CMakeFiles/openbabel.dir/typer.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/typer.cpp --- src/CMakeFiles/openbabel.dir/parsmart.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/parsmart.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/parsmart.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/parsmart.cpp: In destructor 'virtual OpenBabel::OBSmartsPattern::~OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/parsmart.cpp:1745:37: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern::~OBSmartsPattern() ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/parsmart.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/parsmart.cpp:1745:37: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern::~OBSmartsPattern() ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/parsmart.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/CMakeFiles/openbabel.dir/obmolecformat.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/openbabel.dir/obmolecformat.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/obmolecformat.cpp.o -MF CMakeFiles/openbabel.dir/obmolecformat.cpp.o.d -o CMakeFiles/openbabel.dir/obmolecformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/obmolecformat.cpp --- src/CMakeFiles/openbabel.dir/residue.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/residue.cpp:34: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/conformersearch.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/openbabel.dir/conformersearch.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/conformersearch.cpp.o -MF CMakeFiles/openbabel.dir/conformersearch.cpp.o.d -o CMakeFiles/openbabel.dir/conformersearch.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp --- src/CMakeFiles/openbabel.dir/confsearch.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/openbabel.dir/confsearch.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/confsearch.cpp.o -MF CMakeFiles/openbabel.dir/confsearch.cpp.o.d -o CMakeFiles/openbabel.dir/confsearch.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/confsearch.cpp --- src/CMakeFiles/openbabel.dir/pointgroup.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/pointgroup.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/distgeom.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/openbabel.dir/distgeom.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/distgeom.cpp.o -MF CMakeFiles/openbabel.dir/distgeom.cpp.o.d -o CMakeFiles/openbabel.dir/distgeom.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/distgeom.cpp --- src/CMakeFiles/openbabel.dir/ring.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp: In destructor 'OpenBabel::OBRingSearch::~OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp:479:31: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch::~OBRingSearch() ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp:479:31: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch::~OBRingSearch() ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ring.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ --- src/CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o -MF CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o.d -o CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/dlhandler_unix.cpp --- src/CMakeFiles/openbabel.dir/tautomer.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/tautomer.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/depict/depict.cpp.o --- [ 17%] Building CXX object src/CMakeFiles/openbabel.dir/depict/depict.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/depict/depict.cpp.o -MF CMakeFiles/openbabel.dir/depict/depict.cpp.o.d -o CMakeFiles/openbabel.dir/depict/depict.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/depict/depict.cpp --- src/CMakeFiles/openbabel.dir/rotor.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp: In member function 'bool OpenBabel::OBRotorList::FindRotors(OpenBabel::OBMol&, bool)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:114:28: warning: 'bool OpenBabel::OBRotorList::HasFixedAtoms()' is deprecated: See HasFixedBonds() [-Wdeprecated-declarations] if ((HasFixedAtoms() || HasFixedBonds()) && IsFixedBond(bond)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:644:10: note: declared here bool HasFixedAtoms() ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:138:43: warning: 'void OpenBabel::OBRotor::SetNumCoords(int)' is deprecated [-Wdeprecated-declarations] rotor->SetNumCoords(mol.NumAtoms()*3); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:453:10: note: declared here void SetNumCoords(int UNUSED(nc)) {} ^~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp: In member function 'bool OpenBabel::OBRotorList::SetEvalAtoms(OpenBabel::OBMol&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:318:79: warning: 'bool OpenBabel::OBRotorList::HasFixedAtoms()' is deprecated: See HasFixedBonds() [-Wdeprecated-declarations] if (!((OBBond*)*k)->IsRotor(_ringRotors)||((HasFixedAtoms()||HasFixedBonds())&&IsFixedBond((OBBond*)*k))) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:644:10: note: declared here bool HasFixedAtoms() ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:336:33: warning: 'void OpenBabel::OBRotor::SetEvalAtoms(OpenBabel::OBBitVec&)' is deprecated [-Wdeprecated-declarations] rotor->SetEvalAtoms(eval); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:444:10: note: declared here void SetEvalAtoms(OBBitVec &bv) { _evalatoms = bv; } ^~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp: In member function 'bool OpenBabel::OBRotorList::AssignTorVals(OpenBabel::OBMol&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:355:28: warning: 'void OpenBabel::OBRotor::SetDelta(double)' is deprecated: Has no effect. [-Wdeprecated-declarations] rotor->SetDelta(delta); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotor.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:429:10: note: declared here void SetDelta(double UNUSED(d)) {} ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o --- [ 17%] Building CXX object src/CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o -MF CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o.d -o CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/depict/svgpainter.cpp --- src/CMakeFiles/openbabel.dir/spectrophore.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/spectrophore.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o --- [ 17%] Building CXX object src/CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o -MF CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o.d -o CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp --- src/CMakeFiles/openbabel.dir/math/spacegroup.cpp.o --- [ 17%] Building CXX object src/CMakeFiles/openbabel.dir/math/spacegroup.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/math/spacegroup.cpp.o -MF CMakeFiles/openbabel.dir/math/spacegroup.cpp.o.d -o CMakeFiles/openbabel.dir/math/spacegroup.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/spacegroup.cpp --- src/CMakeFiles/openbabel.dir/mol.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp: In member function 'bool OpenBabel::OBMol::HasNonZeroCoords()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2786:32: warning: 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] if (atom->GetVector() != VZero) ^~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:279:10: note: declared here bool operator!= ( const vector3& other ) const ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp: In member function 'bool OpenBabel::OBMol::Has2D(bool)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2801:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasX && !IsNearZero(atom->x())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2801:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasX && !IsNearZero(atom->x())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2803:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasY && !IsNearZero(atom->y())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2803:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasY && !IsNearZero(atom->y())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp: In member function 'bool OpenBabel::OBMol::Has3D()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2824:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasX && !IsNearZero(atom->x())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2824:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasX && !IsNearZero(atom->x())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2826:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasY && !IsNearZero(atom->y())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2826:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasY && !IsNearZero(atom->y())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2828:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasZ && !IsNearZero(atom->z())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:2828:43: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!hasZ && !IsNearZero(atom->z())) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp: In member function 'void OpenBabel::OBMol::PerceiveBondOrders()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:3250:33: warning: 'size_t OpenBabel::OBRing::PathSize() const' is deprecated: Use Size() instead [-Wdeprecated-declarations] if ((*ringit)->PathSize() == 5) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:66:15: note: declared here size_t PathSize() const { return(_path.size()); } ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:3272:38: warning: 'size_t OpenBabel::OBRing::PathSize() const' is deprecated: Use Size() instead [-Wdeprecated-declarations] else if ((*ringit)->PathSize() == 6) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:66:15: note: declared here size_t PathSize() const { return(_path.size()); } ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:3341:40: warning: 'size_t OpenBabel::OBRing::PathSize() const' is deprecated: Use Size() instead [-Wdeprecated-declarations] loopSize = (*ringit)->PathSize(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mol.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:66:15: note: declared here size_t PathSize() const { return(_path.size()); } ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/math/transform3d.cpp.o --- [ 17%] Building CXX object src/CMakeFiles/openbabel.dir/math/transform3d.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/math/transform3d.cpp.o -MF CMakeFiles/openbabel.dir/math/transform3d.cpp.o.d -o CMakeFiles/openbabel.dir/math/transform3d.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/transform3d.cpp --- src/CMakeFiles/openbabel.dir/transform.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/transform.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/transform.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/CMakeFiles/openbabel.dir/math/vector3.cpp.o --- [ 17%] Building CXX object src/CMakeFiles/openbabel.dir/math/vector3.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/math/vector3.cpp.o -MF CMakeFiles/openbabel.dir/math/vector3.cpp.o.d -o CMakeFiles/openbabel.dir/math/vector3.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/vector3.cpp--- src/CMakeFiles/openbabel.dir/rotamer.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotamer.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotamer.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotamer.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotamer.cpp: In member function 'void OpenBabel::OBRotamerList::Setup(OpenBabel::OBMol&, OpenBabel::OBRotorList&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotamer.cpp:232:46: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] _vres.push_back(rotor->GetResolution()); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/rotamer.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ --- src/CMakeFiles/openbabel.dir/math/align.cpp.o --- [ 18%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/math/align.cpp.o -MF CMakeFiles/openbabel.dir/math/align.cpp.o.d -o CMakeFiles/openbabel.dir/math/align.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/align.cpp --- src/CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp: In member function 'OpenBabel::vector3& OpenBabel::vector3::operator*=(const OpenBabel::matrix3x3&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:273:26: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetX(x()*m.Get(0,0) + y()*m.Get(0,1) + z()*m.Get(0,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:273:43: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetX(x()*m.Get(0,0) + y()*m.Get(0,1) + z()*m.Get(0,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:273:60: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetX(x()*m.Get(0,0) + y()*m.Get(0,1) + z()*m.Get(0,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:274:26: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetY(x()*m.Get(1,0) + y()*m.Get(1,1) + z()*m.Get(1,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:274:43: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetY(x()*m.Get(1,0) + y()*m.Get(1,1) + z()*m.Get(1,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:274:60: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetY(x()*m.Get(1,0) + y()*m.Get(1,1) + z()*m.Get(1,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:275:26: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetZ(x()*m.Get(2,0) + y()*m.Get(2,1) + z()*m.Get(2,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:275:43: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetZ(x()*m.Get(2,0) + y()*m.Get(2,1) + z()*m.Get(2,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:275:60: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] vv.SetZ(x()*m.Get(2,0) + y()*m.Get(2,1) + z()*m.Get(2,2)); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/matrix3x3.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ --- src/CMakeFiles/openbabel.dir/stereo/stereo.cpp.o --- [ 18%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/stereo.cpp.o -MF CMakeFiles/openbabel.dir/stereo/stereo.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/stereo.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/stereo.cpp --- src/CMakeFiles/openbabel.dir/math/transform3d.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/transform3d.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o --- [ 18%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o -MF CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/tetranonplanar.cpp --- src/CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o --- [ 18%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o -MF CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/tetraplanar.cpp --- src/CMakeFiles/openbabel.dir/math/vector3.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/vector3.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o --- [ 18%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o -MF CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/squareplanar.cpp --- src/CMakeFiles/openbabel.dir/typer.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/typer.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/typer.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/typer.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ --- src/CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o --- [ 18%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o -MF CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/cistrans.cpp --- src/CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o --- [ 19%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o -MF CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/tetrahedral.cpp --- src/CMakeFiles/openbabel.dir/stereo/perception.cpp.o --- [ 19%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/perception.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/perception.cpp.o -MF CMakeFiles/openbabel.dir/stereo/perception.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/perception.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp --- src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o --- [ 19%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o -MF CMakeFiles/openbabel.dir/stereo/facade.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/facade.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/facade.cpp --- src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o --- [ 19%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -pthread -MD -MT src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o -MF CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/gen3dstereohelper.cpp --- src/CMakeFiles/openbabel.dir/confsearch.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/confsearch.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/confsearch.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/confsearch.cpp: In member function 'int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/confsearch.cpp:361:25: warning: 'void OpenBabel::OBRotorList::SetFixAtoms(OpenBabel::OBBitVec&)' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations] rl.SetFixAtoms(fixed); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/confsearch.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:634:10: note: declared here void SetFixAtoms(OBBitVec &fix) ^~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/confsearch.cpp:382:42: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] size_t size = rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/confsearch.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ --- src/CMakeFiles/openbabel.dir/math/spacegroup.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/spacegroup.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/gen3dstereohelper.cpp:31: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/facade.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/depict/depict.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/depict/depict.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/depict/depict.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/depict/depict.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ --- src/CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/cistrans.cpp:3: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/conformersearch.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp: In member function 'bool OpenBabel::OBConformerSearch::Setup(const OpenBabel::OBMol&, int, int, int, int)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:411:68: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] rotorKey[i] = generator.NextInt() % rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp: In member function 'void OpenBabel::OBConformerSearch::NextGeneration()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:477:72: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] rotorKey[i] = generator.NextInt() % rotor->GetResolution().size(); // permutate gene ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp: In member function 'void OpenBabel::OBConformerSearch::Search()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:643:35: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(last_score, score)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:643:35: warning: 'bool OpenBabel::IsNear(const double&, const double&, double)' is deprecated: Use IsApprox() instead [-Wdeprecated-declarations] if (IsNear(last_score, score)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:190:14: note: declared here OBAPI bool IsNear(const double &, const double &, const double epsilon=2e-6); ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp: In member function 'int OpenBabel::OBConformerSearch::local_opt()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:795:68: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] new_val = ((OBRandom*)d)->NextInt() % rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:797:70: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] new_val = ((OBRandom*)d)->NextInt() % rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp: In member function 'int OpenBabel::OBConformerSearch::reproduce(OpenBabel::RotorKey&, OpenBabel::RotorKey&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:904:70: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] key1[i] = ((OBRandom*)d)->NextInt() % rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:906:70: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] key2[i] = ((OBRandom*)d)->NextInt() % rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/conformersearch.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ --- src/CMakeFiles/openbabel.dir/mcdlutil.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/mcdlutil.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/math/align.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/align.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/math/align.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/openbabel.dir/stereo/perception.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:31: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:31: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp: In function 'double OpenBabel::GetAngle(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:2401:39: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(v1.length(), 1.0e-3) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:2401:39: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(v1.length(), 1.0e-3) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:2402:40: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] || IsNearZero(v2.length(), 1.0e-3)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:2402:40: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] || IsNearZero(v2.length(), 1.0e-3)) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/stereo/perception.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- src/CMakeFiles/openbabel.dir/distgeom.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/distgeom.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/distgeom.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/distgeom.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ --- lib/libopenbabel.so.7.0.0 --- [ 19%] Linking CXX shared library ../lib/libopenbabel.so cd /construction/science/openbabel/.build/src && /usr/local/bin/cmake -E 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CMakeFiles/openbabel.dir/residue.cpp.o CMakeFiles/openbabel.dir/ring.cpp.o CMakeFiles/openbabel.dir/rotamer.cpp.o CMakeFiles/openbabel.dir/rotor.cpp.o CMakeFiles/openbabel.dir/spectrophore.cpp.o CMakeFiles/openbabel.dir/tautomer.cpp.o CMakeFiles/openbabel.dir/tokenst.cpp.o CMakeFiles/openbabel.dir/transform.cpp.o CMakeFiles/openbabel.dir/typer.cpp.o CMakeFiles/openbabel.dir/obmolecformat.cpp.o CMakeFiles/openbabel.dir/conformersearch.cpp.o CMakeFiles/openbabel.dir/confsearch.cpp.o CMakeFiles/openbabel.dir/distgeom.cpp.o CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o CMakeFiles/openbabel.dir/depict/depict.cpp.o CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o CMakeFiles/openbabel.dir/math/spacegroup.cpp.o CMakeFiles/openbabel.dir/math/transform3d.cpp.o CMakeFiles/openbabel.dir/math/vector3.cpp.o CMakeFiles/openbabel.dir/math/align.cpp.o CMakeFiles/openbabel.dir/stereo/stereo.cpp.o CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o CMakeFiles/openbabel.dir/stereo/perception.cpp.o CMakeFiles/openbabel.dir/stereo/facade.cpp.o CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz -pthread cd /construction/science/openbabel/.build/src && /usr/local/bin/cmake -E cmake_symlink_library ../lib/libopenbabel.so.7.0.0 ../lib/libopenbabel.so.7 ../lib/libopenbabel.so [ 19%] Built target openbabel --- src/CMakeFiles/plugin_descriptors.dir/all --- --- src/CMakeFiles/plugin_fingerprints.dir/all --- --- src/CMakeFiles/plugin_forcefields.dir/all --- --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_charges.dir/all --- --- src/formats/CMakeFiles/smilesformat.dir/all --- --- 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cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/mol2format.dir/DependInfo.cmake --- src/CMakeFiles/plugin_charges.dir/all --- /usr/bin/make -f src/CMakeFiles/plugin_charges.dir/build.make src/CMakeFiles/plugin_charges.dir/build --- src/formats/CMakeFiles/inchiformat.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats 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src/formats/CMakeFiles/inchiformat.dir/inchiformat.cpp.o --- --- src/formats/CMakeFiles/pdbformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pdbformat.dir/build.make src/formats/CMakeFiles/pdbformat.dir/build --- src/formats/CMakeFiles/asciiformat.dir/all --- --- src/formats/CMakeFiles/asciiformat.dir/asciiformat.cpp.o --- --- src/CMakeFiles/plugin_charges.dir/all --- cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/eem.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/eem.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/eem.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/eem.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/addfilename.cpp.o --- --- src/formats/CMakeFiles/smilesformat.dir/all --- [ 19%] Building CXX object src/formats/CMakeFiles/smilesformat.dir/smilesformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dsmilesformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include 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/usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/inchiformat.dir/inchiformat.cpp.o -MF CMakeFiles/inchiformat.dir/inchiformat.cpp.o.d -o CMakeFiles/inchiformat.dir/inchiformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/inchiformat.cpp --- src/CMakeFiles/plugin_forcefields.dir/all --- /usr/bin/make -f src/CMakeFiles/plugin_forcefields.dir/build.make src/CMakeFiles/plugin_forcefields.dir/build --- src/formats/CMakeFiles/copyformat.dir/all --- --- src/formats/CMakeFiles/copyformat.dir/copyformat.cpp.o --- --- src/CMakeFiles/plugin_ops.dir/all --- [ 19%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addfilename.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS 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/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp --- src/formats/CMakeFiles/mdlformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmdlformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/mdlformat.dir/mdlformat.cpp.o -MF CMakeFiles/mdlformat.dir/mdlformat.cpp.o.d -o CMakeFiles/mdlformat.dir/mdlformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mdlformat.cpp --- src/CMakeFiles/plugin_fingerprints.dir/all --- [ 20%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_fingerprints_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o -MF CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o.d -o CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/fingerprints/finger2.cpp --- src/formats/CMakeFiles/asciiformat.dir/all --- [ 20%] Building CXX object src/formats/CMakeFiles/asciiformat.dir/asciiformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dasciiformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/asciiformat.dir/asciiformat.cpp.o -MF CMakeFiles/asciiformat.dir/asciiformat.cpp.o.d -o CMakeFiles/asciiformat.dir/asciiformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/asciiformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o --- [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/addinindex.cpp --- src/formats/CMakeFiles/copyformat.dir/all --- --- lib/copyformat.so --- [ 20%] Linking CXX shared module ../../lib/copyformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/copyformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/copyformat.so CMakeFiles/copyformat.dir/copyformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 20%] Built target copyformat --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o --- [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/addpolarh.cpp --- src/CMakeFiles/plugin_descriptors.dir/all --- --- src/CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o --- [ 20%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/cmpdfilter.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o --- [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/addnonpolarh.cpp --- src/CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o --- [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/canonical.cpp --- src/formats/CMakeFiles/asciiformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/asciiformat.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o --- [ 21%] Building CXX object src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dasciiformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o -MF CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o.d -o CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/depict/asciipainter.cpp --- src/CMakeFiles/plugin_fingerprints.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/fingerprints/finger2.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o --- [ 21%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_fingerprints_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o -MF CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o.d -o CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/fingerprints/finger3.cpp --- src/CMakeFiles/plugin_charges.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/chargemodel.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/eem.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o --- [ 21%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/gasteiger.cpp --- src/CMakeFiles/plugin_descriptors.dir/all --- --- src/CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o --- [ 21%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/groupcontrib.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o --- [ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/changecell.cpp --- src/formats/CMakeFiles/MNAformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/MNAformat.cpp:33: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/MNAformat.cpp:37: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/MNAformat.cpp:37: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ --- lib/MNAformat.so --- [ 22%] Linking CXX shared module ../../lib/MNAformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MNAformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/MNAformat.so CMakeFiles/MNAformat.dir/MNAformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 22%] Built target MNAformat --- src/formats/CMakeFiles/molreport.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/molreport.dir/build.make src/formats/CMakeFiles/molreport.dir/depend --- src/formats/CMakeFiles/molreport.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/molreport.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/molreport.dir/build.make src/formats/CMakeFiles/molreport.dir/build --- src/formats/CMakeFiles/molreport.dir/molreport.cpp.o --- [ 22%] Building CXX object src/formats/CMakeFiles/molreport.dir/molreport.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmolreport_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/molreport.dir/molreport.cpp.o -MF CMakeFiles/molreport.dir/molreport.cpp.o.d -o CMakeFiles/molreport.dir/molreport.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/molreport.cpp --- src/formats/CMakeFiles/asciiformat.dir/all --- --- lib/asciiformat.so --- [ 22%] Linking CXX shared module ../../lib/asciiformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/asciiformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/asciiformat.so CMakeFiles/asciiformat.dir/asciiformat.cpp.o CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 22%] Built target asciiformat --- src/formats/CMakeFiles/nulformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/nulformat.dir/build.make src/formats/CMakeFiles/nulformat.dir/depend --- src/formats/CMakeFiles/nulformat.dir/depend --- --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o --- --- src/formats/CMakeFiles/nulformat.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/nulformat.dir/DependInfo.cmake --- src/CMakeFiles/plugin_ops.dir/all --- [ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/delpolarh.cpp --- src/formats/CMakeFiles/nulformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/nulformat.dir/build.make src/formats/CMakeFiles/nulformat.dir/build --- src/formats/CMakeFiles/nulformat.dir/nulformat.cpp.o --- --- src/CMakeFiles/plugin_charges.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/chargemodel.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/gasteiger.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_charges.dir/charges/none.cpp.o --- --- src/formats/CMakeFiles/nulformat.dir/all --- [ 22%] Building CXX object src/formats/CMakeFiles/nulformat.dir/nulformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dnulformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/nulformat.dir/nulformat.cpp.o -MF CMakeFiles/nulformat.dir/nulformat.cpp.o.d -o CMakeFiles/nulformat.dir/nulformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/nulformat.cpp --- src/CMakeFiles/plugin_charges.dir/all --- [ 22%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/none.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/none.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/none.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/none.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/none.cpp --- src/formats/CMakeFiles/mol2format.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mol2format.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mol2format.cpp: In member function 'virtual bool OpenBabel::MOL2Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mol2format.cpp:371:32: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!IsNearZero(pcharge)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mol2format.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mol2format.cpp:371:32: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (!IsNearZero(pcharge)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mol2format.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- lib/mol2format.so --- [ 23%] Linking CXX shared module ../../lib/mol2format.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mol2format.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/mol2format.so CMakeFiles/mol2format.dir/mol2format.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 23%] Built target mol2format --- src/formats/CMakeFiles/painterformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/painterformat.dir/build.make src/formats/CMakeFiles/painterformat.dir/depend --- src/formats/CMakeFiles/painterformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/painterformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/painterformat.dir/build.make src/formats/CMakeFiles/painterformat.dir/build --- src/formats/CMakeFiles/painterformat.dir/painterformat.cpp.o --- [ 23%] Building CXX object src/formats/CMakeFiles/painterformat.dir/painterformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpainterformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/painterformat.dir/painterformat.cpp.o -MF CMakeFiles/painterformat.dir/painterformat.cpp.o.d -o CMakeFiles/painterformat.dir/painterformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/painterformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o --- [ 23%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/delnonpolarh.cpp --- src/formats/CMakeFiles/molreport.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/molreport.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/molreport.so --- [ 23%] Linking CXX shared module ../../lib/molreport.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molreport.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/molreport.so CMakeFiles/molreport.dir/molreport.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 23%] Built target molreport --- src/formats/CMakeFiles/painterformat.dir/all --- --- src/formats/CMakeFiles/painterformat.dir/__/depict/commandpainter.cpp.o --- [ 23%] Building CXX object src/formats/CMakeFiles/painterformat.dir/__/depict/commandpainter.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpainterformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/painterformat.dir/__/depict/commandpainter.cpp.o -MF CMakeFiles/painterformat.dir/__/depict/commandpainter.cpp.o.d -o CMakeFiles/painterformat.dir/__/depict/commandpainter.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/depict/commandpainter.cpp --- src/formats/CMakeFiles/inchiformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/inchiformat.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/inchiformat.dir/getinchi.cpp.o --- [ 23%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/getinchi.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dinchiformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/inchiformat.dir/getinchi.cpp.o -MF CMakeFiles/inchiformat.dir/getinchi.cpp.o.d -o CMakeFiles/inchiformat.dir/getinchi.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/getinchi.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/changecell.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o --- [ 23%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/gen2D.cpp --- src/CMakeFiles/plugin_charges.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/chargemodel.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/none.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o --- [ 24%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/mmff94.cpp --- src/formats/CMakeFiles/povrayformat.dir/all --- --- src/CMakeFiles/plugin_fingerprints.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/fingerprints/finger3.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/formats/CMakeFiles/povrayformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/povrayformat.dir/build.make src/formats/CMakeFiles/povrayformat.dir/depend --- src/CMakeFiles/plugin_fingerprints.dir/all --- --- src/CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o --- --- src/formats/CMakeFiles/povrayformat.dir/all --- --- src/formats/CMakeFiles/povrayformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/povrayformat.dir/DependInfo.cmake --- src/CMakeFiles/plugin_fingerprints.dir/all --- [ 24%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_fingerprints_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o -MF CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o.d -o CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/fingerprints/fingerecfp.cpp --- src/formats/CMakeFiles/povrayformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/povrayformat.dir/build.make src/formats/CMakeFiles/povrayformat.dir/build --- src/formats/CMakeFiles/povrayformat.dir/povrayformat.cpp.o --- [ 24%] Building CXX object src/formats/CMakeFiles/povrayformat.dir/povrayformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpovrayformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/povrayformat.dir/povrayformat.cpp.o -MF CMakeFiles/povrayformat.dir/povrayformat.cpp.o.d -o CMakeFiles/povrayformat.dir/povrayformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/povrayformat.cpp --- src/formats/CMakeFiles/reportformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/reportformat.dir/build.make src/formats/CMakeFiles/reportformat.dir/depend --- src/formats/CMakeFiles/reportformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/reportformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/reportformat.dir/build.make src/formats/CMakeFiles/reportformat.dir/build --- src/formats/CMakeFiles/reportformat.dir/reportformat.cpp.o --- [ 24%] Building CXX object src/formats/CMakeFiles/reportformat.dir/reportformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dreportformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/reportformat.dir/reportformat.cpp.o -MF CMakeFiles/reportformat.dir/reportformat.cpp.o.d -o CMakeFiles/reportformat.dir/reportformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/reportformat.cpp --- src/formats/CMakeFiles/inchiformat.dir/all --- --- src/formats/CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o --- --- src/formats/CMakeFiles/nulformat.dir/all --- --- lib/nulformat.so --- --- src/formats/CMakeFiles/inchiformat.dir/all --- [ 24%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o --- src/formats/CMakeFiles/nulformat.dir/all --- [ 24%] Linking CXX shared module ../../lib/nulformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/nulformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/inchiformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dinchiformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o -MF CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o.d -o CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/unique.cpp --- src/formats/CMakeFiles/nulformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/nulformat.so CMakeFiles/nulformat.dir/nulformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 24%] Built target nulformat --- src/formats/CMakeFiles/svgformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/svgformat.dir/build.make src/formats/CMakeFiles/svgformat.dir/depend --- src/formats/CMakeFiles/svgformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/svgformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/svgformat.dir/build.make src/formats/CMakeFiles/svgformat.dir/build --- src/formats/CMakeFiles/svgformat.dir/svgformat.cpp.o --- [ 25%] Building CXX object src/formats/CMakeFiles/svgformat.dir/svgformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dsvgformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/svgformat.dir/svgformat.cpp.o -MF CMakeFiles/svgformat.dir/svgformat.cpp.o.d -o CMakeFiles/svgformat.dir/svgformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/svgformat.cpp --- src/formats/CMakeFiles/painterformat.dir/all --- --- src/formats/CMakeFiles/painterformat.dir/painterformat.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/depict/depict.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/painterformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/painterformat.so --- [ 25%] Linking CXX shared module ../../lib/painterformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/painterformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/painterformat.so CMakeFiles/painterformat.dir/painterformat.cpp.o CMakeFiles/painterformat.dir/__/depict/commandpainter.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 25%] Built target painterformat --- src/formats/CMakeFiles/textformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/textformat.dir/build.make src/formats/CMakeFiles/textformat.dir/depend --- src/formats/CMakeFiles/textformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/textformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/textformat.dir/build.make src/formats/CMakeFiles/textformat.dir/build --- src/formats/CMakeFiles/pdbformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obfunctions.h:22, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pdbformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/pdbformat.so --- --- src/CMakeFiles/plugin_descriptors.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/groupcontrib.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/groupcontrib.cpp:31: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/formats/CMakeFiles/textformat.dir/all --- --- src/formats/CMakeFiles/textformat.dir/textformat.cpp.o --- --- src/CMakeFiles/plugin_descriptors.dir/all --- --- src/CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o --- --- src/formats/CMakeFiles/pdbformat.dir/all --- [ 25%] Linking CXX shared module ../../lib/pdbformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pdbformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/textformat.dir/all --- [ 25%] Building CXX object src/formats/CMakeFiles/textformat.dir/textformat.cpp.o --- src/CMakeFiles/plugin_descriptors.dir/all --- [ 25%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o --- src/formats/CMakeFiles/pdbformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pdbformat.so CMakeFiles/pdbformat.dir/pdbformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/textformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dtextformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/textformat.dir/textformat.cpp.o -MF CMakeFiles/textformat.dir/textformat.cpp.o.d -o CMakeFiles/textformat.dir/textformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/textformat.cpp --- src/CMakeFiles/plugin_descriptors.dir/all --- cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/filters.cpp --- src/formats/CMakeFiles/pdbformat.dir/all --- [ 25%] Built target pdbformat --- src/formats/CMakeFiles/titleformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/titleformat.dir/build.make src/formats/CMakeFiles/titleformat.dir/depend --- src/formats/CMakeFiles/titleformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/titleformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/titleformat.dir/build.make src/formats/CMakeFiles/titleformat.dir/build --- src/formats/CMakeFiles/titleformat.dir/titleformat.cpp.o --- [ 26%] Building CXX object src/formats/CMakeFiles/titleformat.dir/titleformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dtitleformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/titleformat.dir/titleformat.cpp.o -MF CMakeFiles/titleformat.dir/titleformat.cpp.o.d -o CMakeFiles/titleformat.dir/titleformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/titleformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o --- [ 26%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/fillUC.cpp --- src/CMakeFiles/plugin_fingerprints.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/fingerprints/fingerecfp.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/plugin_fingerprints.so --- [ 26%] Linking CXX shared module ../lib/plugin_fingerprints.so cd /construction/science/openbabel/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/plugin_fingerprints.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../lib/plugin_fingerprints.so CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz ../lib/libopenbabel.so.7.0.0 [ 27%] Built target plugin_fingerprints --- src/formats/CMakeFiles/confabreport.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/confabreport.dir/build.make src/formats/CMakeFiles/confabreport.dir/depend --- src/formats/CMakeFiles/confabreport.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/confabreport.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/confabreport.dir/build.make src/formats/CMakeFiles/confabreport.dir/build --- src/formats/CMakeFiles/confabreport.dir/confabreport.cpp.o --- [ 27%] Building CXX object src/formats/CMakeFiles/confabreport.dir/confabreport.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dconfabreport_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/confabreport.dir/confabreport.cpp.o -MF CMakeFiles/confabreport.dir/confabreport.cpp.o.d -o CMakeFiles/confabreport.dir/confabreport.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/confabreport.cpp --- src/formats/CMakeFiles/reportformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/reportformat.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/reportformat.so --- [ 27%] Linking CXX shared module ../../lib/reportformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/reportformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/reportformat.so CMakeFiles/reportformat.dir/reportformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 28%] Built target reportformat --- src/formats/CMakeFiles/pngformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pngformat.dir/build.make src/formats/CMakeFiles/pngformat.dir/depend --- src/formats/CMakeFiles/pngformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/pngformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/pngformat.dir/build.make src/formats/CMakeFiles/pngformat.dir/build --- src/formats/CMakeFiles/pngformat.dir/pngformat.cpp.o --- [ 28%] Building CXX object src/formats/CMakeFiles/pngformat.dir/pngformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpngformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pngformat.dir/pngformat.cpp.o -MF CMakeFiles/pngformat.dir/pngformat.cpp.o.d -o CMakeFiles/pngformat.dir/pngformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pngformat.cpp --- src/CMakeFiles/plugin_charges.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/chargemodel.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/mmff94.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o --- [ 28%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/fromfile.cpp --- src/formats/CMakeFiles/textformat.dir/all --- --- lib/textformat.so --- [ 28%] Linking CXX shared module ../../lib/textformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/textformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/textformat.so CMakeFiles/textformat.dir/textformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 28%] Built target textformat --- src/formats/CMakeFiles/acesformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/acesformat.dir/build.make src/formats/CMakeFiles/acesformat.dir/depend --- src/formats/CMakeFiles/acesformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/acesformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/acesformat.dir/build.make src/formats/CMakeFiles/acesformat.dir/build --- src/formats/CMakeFiles/acesformat.dir/acesformat.cpp.o --- [ 29%] Building CXX object src/formats/CMakeFiles/acesformat.dir/acesformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dacesformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/acesformat.dir/acesformat.cpp.o -MF CMakeFiles/acesformat.dir/acesformat.cpp.o.d -o CMakeFiles/acesformat.dir/acesformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/acesformat.cpp --- src/CMakeFiles/plugin_descriptors.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/filters.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o --- [ 29%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/inchidescriptor.cpp --- src/formats/CMakeFiles/titleformat.dir/all --- --- lib/titleformat.so --- [ 29%] Linking CXX shared module ../../lib/titleformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/titleformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/titleformat.so CMakeFiles/titleformat.dir/titleformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 29%] Built target titleformat --- src/formats/CMakeFiles/abinitformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/abinitformat.dir/build.make src/formats/CMakeFiles/abinitformat.dir/depend --- src/formats/CMakeFiles/abinitformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/abinitformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/abinitformat.dir/build.make src/formats/CMakeFiles/abinitformat.dir/build --- src/formats/CMakeFiles/abinitformat.dir/abinitformat.cpp.o --- [ 29%] Building CXX object src/formats/CMakeFiles/abinitformat.dir/abinitformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dabinitformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/abinitformat.dir/abinitformat.cpp.o -MF CMakeFiles/abinitformat.dir/abinitformat.cpp.o.d -o CMakeFiles/abinitformat.dir/abinitformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/abinitformat.cpp --- src/formats/CMakeFiles/inchiformat.dir/all --- --- lib/inchiformat.so --- [ 29%] Linking CXX shared module ../../lib/inchiformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/inchiformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/inchiformat.so CMakeFiles/inchiformat.dir/inchiformat.cpp.o CMakeFiles/inchiformat.dir/getinchi.cpp.o CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 29%] Built target inchiformat --- src/formats/CMakeFiles/adfformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/adfformat.dir/build.make src/formats/CMakeFiles/adfformat.dir/depend --- src/formats/CMakeFiles/adfformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/adfformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/adfformat.dir/build.make src/formats/CMakeFiles/adfformat.dir/build --- src/formats/CMakeFiles/adfformat.dir/adfformat.cpp.o --- [ 30%] Building CXX object src/formats/CMakeFiles/adfformat.dir/adfformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dadfformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/adfformat.dir/adfformat.cpp.o -MF CMakeFiles/adfformat.dir/adfformat.cpp.o.d -o CMakeFiles/adfformat.dir/adfformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/adfformat.cpp --- src/formats/CMakeFiles/povrayformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/povrayformat.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/povrayformat.so --- [ 30%] Linking CXX shared module ../../lib/povrayformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/povrayformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/povrayformat.so CMakeFiles/povrayformat.dir/povrayformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 31%] Built target povrayformat --- src/formats/CMakeFiles/aoforceformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/aoforceformat.dir/build.make src/formats/CMakeFiles/aoforceformat.dir/depend --- src/formats/CMakeFiles/aoforceformat.dir/depend --- --- src/CMakeFiles/plugin_ops.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/fillUC.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/aoforceformat.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/aoforceformat.dir/DependInfo.cmake --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o --- --- src/formats/CMakeFiles/aoforceformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/aoforceformat.dir/build.make src/formats/CMakeFiles/aoforceformat.dir/build --- src/CMakeFiles/plugin_ops.dir/all --- [ 31%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/forcefield.cpp --- src/formats/CMakeFiles/aoforceformat.dir/all --- --- src/formats/CMakeFiles/aoforceformat.dir/aoforceformat.cpp.o --- [ 31%] Building CXX object src/formats/CMakeFiles/aoforceformat.dir/aoforceformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Daoforceformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/aoforceformat.dir/aoforceformat.cpp.o -MF CMakeFiles/aoforceformat.dir/aoforceformat.cpp.o.d -o CMakeFiles/aoforceformat.dir/aoforceformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/aoforceformat.cpp --- src/formats/CMakeFiles/svgformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/depict/depict.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/svgformat.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/svgformat.so --- [ 31%] Linking CXX shared module ../../lib/svgformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/svgformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/svgformat.so CMakeFiles/svgformat.dir/svgformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 31%] Built target svgformat --- src/formats/CMakeFiles/castepformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/castepformat.dir/build.make src/formats/CMakeFiles/castepformat.dir/depend --- src/formats/CMakeFiles/castepformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/castepformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/castepformat.dir/build.make src/formats/CMakeFiles/castepformat.dir/build --- src/formats/CMakeFiles/castepformat.dir/castepformat.cpp.o --- [ 31%] Building CXX object src/formats/CMakeFiles/castepformat.dir/castepformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcastepformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/castepformat.dir/castepformat.cpp.o -MF CMakeFiles/castepformat.dir/castepformat.cpp.o.d -o CMakeFiles/castepformat.dir/castepformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/castepformat.cpp --- src/CMakeFiles/plugin_forcefields.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp: In member function 'void OpenBabel::OBFFElectrostaticCalculationGaff::Compute()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:31: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp: In instantiation of 'void OpenBabel::OBFFElectrostaticCalculationGaff::Compute() [with bool = true]': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:468:7: required from 'double OpenBabel::OBForceFieldGaff::E_Electrostatic() [with bool = true]' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.h:201:50: required from here /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp: In instantiation of 'void OpenBabel::OBFFElectrostaticCalculationGaff::Compute() [with bool = false]': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:468:7: required from 'double OpenBabel::OBForceFieldGaff::E_Electrostatic() [with bool = false]' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.h:201:77: required from here /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:441:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldgaff.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o --- [ 31%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_forcefields_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o -MF CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o.d -o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp --- src/CMakeFiles/plugin_descriptors.dir/all --- --- src/CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o --- [ 31%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/smartsdescriptors.cpp --- src/formats/CMakeFiles/pngformat.dir/all --- --- lib/pngformat.so --- [ 31%] Linking CXX shared module ../../lib/pngformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pngformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pngformat.so CMakeFiles/pngformat.dir/pngformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 31%] Built target pngformat --- src/formats/CMakeFiles/crystal09format.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/crystal09format.dir/build.make src/formats/CMakeFiles/crystal09format.dir/depend --- src/formats/CMakeFiles/crystal09format.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/crystal09format.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/crystal09format.dir/build.make src/formats/CMakeFiles/crystal09format.dir/build --- src/formats/CMakeFiles/crystal09format.dir/crystal09format.cpp.o --- [ 32%] Building CXX object src/formats/CMakeFiles/crystal09format.dir/crystal09format.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcrystal09format_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/crystal09format.dir/crystal09format.cpp.o -MF CMakeFiles/crystal09format.dir/crystal09format.cpp.o.d -o CMakeFiles/crystal09format.dir/crystal09format.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/crystal09format.cpp --- src/formats/CMakeFiles/abinitformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/abinitformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/abinitformat.so --- [ 32%] Linking CXX shared module ../../lib/abinitformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/abinitformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/abinitformat.so CMakeFiles/abinitformat.dir/abinitformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 32%] Built target abinitformat --- src/formats/CMakeFiles/daltonformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/daltonformat.dir/build.make src/formats/CMakeFiles/daltonformat.dir/depend --- src/formats/CMakeFiles/daltonformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/daltonformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/daltonformat.dir/build.make src/formats/CMakeFiles/daltonformat.dir/build --- src/formats/CMakeFiles/daltonformat.dir/daltonformat.cpp.o --- [ 33%] Building CXX object src/formats/CMakeFiles/daltonformat.dir/daltonformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Ddaltonformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/daltonformat.dir/daltonformat.cpp.o -MF CMakeFiles/daltonformat.dir/daltonformat.cpp.o.d -o CMakeFiles/daltonformat.dir/daltonformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/daltonformat.cpp --- src/formats/CMakeFiles/mdlformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mdlformat.cpp:31: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/mdlformat.so --- [ 33%] Linking CXX shared module ../../lib/mdlformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mdlformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/mdlformat.so CMakeFiles/mdlformat.dir/mdlformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 33%] Built target mdlformat --- src/formats/CMakeFiles/dmolformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/dmolformat.dir/build.make src/formats/CMakeFiles/dmolformat.dir/depend --- src/formats/CMakeFiles/dmolformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/dmolformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/dmolformat.dir/build.make src/formats/CMakeFiles/dmolformat.dir/build --- src/formats/CMakeFiles/dmolformat.dir/dmolformat.cpp.o --- [ 33%] Building CXX object src/formats/CMakeFiles/dmolformat.dir/dmolformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Ddmolformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/dmolformat.dir/dmolformat.cpp.o -MF CMakeFiles/dmolformat.dir/dmolformat.cpp.o.d -o CMakeFiles/dmolformat.dir/dmolformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/dmolformat.cpp --- src/formats/CMakeFiles/confabreport.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/align.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/confabreport.cpp:35: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/confabreport.so --- [ 33%] Linking CXX shared module ../../lib/confabreport.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/confabreport.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/confabreport.so CMakeFiles/confabreport.dir/confabreport.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 33%] Built target confabreport --- src/formats/CMakeFiles/fchkformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/fchkformat.dir/build.make src/formats/CMakeFiles/fchkformat.dir/depend --- src/formats/CMakeFiles/fchkformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fchkformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/acesformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/acesformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/acesformat.so --- --- src/formats/CMakeFiles/fchkformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/fchkformat.dir/build.make src/formats/CMakeFiles/fchkformat.dir/build --- src/formats/CMakeFiles/fchkformat.dir/fchkformat.cpp.o --- [ 33%] Building CXX object src/formats/CMakeFiles/fchkformat.dir/fchkformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfchkformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/fchkformat.dir/fchkformat.cpp.o -MF CMakeFiles/fchkformat.dir/fchkformat.cpp.o.d -o CMakeFiles/fchkformat.dir/fchkformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fchkformat.cpp --- src/formats/CMakeFiles/acesformat.dir/all --- [ 33%] Linking CXX shared module ../../lib/acesformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/acesformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/acesformat.so CMakeFiles/acesformat.dir/acesformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/CMakeFiles/plugin_charges.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/chargemodel.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/fromfile.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o --- [ 33%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/eqeq.cpp --- src/formats/CMakeFiles/acesformat.dir/all --- [ 33%] Built target acesformat --- src/formats/CMakeFiles/fhiaimsformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/fhiaimsformat.dir/build.make src/formats/CMakeFiles/fhiaimsformat.dir/depend --- src/formats/CMakeFiles/fhiaimsformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fhiaimsformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/fhiaimsformat.dir/build.make src/formats/CMakeFiles/fhiaimsformat.dir/build --- src/formats/CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o --- [ 33%] Building CXX object src/formats/CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfhiaimsformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o -MF CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o.d -o CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fhiaimsformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/forcefield.cpp:33: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o --- [ 33%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/gen3d.cpp --- src/CMakeFiles/plugin_descriptors.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/descriptors/smartsdescriptors.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- lib/plugin_descriptors.so --- [ 34%] Linking CXX shared module ../lib/plugin_descriptors.so cd /construction/science/openbabel/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/plugin_descriptors.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../lib/plugin_descriptors.so CMakeFiles/plugin_descriptors.dir/descriptors/cansmidescriptor.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz ../lib/libopenbabel.so.7.0.0 --- src/formats/CMakeFiles/aoforceformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/aoforceformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/aoforceformat.so --- --- src/CMakeFiles/plugin_descriptors.dir/all --- [ 34%] Built target plugin_descriptors --- src/formats/CMakeFiles/aoforceformat.dir/all --- [ 34%] Linking CXX shared module ../../lib/aoforceformat.so --- src/formats/CMakeFiles/gamessformat.dir/all --- --- src/formats/CMakeFiles/aoforceformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/aoforceformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/gamessformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/gamessformat.dir/build.make src/formats/CMakeFiles/gamessformat.dir/depend --- src/formats/CMakeFiles/gamessformat.dir/depend --- --- src/formats/CMakeFiles/aoforceformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/aoforceformat.so CMakeFiles/aoforceformat.dir/aoforceformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/gamessformat.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/gamessformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/gamessformat.dir/build.make src/formats/CMakeFiles/gamessformat.dir/build --- src/formats/CMakeFiles/gamessformat.dir/gamessformat.cpp.o --- [ 34%] Building CXX object src/formats/CMakeFiles/gamessformat.dir/gamessformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgamessformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gamessformat.dir/gamessformat.cpp.o -MF CMakeFiles/gamessformat.dir/gamessformat.cpp.o.d -o CMakeFiles/gamessformat.dir/gamessformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gamessformat.cpp --- src/formats/CMakeFiles/smilesformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/smilesformat.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/smilesformat.so --- [ 34%] Linking CXX shared module ../../lib/smilesformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/smilesformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/smilesformat.so CMakeFiles/smilesformat.dir/smilesformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/aoforceformat.dir/all --- [ 34%] Built target aoforceformat --- src/formats/CMakeFiles/gaussformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/gaussformat.dir/build.make src/formats/CMakeFiles/gaussformat.dir/depend --- src/formats/CMakeFiles/gaussformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/gaussformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/gaussformat.dir/build.make src/formats/CMakeFiles/gaussformat.dir/build --- src/formats/CMakeFiles/castepformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/castepformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/castepformat.so --- --- src/formats/CMakeFiles/gaussformat.dir/all --- --- src/formats/CMakeFiles/gaussformat.dir/gaussformat.cpp.o --- --- src/formats/CMakeFiles/castepformat.dir/all --- [ 34%] Linking CXX shared module ../../lib/castepformat.so --- src/formats/CMakeFiles/gaussformat.dir/all --- [ 34%] Building CXX object src/formats/CMakeFiles/gaussformat.dir/gaussformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgaussformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gaussformat.dir/gaussformat.cpp.o -MF CMakeFiles/gaussformat.dir/gaussformat.cpp.o.d -o CMakeFiles/gaussformat.dir/gaussformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gaussformat.cpp --- src/formats/CMakeFiles/castepformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/castepformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/castepformat.so CMakeFiles/castepformat.dir/castepformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/smilesformat.dir/all --- [ 35%] Built target smilesformat --- src/formats/CMakeFiles/gausscubeformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/gausscubeformat.dir/build.make src/formats/CMakeFiles/gausscubeformat.dir/depend --- src/formats/CMakeFiles/gausscubeformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/gausscubeformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/gausscubeformat.dir/build.make src/formats/CMakeFiles/gausscubeformat.dir/build --- src/formats/CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o --- [ 35%] Building CXX object src/formats/CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgausscubeformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o -MF CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o.d -o CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gausscubeformat.cpp --- src/formats/CMakeFiles/castepformat.dir/all --- [ 35%] Built target castepformat --- src/formats/CMakeFiles/gausszmatformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/gausszmatformat.dir/build.make src/formats/CMakeFiles/gausszmatformat.dir/depend --- src/formats/CMakeFiles/gausszmatformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/gausszmatformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/gausszmatformat.dir/build.make src/formats/CMakeFiles/gausszmatformat.dir/build --- src/formats/CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o --- [ 35%] Building CXX object src/formats/CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgausszmatformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o -MF CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o.d -o CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gausszmatformat.cpp --- src/formats/CMakeFiles/daltonformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/daltonformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/daltonformat.so --- [ 35%] Linking CXX shared module ../../lib/daltonformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/daltonformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/daltonformat.so CMakeFiles/daltonformat.dir/daltonformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 35%] Built target daltonformat --- src/formats/CMakeFiles/gulpformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/gulpformat.dir/build.make src/formats/CMakeFiles/gulpformat.dir/depend --- src/formats/CMakeFiles/gulpformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/gulpformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/gulpformat.dir/build.make src/formats/CMakeFiles/gulpformat.dir/build --- src/formats/CMakeFiles/gulpformat.dir/gulpformat.cpp.o --- [ 35%] Building CXX object src/formats/CMakeFiles/gulpformat.dir/gulpformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgulpformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gulpformat.dir/gulpformat.cpp.o -MF CMakeFiles/gulpformat.dir/gulpformat.cpp.o.d -o CMakeFiles/gulpformat.dir/gulpformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gulpformat.cpp --- src/formats/CMakeFiles/fhiaimsformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fhiaimsformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/fhiaimsformat.so --- [ 36%] Linking CXX shared module ../../lib/fhiaimsformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/fhiaimsformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/fhiaimsformat.so CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 36%] Built target fhiaimsformat --- src/formats/CMakeFiles/hinformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/hinformat.dir/build.make src/formats/CMakeFiles/hinformat.dir/depend --- src/formats/CMakeFiles/hinformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/hinformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/hinformat.dir/build.make src/formats/CMakeFiles/hinformat.dir/build --- src/formats/CMakeFiles/hinformat.dir/hinformat.cpp.o --- [ 37%] Building CXX object src/formats/CMakeFiles/hinformat.dir/hinformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dhinformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/hinformat.dir/hinformat.cpp.o -MF CMakeFiles/hinformat.dir/hinformat.cpp.o.d -o CMakeFiles/hinformat.dir/hinformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/hinformat.cpp --- src/formats/CMakeFiles/crystal09format.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/crystal09format.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/crystal09format.so --- [ 37%] Linking CXX shared module ../../lib/crystal09format.so --- src/formats/CMakeFiles/fchkformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fchkformat.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/crystal09format.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/crystal09format.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/crystal09format.so CMakeFiles/crystal09format.dir/crystal09format.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/dmolformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/dmolformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/gausszmatformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gausszmatformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/hinformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/hinformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/hinformat.so --- --- src/formats/CMakeFiles/dmolformat.dir/all --- --- lib/dmolformat.so --- --- src/formats/CMakeFiles/gausszmatformat.dir/all --- --- lib/gausszmatformat.so --- --- src/formats/CMakeFiles/fchkformat.dir/all --- --- lib/fchkformat.so --- --- src/formats/CMakeFiles/hinformat.dir/all --- [ 37%] Linking CXX shared module ../../lib/hinformat.so --- src/CMakeFiles/plugin_ops.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/gen3d.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/gen3d.cpp: In member function 'virtual bool OpenBabel::OpGen3D::Do(OpenBabel::OBBase*, const char*, OpenBabel::OBOp::OpMap*, OpenBabel::OBConversion*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/gen3d.cpp:169:37: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(molCopy); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/gen3d.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/gen3d.cpp:187:35: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(molCopy); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/gen3d.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ --- src/formats/CMakeFiles/gausszmatformat.dir/all --- [ 37%] Linking CXX shared module ../../lib/gausszmatformat.so --- src/formats/CMakeFiles/dmolformat.dir/all --- [ 37%] Linking CXX shared module ../../lib/dmolformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/dmolformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/gausszmatformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gausszmatformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/hinformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hinformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/dmolformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/dmolformat.so CMakeFiles/dmolformat.dir/dmolformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/gausszmatformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/gausszmatformat.so CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/fchkformat.dir/all --- [ 37%] Linking CXX shared module ../../lib/fchkformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/fchkformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/hinformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/hinformat.so CMakeFiles/hinformat.dir/hinformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/fchkformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/fchkformat.so CMakeFiles/fchkformat.dir/fchkformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/crystal09format.dir/all --- [ 37%] Built target crystal09format --- src/formats/CMakeFiles/jaguarformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/jaguarformat.dir/build.make src/formats/CMakeFiles/jaguarformat.dir/depend --- src/formats/CMakeFiles/hinformat.dir/all --- [ 37%] Built target hinformat --- src/formats/CMakeFiles/molproformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/molproformat.dir/build.make src/formats/CMakeFiles/molproformat.dir/depend --- src/formats/CMakeFiles/gausszmatformat.dir/all --- [ 38%] Built target gausszmatformat --- src/formats/CMakeFiles/mopacformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/mopacformat.dir/build.make src/formats/CMakeFiles/mopacformat.dir/depend --- src/formats/CMakeFiles/fchkformat.dir/all --- [ 38%] Built target fchkformat --- src/formats/CMakeFiles/nwchemformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/nwchemformat.dir/build.make src/formats/CMakeFiles/nwchemformat.dir/depend --- src/formats/CMakeFiles/mopacformat.dir/all --- --- src/formats/CMakeFiles/mopacformat.dir/depend --- --- src/formats/CMakeFiles/jaguarformat.dir/all --- --- src/formats/CMakeFiles/jaguarformat.dir/depend --- --- src/formats/CMakeFiles/mopacformat.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/mopacformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/molproformat.dir/all --- --- src/formats/CMakeFiles/molproformat.dir/depend --- --- src/formats/CMakeFiles/jaguarformat.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/jaguarformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/molproformat.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/molproformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/nwchemformat.dir/all --- --- src/formats/CMakeFiles/nwchemformat.dir/depend --- --- src/formats/CMakeFiles/jaguarformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/jaguarformat.dir/build.make src/formats/CMakeFiles/jaguarformat.dir/build --- src/formats/CMakeFiles/molproformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/molproformat.dir/build.make src/formats/CMakeFiles/molproformat.dir/build --- src/formats/CMakeFiles/nwchemformat.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/nwchemformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/molproformat.dir/all --- --- src/formats/CMakeFiles/molproformat.dir/molproformat.cpp.o --- --- src/formats/CMakeFiles/jaguarformat.dir/all --- --- src/formats/CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o --- --- src/formats/CMakeFiles/mopacformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/mopacformat.dir/build.make src/formats/CMakeFiles/mopacformat.dir/build --- src/formats/CMakeFiles/molproformat.dir/all --- [ 38%] Building CXX object src/formats/CMakeFiles/molproformat.dir/molproformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmolproformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/molproformat.dir/molproformat.cpp.o -MF CMakeFiles/molproformat.dir/molproformat.cpp.o.d -o CMakeFiles/molproformat.dir/molproformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/molproformat.cpp --- src/formats/CMakeFiles/mopacformat.dir/all --- --- src/formats/CMakeFiles/mopacformat.dir/mopacformat.cpp.o --- --- src/formats/CMakeFiles/nwchemformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/nwchemformat.dir/build.make src/formats/CMakeFiles/nwchemformat.dir/build --- src/formats/CMakeFiles/jaguarformat.dir/all --- [ 39%] Building CXX object src/formats/CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Djaguarformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o -MF CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o.d -o CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/jaguarformat.cpp --- src/formats/CMakeFiles/nwchemformat.dir/all --- --- src/formats/CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o --- [ 39%] Building CXX object src/formats/CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dnwchemformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o -MF CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o.d -o CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/nwchemformat.cpp --- src/formats/CMakeFiles/mopacformat.dir/all --- [ 39%] Building CXX object src/formats/CMakeFiles/mopacformat.dir/mopacformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmopacformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/mopacformat.dir/mopacformat.cpp.o -MF CMakeFiles/mopacformat.dir/mopacformat.cpp.o.d -o CMakeFiles/mopacformat.dir/mopacformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mopacformat.cpp --- src/formats/CMakeFiles/adfformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/adfformat.cpp:38: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/adfformat.cpp: In member function 'OpenBabel::OBGridData* OpenBabel::OBT41Format::NewData(const OpenBabel::OBT41Format::T41GridData&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/adfformat.cpp:795:73: warning: 'void OpenBabel::OBGridData::SetLimits(const double*, const double*, const double*, const double*)' is deprecated: Use vector version instead [-Wdeprecated-declarations] t41Data->SetLimits( gd.startPoint, gd.xAxis, gd.yAxis, gd.zAxis ); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/adfformat.cpp:46: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/griddata.h:112:10: note: declared here void SetLimits(const double origin[3], const double x[3], const double y[3], ^~~~~~~~~ --- src/formats/CMakeFiles/gulpformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gulpformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/dmolformat.dir/all --- [ 39%] Built target dmolformat --- src/formats/CMakeFiles/pwscfformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pwscfformat.dir/build.make src/formats/CMakeFiles/pwscfformat.dir/depend --- src/formats/CMakeFiles/pwscfformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/pwscfformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/pwscfformat.dir/build.make 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-fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o -MF CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o.d -o CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pwscfformat.cpp --- src/formats/CMakeFiles/adfformat.dir/all --- --- lib/adfformat.so --- --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/largest.cpp.o --- --- src/formats/CMakeFiles/adfformat.dir/all --- [ 39%] Linking CXX shared module ../../lib/adfformat.so --- src/CMakeFiles/plugin_ops.dir/all --- [ 40%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/largest.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/largest.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/largest.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/largest.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/largest.cpp --- src/formats/CMakeFiles/adfformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script 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cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/qchemformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/qchemformat.dir/build.make src/formats/CMakeFiles/qchemformat.dir/build --- src/formats/CMakeFiles/qchemformat.dir/qchemformat.cpp.o --- [ 40%] Building CXX object src/formats/CMakeFiles/qchemformat.dir/qchemformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dqchemformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/qchemformat.dir/qchemformat.cpp.o -MF CMakeFiles/qchemformat.dir/qchemformat.cpp.o.d -o CMakeFiles/qchemformat.dir/qchemformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/qchemformat.cpp --- src/formats/CMakeFiles/gausscubeformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gausscubeformat.cpp:31: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gausscubeformat.cpp: In member function 'virtual bool OpenBabel::OBGaussianCubeFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gausscubeformat.cpp:589:31: warning: 'void OpenBabel::OBGridData::GetOriginVector(double*) const' is deprecated: Use GetOriginVector() instead [-Wdeprecated-declarations] gd->GetOriginVector(origin); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gausscubeformat.cpp:36: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/griddata.h:89:10: note: declared here void GetOriginVector(double o[3]) const; ^~~~~~~~~~~~~~~ --- lib/gausscubeformat.so --- [ 40%] Linking CXX shared module ../../lib/gausscubeformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gausscubeformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/gausscubeformat.so CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 41%] Built target gausscubeformat --- src/formats/CMakeFiles/siestaformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/siestaformat.dir/build.make src/formats/CMakeFiles/siestaformat.dir/depend --- src/formats/CMakeFiles/siestaformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/siestaformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/jaguarformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/jaguarformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/jaguarformat.so --- --- src/formats/CMakeFiles/siestaformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/siestaformat.dir/build.make src/formats/CMakeFiles/siestaformat.dir/build --- src/formats/CMakeFiles/jaguarformat.dir/all --- [ 41%] Linking CXX shared module ../../lib/jaguarformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/jaguarformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/siestaformat.dir/all --- --- src/formats/CMakeFiles/siestaformat.dir/siestaformat.cpp.o --- --- src/formats/CMakeFiles/jaguarformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/jaguarformat.so CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/siestaformat.dir/all --- [ 41%] Building CXX object src/formats/CMakeFiles/siestaformat.dir/siestaformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dsiestaformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/siestaformat.dir/siestaformat.cpp.o -MF CMakeFiles/siestaformat.dir/siestaformat.cpp.o.d -o CMakeFiles/siestaformat.dir/siestaformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/siestaformat.cpp --- src/formats/CMakeFiles/jaguarformat.dir/all --- [ 41%] Built target jaguarformat --- src/formats/CMakeFiles/turbomoleformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/turbomoleformat.dir/build.make src/formats/CMakeFiles/turbomoleformat.dir/depend --- src/formats/CMakeFiles/turbomoleformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/turbomoleformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/turbomoleformat.dir/build.make src/formats/CMakeFiles/turbomoleformat.dir/build --- src/formats/CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o --- [ 41%] Building CXX object src/formats/CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dturbomoleformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o -MF CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o.d -o CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/turbomoleformat.cpp --- src/formats/CMakeFiles/gulpformat.dir/all --- --- lib/gulpformat.so --- [ 41%] Linking CXX shared module ../../lib/gulpformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gulpformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/gulpformat.so CMakeFiles/gulpformat.dir/gulpformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 41%] Built target gulpformat --- src/formats/CMakeFiles/vaspformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/vaspformat.dir/build.make src/formats/CMakeFiles/vaspformat.dir/depend --- src/formats/CMakeFiles/vaspformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/vaspformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/vaspformat.dir/build.make src/formats/CMakeFiles/vaspformat.dir/build --- src/formats/CMakeFiles/pwscfformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pwscfformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/pwscfformat.so --- --- src/formats/CMakeFiles/vaspformat.dir/all --- --- src/formats/CMakeFiles/vaspformat.dir/vaspformat.cpp.o --- --- src/formats/CMakeFiles/pwscfformat.dir/all --- [ 42%] Linking CXX shared module ../../lib/pwscfformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pwscfformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pwscfformat.so CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/vaspformat.dir/all --- [ 42%] Building CXX object src/formats/CMakeFiles/vaspformat.dir/vaspformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dvaspformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo 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-I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xsfformat.dir/xsfformat.cpp.o -MF CMakeFiles/xsfformat.dir/xsfformat.cpp.o.d -o CMakeFiles/xsfformat.dir/xsfformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xsfformat.cpp --- src/formats/CMakeFiles/gamessformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gamessformat.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/gaussformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gaussformat.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/gamessformat.dir/all --- --- lib/gamessformat.so --- [ 42%] Linking CXX shared module ../../lib/gamessformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gamessformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/gamessformat.so CMakeFiles/gamessformat.dir/gamessformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 43%] Built target gamessformat --- src/formats/CMakeFiles/zindoformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/zindoformat.dir/build.make src/formats/CMakeFiles/zindoformat.dir/depend --- src/formats/CMakeFiles/zindoformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/zindoformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/zindoformat.dir/build.make src/formats/CMakeFiles/zindoformat.dir/build --- src/formats/CMakeFiles/zindoformat.dir/zindoformat.cpp.o --- [ 43%] Building CXX object src/formats/CMakeFiles/zindoformat.dir/zindoformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dzindoformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/zindoformat.dir/zindoformat.cpp.o -MF CMakeFiles/zindoformat.dir/zindoformat.cpp.o.d -o CMakeFiles/zindoformat.dir/zindoformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/zindoformat.cpp --- src/formats/CMakeFiles/gaussformat.dir/all --- --- lib/gaussformat.so --- [ 43%] Linking CXX shared module ../../lib/gaussformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gaussformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/gaussformat.so CMakeFiles/gaussformat.dir/gaussformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 43%] Built target gaussformat --- src/formats/CMakeFiles/maeformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/maeformat.dir/build.make src/formats/CMakeFiles/maeformat.dir/depend --- src/formats/CMakeFiles/maeformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/maeformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/qchemformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/qchemformat.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/maeformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/maeformat.dir/build.make src/formats/CMakeFiles/maeformat.dir/build --- src/formats/CMakeFiles/maeformat.dir/maeformat.cpp.o --- [ 43%] Building CXX object src/formats/CMakeFiles/maeformat.dir/maeformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmaeformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/maeformat.dir/maeformat.cpp.o -MF CMakeFiles/maeformat.dir/maeformat.cpp.o.d -o CMakeFiles/maeformat.dir/maeformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/maeformat.cpp --- src/formats/CMakeFiles/qchemformat.dir/all --- --- lib/qchemformat.so --- [ 43%] Linking CXX shared module ../../lib/qchemformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/qchemformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/qchemformat.so CMakeFiles/qchemformat.dir/qchemformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 43%] Built target qchemformat --- src/formats/CMakeFiles/gamessukformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/gamessukformat.dir/build.make src/formats/CMakeFiles/gamessukformat.dir/depend --- src/formats/CMakeFiles/gamessukformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/gamessukformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/gamessukformat.dir/build.make src/formats/CMakeFiles/gamessukformat.dir/build --- src/formats/CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o --- [ 43%] Building CXX object src/formats/CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgamessukformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o -MF CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o.d -o CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gamessukformat.cpp --- src/formats/CMakeFiles/molproformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/molproformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/loader.cpp.o --- [ 43%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/loader.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/loader.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/loader.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/loader.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/loader.cpp --- src/formats/CMakeFiles/turbomoleformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/turbomoleformat.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/molproformat.dir/all --- --- lib/molproformat.so --- [ 44%] Linking CXX shared module ../../lib/molproformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/molproformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/molproformat.so CMakeFiles/molproformat.dir/molproformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 44%] Built target molproformat --- src/CMakeFiles/plugin_forcefields.dir/all --- --- src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o --- [ 44%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_forcefields_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o -MF CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o.d -o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldmmff94.cpp --- src/formats/CMakeFiles/turbomoleformat.dir/all --- --- lib/turbomoleformat.so --- [ 44%] Linking CXX shared module ../../lib/turbomoleformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/turbomoleformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/turbomoleformat.so CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 44%] Built target turbomoleformat --- src/formats/CMakeFiles/orcaformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/orcaformat.dir/build.make src/formats/CMakeFiles/orcaformat.dir/depend --- src/formats/CMakeFiles/orcaformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/orcaformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/orcaformat.dir/build.make src/formats/CMakeFiles/orcaformat.dir/build --- src/formats/CMakeFiles/orcaformat.dir/orcaformat.cpp.o --- [ 44%] Building CXX object src/formats/CMakeFiles/orcaformat.dir/orcaformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dorcaformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/orcaformat.dir/orcaformat.cpp.o -MF CMakeFiles/orcaformat.dir/orcaformat.cpp.o.d -o CMakeFiles/orcaformat.dir/orcaformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/orcaformat.cpp --- src/formats/CMakeFiles/mopacformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mopacformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/mopacformat.so --- [ 45%] Linking CXX shared module ../../lib/mopacformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mopacformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/mopacformat.so CMakeFiles/mopacformat.dir/mopacformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 45%] Built target mopacformat --- src/CMakeFiles/plugin_forcefields.dir/all --- --- src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o --- --- src/formats/CMakeFiles/xsfformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xsfformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_forcefields.dir/all --- [ 45%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_forcefields_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o -MF CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o.d -o CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp --- src/formats/CMakeFiles/xsfformat.dir/all --- --- lib/xsfformat.so --- [ 45%] Linking CXX shared module ../../lib/xsfformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/xsfformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/xsfformat.so CMakeFiles/xsfformat.dir/xsfformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 45%] Built target xsfformat --- src/CMakeFiles/plugin_charges.dir/all --- --- src/CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o --- [ 45%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/qeq.cpp --- src/formats/CMakeFiles/siestaformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/siestaformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/siestaformat.so --- [ 45%] Linking CXX shared module ../../lib/siestaformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/siestaformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/siestaformat.so CMakeFiles/siestaformat.dir/siestaformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 45%] Built target siestaformat --- src/formats/CMakeFiles/APIInterface.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/APIInterface.dir/build.make src/formats/CMakeFiles/APIInterface.dir/depend --- src/formats/CMakeFiles/APIInterface.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/APIInterface.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/APIInterface.dir/build.make src/formats/CMakeFiles/APIInterface.dir/build --- src/formats/CMakeFiles/APIInterface.dir/APIInterface.cpp.o --- [ 45%] Building CXX object src/formats/CMakeFiles/APIInterface.dir/APIInterface.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DAPIInterface_EXPORTS -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/APIInterface.dir/APIInterface.cpp.o -MF CMakeFiles/APIInterface.dir/APIInterface.cpp.o.d -o CMakeFiles/APIInterface.dir/APIInterface.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/APIInterface.cpp --- src/formats/CMakeFiles/zindoformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/zindoformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/zindoformat.so --- [ 45%] Linking CXX shared module ../../lib/zindoformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/zindoformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/zindoformat.so CMakeFiles/zindoformat.dir/zindoformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 46%] Built target zindoformat --- src/formats/CMakeFiles/CSRformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/CSRformat.dir/build.make src/formats/CMakeFiles/CSRformat.dir/depend --- src/formats/CMakeFiles/CSRformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/CSRformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/CSRformat.dir/build.make src/formats/CMakeFiles/CSRformat.dir/build --- src/formats/CMakeFiles/CSRformat.dir/CSRformat.cpp.o --- [ 46%] Building CXX object src/formats/CMakeFiles/CSRformat.dir/CSRformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DCSRformat_EXPORTS -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/CSRformat.dir/CSRformat.cpp.o -MF CMakeFiles/CSRformat.dir/CSRformat.cpp.o.d -o CMakeFiles/CSRformat.dir/CSRformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/CSRformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o --- [ 46%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/neutralize.cpp --- src/formats/CMakeFiles/nwchemformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/nwchemformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/nwchemformat.cpp: In member function 'void OpenBabel::NWChemOutputFormat::ReadMultipoleMoment(std::istream*, OpenBabel::OBMol*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/nwchemformat.cpp:321:45: warning: 'void OpenBabel::matrix3x3::Set(int, int, double)' is deprecated: use the non-constant operator() instead [-Wdeprecated-declarations] quadrupole.Set(i[0], i[1], value); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/nwchemformat.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:189:12: note: declared here void Set(int row,int column, double v) ^~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/nwchemformat.cpp:322:45: warning: 'void OpenBabel::matrix3x3::Set(int, int, double)' is deprecated: use the non-constant operator() instead [-Wdeprecated-declarations] quadrupole.Set(i[1], i[0], value); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/nwchemformat.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:189:12: note: declared here void Set(int row,int column, double v) ^~~ --- lib/nwchemformat.so --- [ 46%] Linking CXX shared module ../../lib/nwchemformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/nwchemformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/nwchemformat.so CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 47%] Built target nwchemformat --- src/formats/CMakeFiles/PQSformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/PQSformat.dir/build.make src/formats/CMakeFiles/PQSformat.dir/depend --- src/formats/CMakeFiles/PQSformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/PQSformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/PQSformat.dir/build.make src/formats/CMakeFiles/PQSformat.dir/build --- src/formats/CMakeFiles/PQSformat.dir/PQSformat.cpp.o --- [ 48%] Building CXX object src/formats/CMakeFiles/PQSformat.dir/PQSformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DPQSformat_EXPORTS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/PQSformat.dir/PQSformat.cpp.o -MF CMakeFiles/PQSformat.dir/PQSformat.cpp.o.d -o CMakeFiles/PQSformat.dir/PQSformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/PQSformat.cpp --- src/formats/CMakeFiles/APIInterface.dir/all --- --- lib/APIInterface.so --- [ 48%] Linking CXX shared module ../../lib/APIInterface.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/APIInterface.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/APIInterface.so CMakeFiles/APIInterface.dir/APIInterface.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 48%] Built target APIInterface --- src/formats/CMakeFiles/MCDLformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/MCDLformat.dir/build.make src/formats/CMakeFiles/MCDLformat.dir/depend --- src/formats/CMakeFiles/MCDLformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/MCDLformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/MCDLformat.dir/build.make src/formats/CMakeFiles/MCDLformat.dir/build --- src/formats/CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o --- [ 49%] Building CXX object src/formats/CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DMCDLformat_EXPORTS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o -MF CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o.d -o CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/MCDLformat.cpp --- src/CMakeFiles/plugin_forcefields.dir/all --- --- src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:27: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp: In member function 'void OpenBabel::OBFFElectrostaticCalculationGhemical::Compute()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:31: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp: In instantiation of 'void OpenBabel::OBFFElectrostaticCalculationGhemical::Compute() [with bool = true]': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:371:7: required from 'double OpenBabel::OBForceFieldGhemical::E_Electrostatic() [with bool = true]' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.h:186:50: required from here /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp: In instantiation of 'void OpenBabel::OBFFElectrostaticCalculationGhemical::Compute() [with bool = false]': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:371:7: required from 'double OpenBabel::OBForceFieldGhemical::E_Electrostatic() [with bool = false]' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.h:186:77: required from here /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:344:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldghemical.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- src/CMakeFiles/plugin_charges.dir/all --- --- src/CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o --- [ 49%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/qtpie.cpp --- src/formats/CMakeFiles/CSRformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/CSRformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/CSRformat.cpp: In member function 'char* OpenBabel::CSRFormat::PadString(char*, int)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/CSRformat.cpp:192:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(output, input, strlen(input)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- lib/CSRformat.so --- [ 49%] Linking CXX shared module ../../lib/CSRformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/CSRformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/CSRformat.so CMakeFiles/CSRformat.dir/CSRformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 49%] Built target CSRformat --- src/formats/CMakeFiles/alchemyformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/alchemyformat.dir/build.make src/formats/CMakeFiles/alchemyformat.dir/depend --- src/formats/CMakeFiles/alchemyformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/alchemyformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/alchemyformat.dir/build.make src/formats/CMakeFiles/alchemyformat.dir/build --- src/formats/CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o --- [ 49%] Building CXX object src/formats/CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dalchemyformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o -MF CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o.d -o CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/alchemyformat.cpp --- src/formats/CMakeFiles/PQSformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/PQSformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/PQSformat.so --- [ 49%] Linking CXX shared module ../../lib/PQSformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/PQSformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/PQSformat.so CMakeFiles/PQSformat.dir/PQSformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 49%] Built target PQSformat --- src/formats/CMakeFiles/acrformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/acrformat.dir/build.make src/formats/CMakeFiles/acrformat.dir/depend --- src/formats/CMakeFiles/acrformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/acrformat.dir/DependInfo.cmake --- src/CMakeFiles/plugin_ops.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/neutralize.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/acrformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/acrformat.dir/build.make src/formats/CMakeFiles/acrformat.dir/build --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o --- --- src/formats/CMakeFiles/acrformat.dir/all --- --- src/formats/CMakeFiles/acrformat.dir/acrformat.cpp.o --- --- src/CMakeFiles/plugin_ops.dir/all --- [ 49%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opsplit.cpp --- src/formats/CMakeFiles/acrformat.dir/all --- [ 49%] Building CXX object src/formats/CMakeFiles/acrformat.dir/acrformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dacrformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/acrformat.dir/acrformat.cpp.o -MF CMakeFiles/acrformat.dir/acrformat.cpp.o.d -o CMakeFiles/acrformat.dir/acrformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/acrformat.cpp --- src/formats/CMakeFiles/vaspformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/vaspformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/vaspformat.so --- [ 49%] Linking CXX shared module ../../lib/vaspformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vaspformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/vaspformat.so CMakeFiles/vaspformat.dir/vaspformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 49%] Built target vaspformat --- src/formats/CMakeFiles/amberformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/amberformat.dir/build.make src/formats/CMakeFiles/amberformat.dir/depend --- src/formats/CMakeFiles/amberformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/amberformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/alchemyformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/alchemyformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/alchemyformat.so --- --- src/formats/CMakeFiles/amberformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/amberformat.dir/build.make src/formats/CMakeFiles/amberformat.dir/build --- src/formats/CMakeFiles/amberformat.dir/amberformat.cpp.o --- --- src/formats/CMakeFiles/alchemyformat.dir/all --- [ 49%] Linking CXX shared module ../../lib/alchemyformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/alchemyformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/amberformat.dir/all --- [ 49%] Building CXX object src/formats/CMakeFiles/amberformat.dir/amberformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Damberformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/amberformat.dir/amberformat.cpp.o -MF CMakeFiles/amberformat.dir/amberformat.cpp.o.d -o CMakeFiles/amberformat.dir/amberformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/amberformat.cpp --- src/formats/CMakeFiles/alchemyformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/alchemyformat.so CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 49%] Built target alchemyformat --- src/formats/CMakeFiles/balstformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/balstformat.dir/build.make src/formats/CMakeFiles/balstformat.dir/depend --- src/formats/CMakeFiles/balstformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/balstformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/balstformat.dir/build.make src/formats/CMakeFiles/balstformat.dir/build --- src/formats/CMakeFiles/balstformat.dir/balstformat.cpp.o --- [ 49%] Building CXX object src/formats/CMakeFiles/balstformat.dir/balstformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dbalstformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/balstformat.dir/balstformat.cpp.o -MF CMakeFiles/balstformat.dir/balstformat.cpp.o.d -o CMakeFiles/balstformat.dir/balstformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/balstformat.cpp --- src/formats/CMakeFiles/acrformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/acrformat.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/acrformat.so --- [ 49%] Linking CXX shared module ../../lib/acrformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/acrformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/acrformat.so CMakeFiles/acrformat.dir/acrformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 49%] Built target acrformat --- src/formats/CMakeFiles/bgfformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/bgfformat.dir/build.make src/formats/CMakeFiles/bgfformat.dir/depend --- src/formats/CMakeFiles/bgfformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/bgfformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/bgfformat.dir/build.make src/formats/CMakeFiles/bgfformat.dir/build --- src/formats/CMakeFiles/bgfformat.dir/bgfformat.cpp.o --- [ 50%] Building CXX object src/formats/CMakeFiles/bgfformat.dir/bgfformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dbgfformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/bgfformat.dir/bgfformat.cpp.o -MF CMakeFiles/bgfformat.dir/bgfformat.cpp.o.d -o CMakeFiles/bgfformat.dir/bgfformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/bgfformat.cpp --- src/formats/CMakeFiles/maeformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/maeformat.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/maeformat.so --- [ 50%] Linking CXX shared module ../../lib/maeformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/maeformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/maeformat.so CMakeFiles/maeformat.dir/maeformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 50%] Built target maeformat --- src/formats/CMakeFiles/boxformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/boxformat.dir/build.make src/formats/CMakeFiles/boxformat.dir/depend --- src/formats/CMakeFiles/boxformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/boxformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/boxformat.dir/build.make src/formats/CMakeFiles/boxformat.dir/build --- src/formats/CMakeFiles/boxformat.dir/boxformat.cpp.o --- [ 50%] Building CXX object src/formats/CMakeFiles/boxformat.dir/boxformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dboxformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/boxformat.dir/boxformat.cpp.o -MF CMakeFiles/boxformat.dir/boxformat.cpp.o.d -o CMakeFiles/boxformat.dir/boxformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/boxformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o --- [ 50%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/optransform.cpp --- src/formats/CMakeFiles/amberformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/amberformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/amberformat.so --- [ 51%] Linking CXX shared module ../../lib/amberformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/amberformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/amberformat.so CMakeFiles/amberformat.dir/amberformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 51%] Built target amberformat --- src/formats/CMakeFiles/cacaoformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cacaoformat.dir/build.make src/formats/CMakeFiles/cacaoformat.dir/depend --- src/formats/CMakeFiles/cacaoformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cacaoformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cacaoformat.dir/build.make src/formats/CMakeFiles/cacaoformat.dir/build --- src/formats/CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o --- [ 52%] Building CXX object src/formats/CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcacaoformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o -MF CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o.d -o CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cacaoformat.cpp --- src/CMakeFiles/plugin_charges.dir/all --- --- src/CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/chargemodel.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/eqeq.h:22, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/eqeq.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o --- [ 52%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/partialcharges.cpp --- src/formats/CMakeFiles/balstformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/balstformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/balstformat.so --- [ 52%] Linking CXX shared module ../../lib/balstformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/balstformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/balstformat.so CMakeFiles/balstformat.dir/balstformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 52%] Built target balstformat --- src/formats/CMakeFiles/cacheformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cacheformat.dir/build.make src/formats/CMakeFiles/cacheformat.dir/depend --- src/formats/CMakeFiles/cacheformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cacheformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cacheformat.dir/build.make src/formats/CMakeFiles/cacheformat.dir/build --- src/formats/CMakeFiles/cacheformat.dir/cacheformat.cpp.o --- [ 52%] Building CXX object src/formats/CMakeFiles/cacheformat.dir/cacheformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcacheformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cacheformat.dir/cacheformat.cpp.o -MF CMakeFiles/cacheformat.dir/cacheformat.cpp.o.d -o CMakeFiles/cacheformat.dir/cacheformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cacheformat.cpp --- src/CMakeFiles/plugin_forcefields.dir/all --- --- src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp: In member function 'void OpenBabel::OBFFTorsionCalculationUFF::Compute()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:33: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp: In member function 'void OpenBabel::OBFFElectrostaticCalculationUFF::Compute()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:515:27: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:24, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:515:56: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:24, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:31: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp: In member function 'virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:1325:35: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(torsioncalc.V)) // don't bother calcuating this torsion ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:1325:35: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(torsioncalc.V)) // don't bother calcuating this torsion ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp: In instantiation of 'void OpenBabel::OBFFTorsionCalculationUFF::Compute() [with bool = true]': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:304:7: required from 'double OpenBabel::OBForceFieldUFF::E_Torsion() [with bool = true]' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:181:42: required from here /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:21: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:21: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:21: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:21: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp: In instantiation of 'void OpenBabel::OBFFTorsionCalculationUFF::Compute() [with bool = false]': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:304:7: required from 'double OpenBabel::OBForceFieldUFF::E_Torsion() [with bool = false]' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:181:63: required from here /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:21: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:21: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:21: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:269:21: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(dotAbbcBccd) || !isfinite(tor)) { // stop any NaN or infinity ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp: In instantiation of 'void OpenBabel::OBFFElectrostaticCalculationUFF::Compute() [with bool = true]': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:555:7: required from 'double OpenBabel::OBForceFieldUFF::E_Electrostatic() [with bool = true]' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:199:48: required from here /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:515:49: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:24, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:515:49: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:24, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:515:49: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:24, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp: In instantiation of 'void OpenBabel::OBFFElectrostaticCalculationUFF::Compute() [with bool = false]': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:555:7: required from 'double OpenBabel::OBForceFieldUFF::E_Electrostatic() [with bool = false]' /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:199:75: required from here /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:515:49: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:24, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:515:49: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:24, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:515:49: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] rab = OBForceField::VectorLengthDerivative(da, db); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.h:24, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:32: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:519:19: warning: 'bool OpenBabel::IsNearZero(const double&, double)' is deprecated [-Wdeprecated-declarations] if (IsNearZero(rab, 1.0e-3)) ~~~~~~~~~~^~~~~~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:30, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefielduff.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obutil.h:198:14: note: declared here OBAPI bool IsNearZero(const double &, const double epsilon=2e-6); ^~~~~~~~~~ --- src/formats/CMakeFiles/carformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/carformat.dir/build.make src/formats/CMakeFiles/carformat.dir/depend --- src/formats/CMakeFiles/carformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/carformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/carformat.dir/build.make src/formats/CMakeFiles/carformat.dir/build --- src/formats/CMakeFiles/carformat.dir/carformat.cpp.o --- [ 52%] Building CXX object src/formats/CMakeFiles/carformat.dir/carformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcarformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/carformat.dir/carformat.cpp.o -MF CMakeFiles/carformat.dir/carformat.cpp.o.d -o CMakeFiles/carformat.dir/carformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/carformat.cpp --- src/formats/CMakeFiles/bgfformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/bgfformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/bgfformat.so --- [ 52%] Linking CXX shared module ../../lib/bgfformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bgfformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/bgfformat.so CMakeFiles/bgfformat.dir/bgfformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 52%] Built target bgfformat --- src/formats/CMakeFiles/cccformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cccformat.dir/build.make src/formats/CMakeFiles/cccformat.dir/depend --- src/formats/CMakeFiles/cacheformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cacheformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/cacheformat.so --- --- src/formats/CMakeFiles/cccformat.dir/all --- --- src/formats/CMakeFiles/cccformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cccformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/cacheformat.dir/all --- [ 52%] Linking CXX shared module ../../lib/cacheformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cacheformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/cccformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cccformat.dir/build.make src/formats/CMakeFiles/cccformat.dir/build --- src/formats/CMakeFiles/cccformat.dir/cccformat.cpp.o --- --- src/formats/CMakeFiles/cacheformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cacheformat.so CMakeFiles/cacheformat.dir/cacheformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/CMakeFiles/plugin_ops.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/partialcharges.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/cccformat.dir/all --- [ 52%] Building CXX object src/formats/CMakeFiles/cccformat.dir/cccformat.cpp.o --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o --- --- src/formats/CMakeFiles/cccformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcccformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cccformat.dir/cccformat.cpp.o -MF CMakeFiles/cccformat.dir/cccformat.cpp.o.d -o CMakeFiles/cccformat.dir/cccformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cccformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- [ 53%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/readconformers.cpp --- src/formats/CMakeFiles/cacheformat.dir/all --- [ 53%] Built target cacheformat --- src/formats/CMakeFiles/chem3dformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/chem3dformat.dir/build.make src/formats/CMakeFiles/chem3dformat.dir/depend --- src/formats/CMakeFiles/boxformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/boxformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/chem3dformat.dir/all --- --- src/formats/CMakeFiles/chem3dformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/chem3dformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/boxformat.dir/all --- --- lib/boxformat.so --- [ 53%] Linking CXX shared module ../../lib/boxformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/boxformat.dir/link.txt 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src/formats/CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchem3dformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o -MF CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o.d -o CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chem3dformat.cpp --- src/formats/CMakeFiles/boxformat.dir/all --- [ 54%] Built target boxformat --- src/formats/CMakeFiles/chemdrawcdx.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/chemdrawcdx.dir/build.make src/formats/CMakeFiles/chemdrawcdx.dir/depend --- src/formats/CMakeFiles/chemdrawcdx.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/chemdrawcdx.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/chemdrawcdx.dir/build.make src/formats/CMakeFiles/chemdrawcdx.dir/build --- src/formats/CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o --- [ 55%] Building CXX object src/formats/CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchemdrawcdx_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o -MF CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o.d -o CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chemdrawcdx.cpp --- src/formats/CMakeFiles/cacaoformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cacaoformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/cacaoformat.so --- [ 55%] Linking CXX shared module ../../lib/cacaoformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cacaoformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cacaoformat.so CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 55%] Built target cacaoformat --- src/formats/CMakeFiles/chemdrawct.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/chemdrawct.dir/build.make src/formats/CMakeFiles/chemdrawct.dir/depend --- src/formats/CMakeFiles/chemdrawct.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/chemdrawct.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/chemdrawct.dir/build.make src/formats/CMakeFiles/chemdrawct.dir/build --- src/formats/CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o --- [ 55%] Building CXX object src/formats/CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchemdrawct_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o -MF CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o.d -o CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chemdrawct.cpp --- src/formats/CMakeFiles/gamessukformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gamessukformat.cpp:16: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/gamessukformat.so --- [ 55%] Linking CXX shared module ../../lib/gamessukformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gamessukformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/gamessukformat.so CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 55%] Built target gamessukformat --- src/formats/CMakeFiles/chemkinformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/chemkinformat.dir/build.make src/formats/CMakeFiles/chemkinformat.dir/depend --- src/formats/CMakeFiles/chemkinformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/chemkinformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/chemkinformat.dir/build.make src/formats/CMakeFiles/chemkinformat.dir/build --- src/formats/CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o --- [ 55%] Building CXX object src/formats/CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchemkinformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o -MF CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o.d -o CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chemkinformat.cpp --- src/formats/CMakeFiles/carformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/carformat.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/carformat.so --- [ 56%] Linking CXX shared module ../../lib/carformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/carformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/carformat.so CMakeFiles/carformat.dir/carformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/CMakeFiles/plugin_forcefields.dir/all --- --- src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldmmff94.cpp:35: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldmmff94.cpp:37: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/forcefields/forcefieldmmff94.cpp:37: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ --- lib/plugin_forcefields.so --- [ 56%] Linking CXX shared module ../lib/plugin_forcefields.so cd /construction/science/openbabel/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/plugin_forcefields.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../lib/plugin_forcefields.so CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldgaff.cpp.o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz ../lib/libopenbabel.so.7.0.0 --- src/formats/CMakeFiles/carformat.dir/all --- [ 56%] Built target carformat --- src/formats/CMakeFiles/chemtoolformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/chemtoolformat.dir/build.make src/formats/CMakeFiles/chemtoolformat.dir/depend --- src/formats/CMakeFiles/chemtoolformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/chemtoolformat.dir/DependInfo.cmake --- src/CMakeFiles/plugin_forcefields.dir/all --- [ 57%] Built target plugin_forcefields --- src/formats/CMakeFiles/cifformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cifformat.dir/build.make src/formats/CMakeFiles/cifformat.dir/depend --- src/formats/CMakeFiles/chemtoolformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/chemtoolformat.dir/build.make src/formats/CMakeFiles/chemtoolformat.dir/build --- src/formats/CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o --- [ 57%] Building CXX object src/formats/CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o --- src/formats/CMakeFiles/cifformat.dir/all --- --- src/formats/CMakeFiles/cifformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cifformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cifformat.dir/build.make src/formats/CMakeFiles/cifformat.dir/build --- src/formats/CMakeFiles/chemtoolformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchemtoolformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o -MF CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o.d -o CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chemtoolformat.cpp --- src/formats/CMakeFiles/cifformat.dir/all --- --- src/formats/CMakeFiles/cifformat.dir/cifformat.cpp.o --- [ 57%] Building CXX object src/formats/CMakeFiles/cifformat.dir/cifformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcifformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cifformat.dir/cifformat.cpp.o -MF CMakeFiles/cifformat.dir/cifformat.cpp.o.d -o CMakeFiles/cifformat.dir/cifformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cifformat.cpp --- src/formats/CMakeFiles/MCDLformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/MCDLformat.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/MCDLformat.so --- [ 57%] Linking CXX shared module ../../lib/MCDLformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/MCDLformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/MCDLformat.so CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 57%] Built target MCDLformat --- src/formats/CMakeFiles/cofformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cofformat.dir/build.make src/formats/CMakeFiles/cofformat.dir/depend --- src/formats/CMakeFiles/cofformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cofformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cofformat.dir/build.make src/formats/CMakeFiles/cofformat.dir/build --- src/formats/CMakeFiles/cofformat.dir/cofformat.cpp.o --- [ 57%] Building CXX object src/formats/CMakeFiles/cofformat.dir/cofformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcofformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cofformat.dir/cofformat.cpp.o -MF CMakeFiles/cofformat.dir/cofformat.cpp.o.d -o CMakeFiles/cofformat.dir/cofformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cofformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/sort.cpp.o --- [ 57%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/sort.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/sort.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/sort.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/sort.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/sort.cpp --- src/CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/phmodel.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/optransform.h:19, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/optransform.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o --- [ 57%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opisomorph.cpp --- src/formats/CMakeFiles/cccformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cccformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/cccformat.so --- [ 58%] Linking CXX shared module ../../lib/cccformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cccformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cccformat.so CMakeFiles/cccformat.dir/cccformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 58%] Built target cccformat --- src/formats/CMakeFiles/crkformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/crkformat.dir/build.make src/formats/CMakeFiles/crkformat.dir/depend --- src/formats/CMakeFiles/crkformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/crkformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/crkformat.dir/build.make src/formats/CMakeFiles/crkformat.dir/build --- src/formats/CMakeFiles/crkformat.dir/crkformat.cpp.o --- [ 58%] Building CXX object src/formats/CMakeFiles/crkformat.dir/crkformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcrkformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/crkformat.dir/crkformat.cpp.o -MF CMakeFiles/crkformat.dir/crkformat.cpp.o.d -o CMakeFiles/crkformat.dir/crkformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/crkformat.cpp --- src/formats/CMakeFiles/chemdrawct.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chemdrawct.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/chemdrawct.so --- [ 58%] Linking CXX shared module ../../lib/chemdrawct.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/chemdrawct.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/chemdrawct.so CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 58%] Built target chemdrawct --- src/formats/CMakeFiles/cssrformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cssrformat.dir/build.make src/formats/CMakeFiles/cssrformat.dir/depend --- src/formats/CMakeFiles/cssrformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cssrformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cssrformat.dir/build.make src/formats/CMakeFiles/cssrformat.dir/build --- src/formats/CMakeFiles/cssrformat.dir/cssrformat.cpp.o --- [ 58%] Building CXX object src/formats/CMakeFiles/cssrformat.dir/cssrformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcssrformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cssrformat.dir/cssrformat.cpp.o -MF CMakeFiles/cssrformat.dir/cssrformat.cpp.o.d -o CMakeFiles/cssrformat.dir/cssrformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cssrformat.cpp --- src/formats/CMakeFiles/chem3dformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chem3dformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/chem3dformat.so --- [ 58%] Linking CXX shared module ../../lib/chem3dformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/chem3dformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/chem3dformat.so CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 58%] Built target chem3dformat --- src/formats/CMakeFiles/dlpolyformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/dlpolyformat.dir/build.make src/formats/CMakeFiles/dlpolyformat.dir/depend --- src/formats/CMakeFiles/dlpolyformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/dlpolyformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/dlpolyformat.dir/build.make src/formats/CMakeFiles/dlpolyformat.dir/build --- src/formats/CMakeFiles/dlpolyformat.dir/dlpolyformat.cpp.o --- [ 58%] Building CXX object src/formats/CMakeFiles/dlpolyformat.dir/dlpolyformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Ddlpolyformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/dlpolyformat.dir/dlpolyformat.cpp.o -MF CMakeFiles/dlpolyformat.dir/dlpolyformat.cpp.o.d -o CMakeFiles/dlpolyformat.dir/dlpolyformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/dlpolyformat.cpp --- src/formats/CMakeFiles/chemtoolformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chemtoolformat.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/chemtoolformat.so --- [ 59%] Linking CXX shared module ../../lib/chemtoolformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/chemtoolformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/chemtoolformat.so CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 59%] Built target chemtoolformat --- src/formats/CMakeFiles/exyzformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/exyzformat.dir/build.make src/formats/CMakeFiles/exyzformat.dir/depend --- src/formats/CMakeFiles/exyzformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/exyzformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/exyzformat.dir/build.make src/formats/CMakeFiles/exyzformat.dir/build --- src/formats/CMakeFiles/exyzformat.dir/exyzformat.cpp.o --- [ 59%] Building CXX object src/formats/CMakeFiles/exyzformat.dir/exyzformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dexyzformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/exyzformat.dir/exyzformat.cpp.o -MF CMakeFiles/exyzformat.dir/exyzformat.cpp.o.d -o CMakeFiles/exyzformat.dir/exyzformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/exyzformat.cpp --- src/formats/CMakeFiles/orcaformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/orcaformat.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/orcaformat.so --- [ 59%] Linking CXX shared module ../../lib/orcaformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/orcaformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/orcaformat.so CMakeFiles/orcaformat.dir/orcaformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 59%] Built target orcaformat --- src/formats/CMakeFiles/fastsearchformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/fastsearchformat.dir/build.make src/formats/CMakeFiles/fastsearchformat.dir/depend --- src/formats/CMakeFiles/fastsearchformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fastsearchformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/fastsearchformat.dir/build.make src/formats/CMakeFiles/fastsearchformat.dir/build --- src/formats/CMakeFiles/fastsearchformat.dir/fastsearchformat.cpp.o --- [ 59%] Building CXX object src/formats/CMakeFiles/fastsearchformat.dir/fastsearchformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfastsearchformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/fastsearchformat.dir/fastsearchformat.cpp.o -MF CMakeFiles/fastsearchformat.dir/fastsearchformat.cpp.o.d -o CMakeFiles/fastsearchformat.dir/fastsearchformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fastsearchformat.cpp --- src/formats/CMakeFiles/crkformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/crkformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/crkformat.so --- [ 59%] Linking CXX shared module ../../lib/crkformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/crkformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/crkformat.so CMakeFiles/crkformat.dir/crkformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 59%] Built target crkformat --- src/formats/CMakeFiles/fastaformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/fastaformat.dir/build.make src/formats/CMakeFiles/fastaformat.dir/depend --- src/formats/CMakeFiles/fastaformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fastaformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/fastaformat.dir/build.make src/formats/CMakeFiles/fastaformat.dir/build --- src/formats/CMakeFiles/fastaformat.dir/fastaformat.cpp.o --- [ 59%] Building CXX object src/formats/CMakeFiles/fastaformat.dir/fastaformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfastaformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/fastaformat.dir/fastaformat.cpp.o -MF CMakeFiles/fastaformat.dir/fastaformat.cpp.o.d -o CMakeFiles/fastaformat.dir/fastaformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fastaformat.cpp --- src/formats/CMakeFiles/cofformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cofformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/cofformat.so --- [ 59%] Linking CXX shared module ../../lib/cofformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cofformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cofformat.so CMakeFiles/cofformat.dir/cofformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 59%] Built target cofformat --- src/formats/CMakeFiles/featformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/featformat.dir/build.make src/formats/CMakeFiles/featformat.dir/depend --- src/formats/CMakeFiles/featformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/featformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/featformat.dir/build.make src/formats/CMakeFiles/featformat.dir/build --- src/formats/CMakeFiles/featformat.dir/featformat.cpp.o --- [ 59%] Building CXX object src/formats/CMakeFiles/featformat.dir/featformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfeatformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/featformat.dir/featformat.cpp.o -MF CMakeFiles/featformat.dir/featformat.cpp.o.d -o CMakeFiles/featformat.dir/featformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/featformat.cpp --- src/formats/CMakeFiles/chemdrawcdx.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chemdrawcdx.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/cssrformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cssrformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/chemdrawcdx.dir/all --- --- lib/chemdrawcdx.so --- --- src/CMakeFiles/plugin_ops.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opisomorph.cpp:15: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/query.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opisomorph.h:18, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opisomorph.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/chemdrawcdx.dir/all --- [ 59%] Linking CXX shared module ../../lib/chemdrawcdx.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/chemdrawcdx.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/chemdrawcdx.so CMakeFiles/chemdrawcdx.dir/chemdrawcdx.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 59%] Built target chemdrawcdx --- src/formats/CMakeFiles/fhformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/fhformat.dir/build.make src/formats/CMakeFiles/fhformat.dir/depend --- src/formats/CMakeFiles/fhformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fhformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/fhformat.dir/build.make src/formats/CMakeFiles/fhformat.dir/build --- src/formats/CMakeFiles/fhformat.dir/fhformat.cpp.o --- [ 59%] Building CXX object src/formats/CMakeFiles/fhformat.dir/fhformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfhformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/fhformat.dir/fhformat.cpp.o -MF CMakeFiles/fhformat.dir/fhformat.cpp.o.d -o CMakeFiles/fhformat.dir/fhformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fhformat.cpp --- src/formats/CMakeFiles/cssrformat.dir/all --- --- lib/cssrformat.so --- --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o --- --- src/formats/CMakeFiles/cssrformat.dir/all --- [ 59%] Linking CXX shared module ../../lib/cssrformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cssrformat.dir/link.txt --verbose=1 --- src/CMakeFiles/plugin_ops.dir/all --- [ 59%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o --- src/formats/CMakeFiles/cssrformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cssrformat.so CMakeFiles/cssrformat.dir/cssrformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/CMakeFiles/plugin_ops.dir/all --- cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/ophighlight.cpp --- src/formats/CMakeFiles/cssrformat.dir/all --- [ 59%] Built target cssrformat --- src/formats/CMakeFiles/fingerprintformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/fingerprintformat.dir/build.make src/formats/CMakeFiles/fingerprintformat.dir/depend --- src/formats/CMakeFiles/fingerprintformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fingerprintformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/fingerprintformat.dir/build.make src/formats/CMakeFiles/fingerprintformat.dir/build --- src/formats/CMakeFiles/fingerprintformat.dir/fingerprintformat.cpp.o --- [ 59%] Building CXX object src/formats/CMakeFiles/fingerprintformat.dir/fingerprintformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfingerprintformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/fingerprintformat.dir/fingerprintformat.cpp.o -MF CMakeFiles/fingerprintformat.dir/fingerprintformat.cpp.o.d -o CMakeFiles/fingerprintformat.dir/fingerprintformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fingerprintformat.cpp --- src/formats/CMakeFiles/fastaformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fastaformat.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/fastsearchformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fastsearchformat.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/exyzformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/exyzformat.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/xout.cpp.o --- --- src/formats/CMakeFiles/fastaformat.dir/all --- --- lib/fastaformat.so --- [ 59%] Linking CXX shared module ../../lib/fastaformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/fastaformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/fastaformat.so CMakeFiles/fastaformat.dir/fastaformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/CMakeFiles/plugin_ops.dir/all --- [ 59%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/xout.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/xout.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/xout.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/xout.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/xout.cpp --- src/formats/CMakeFiles/featformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/featformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/featformat.so --- [ 60%] Linking CXX shared module ../../lib/featformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/featformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/featformat.so CMakeFiles/featformat.dir/featformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/fastaformat.dir/all --- [ 60%] Built target fastaformat --- src/formats/CMakeFiles/fpsformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/fpsformat.dir/build.make src/formats/CMakeFiles/fpsformat.dir/depend --- src/formats/CMakeFiles/fpsformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fpsformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/fpsformat.dir/build.make src/formats/CMakeFiles/fpsformat.dir/build --- src/formats/CMakeFiles/fpsformat.dir/fpsformat.cpp.o --- --- 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-I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/freefracformat.dir/freefracformat.cpp.o -MF CMakeFiles/freefracformat.dir/freefracformat.cpp.o.d -o CMakeFiles/freefracformat.dir/freefracformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/freefracformat.cpp --- src/formats/CMakeFiles/fastsearchformat.dir/all --- --- lib/fastsearchformat.so --- --- src/formats/CMakeFiles/exyzformat.dir/all --- --- lib/exyzformat.so --- [ 61%] Linking CXX shared module ../../lib/exyzformat.so cd 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/usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/fastsearchformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/fastsearchformat.so CMakeFiles/fastsearchformat.dir/fastsearchformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/exyzformat.dir/all --- [ 62%] Built target exyzformat --- src/formats/CMakeFiles/ghemicalformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/ghemicalformat.dir/build.make src/formats/CMakeFiles/ghemicalformat.dir/depend --- src/formats/CMakeFiles/ghemicalformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/ghemicalformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/fastsearchformat.dir/all --- [ 62%] Built target fastsearchformat --- src/formats/CMakeFiles/gromos96format.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/gromos96format.dir/build.make src/formats/CMakeFiles/gromos96format.dir/depend --- src/formats/CMakeFiles/ghemicalformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/ghemicalformat.dir/build.make src/formats/CMakeFiles/ghemicalformat.dir/build --- src/formats/CMakeFiles/gromos96format.dir/all --- --- src/formats/CMakeFiles/gromos96format.dir/depend --- --- src/formats/CMakeFiles/ghemicalformat.dir/all --- --- src/formats/CMakeFiles/ghemicalformat.dir/ghemicalformat.cpp.o --- --- src/formats/CMakeFiles/gromos96format.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/gromos96format.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/gromos96format.dir/build.make src/formats/CMakeFiles/gromos96format.dir/build --- src/formats/CMakeFiles/ghemicalformat.dir/all --- [ 62%] Building CXX object src/formats/CMakeFiles/ghemicalformat.dir/ghemicalformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dghemicalformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/ghemicalformat.dir/ghemicalformat.cpp.o -MF CMakeFiles/ghemicalformat.dir/ghemicalformat.cpp.o.d -o CMakeFiles/ghemicalformat.dir/ghemicalformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/ghemicalformat.cpp --- src/formats/CMakeFiles/gromos96format.dir/all --- --- src/formats/CMakeFiles/gromos96format.dir/gromos96format.cpp.o --- [ 63%] Building CXX object src/formats/CMakeFiles/gromos96format.dir/gromos96format.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgromos96format_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gromos96format.dir/gromos96format.cpp.o -MF CMakeFiles/gromos96format.dir/gromos96format.cpp.o.d -o CMakeFiles/gromos96format.dir/gromos96format.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gromos96format.cpp --- src/formats/CMakeFiles/chemkinformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/chemkinformat.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/chemkinformat.so --- [ 63%] Linking CXX shared module ../../lib/chemkinformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/chemkinformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/chemkinformat.so CMakeFiles/chemkinformat.dir/chemkinformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 63%] Built target chemkinformat --- src/formats/CMakeFiles/groformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/groformat.dir/build.make src/formats/CMakeFiles/groformat.dir/depend --- src/formats/CMakeFiles/groformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/groformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/groformat.dir/build.make src/formats/CMakeFiles/groformat.dir/build --- src/formats/CMakeFiles/groformat.dir/groformat.cpp.o --- [ 63%] Building CXX object src/formats/CMakeFiles/groformat.dir/groformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgroformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/groformat.dir/groformat.cpp.o -MF CMakeFiles/groformat.dir/groformat.cpp.o.d -o CMakeFiles/groformat.dir/groformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/groformat.cpp --- src/formats/CMakeFiles/fhformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fhformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/fhformat.so --- [ 63%] Linking CXX shared module ../../lib/fhformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/fhformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/fhformat.so CMakeFiles/fhformat.dir/fhformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 63%] Built target fhformat --- src/formats/CMakeFiles/lmpdatformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/lmpdatformat.dir/build.make src/formats/CMakeFiles/lmpdatformat.dir/depend --- src/formats/CMakeFiles/lmpdatformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/lmpdatformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/lmpdatformat.dir/build.make src/formats/CMakeFiles/lmpdatformat.dir/build --- src/formats/CMakeFiles/lmpdatformat.dir/lmpdatformat.cpp.o --- [ 63%] Building CXX object src/formats/CMakeFiles/lmpdatformat.dir/lmpdatformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dlmpdatformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/lmpdatformat.dir/lmpdatformat.cpp.o -MF CMakeFiles/lmpdatformat.dir/lmpdatformat.cpp.o.d -o CMakeFiles/lmpdatformat.dir/lmpdatformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/lmpdatformat.cpp --- src/formats/CMakeFiles/dlpolyformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/dlpolyformat.cpp:16: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/dlpolyformat.so --- [ 64%] Linking CXX shared module ../../lib/dlpolyformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/dlpolyformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/dlpolyformat.so CMakeFiles/dlpolyformat.dir/dlpolyformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 64%] Built target dlpolyformat --- src/formats/CMakeFiles/lpmdformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/lpmdformat.dir/build.make src/formats/CMakeFiles/lpmdformat.dir/depend --- src/formats/CMakeFiles/lpmdformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/lpmdformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/lpmdformat.dir/build.make src/formats/CMakeFiles/lpmdformat.dir/build --- src/formats/CMakeFiles/lpmdformat.dir/lpmdformat.cpp.o --- [ 65%] Building CXX object src/formats/CMakeFiles/lpmdformat.dir/lpmdformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dlpmdformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/lpmdformat.dir/lpmdformat.cpp.o -MF CMakeFiles/lpmdformat.dir/lpmdformat.cpp.o.d -o CMakeFiles/lpmdformat.dir/lpmdformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/lpmdformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/ophighlight.cpp:16: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/ophighlight.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o --- [ 65%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/conformer.cpp --- src/formats/CMakeFiles/gromos96format.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/gromos96format.cpp:56: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/ghemicalformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/ghemicalformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/fpsformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fpsformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/freefracformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/freefracformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o --- [ 66%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opalign.cpp --- src/formats/CMakeFiles/ghemicalformat.dir/all --- --- lib/ghemicalformat.so --- --- src/formats/CMakeFiles/gromos96format.dir/all --- --- lib/gromos96format.so --- --- src/formats/CMakeFiles/ghemicalformat.dir/all --- [ 66%] Linking CXX shared module ../../lib/ghemicalformat.so --- src/formats/CMakeFiles/gromos96format.dir/all --- [ 66%] Linking CXX shared module ../../lib/gromos96format.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gromos96format.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/ghemicalformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ghemicalformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/gromos96format.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/gromos96format.so CMakeFiles/gromos96format.dir/gromos96format.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/ghemicalformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread 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/usr/bin/make -f src/formats/CMakeFiles/mmodformat.dir/build.make src/formats/CMakeFiles/mmodformat.dir/depend --- src/formats/CMakeFiles/mmodformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/mmodformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/mmodformat.dir/build.make src/formats/CMakeFiles/mmodformat.dir/build --- src/formats/CMakeFiles/mmodformat.dir/mmodformat.cpp.o --- [ 67%] Building CXX object src/formats/CMakeFiles/mmodformat.dir/mmodformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmmodformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/mmodformat.dir/mmodformat.cpp.o -MF CMakeFiles/mmodformat.dir/mmodformat.cpp.o.d -o CMakeFiles/mmodformat.dir/mmodformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mmodformat.cpp --- src/formats/CMakeFiles/fpsformat.dir/all --- [ 68%] Built target fpsformat --- src/formats/CMakeFiles/moldenformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/moldenformat.dir/build.make src/formats/CMakeFiles/moldenformat.dir/depend --- src/formats/CMakeFiles/moldenformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/moldenformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/moldenformat.dir/build.make src/formats/CMakeFiles/moldenformat.dir/build --- src/formats/CMakeFiles/moldenformat.dir/moldenformat.cpp.o --- [ 68%] Building CXX object src/formats/CMakeFiles/moldenformat.dir/moldenformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmoldenformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/moldenformat.dir/moldenformat.cpp.o -MF CMakeFiles/moldenformat.dir/moldenformat.cpp.o.d -o CMakeFiles/moldenformat.dir/moldenformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/moldenformat.cpp --- src/formats/CMakeFiles/fingerprintformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/fingerprintformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/fingerprintformat.so --- [ 68%] Linking CXX shared module ../../lib/fingerprintformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/fingerprintformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/fingerprintformat.so CMakeFiles/fingerprintformat.dir/fingerprintformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 68%] Built target fingerprintformat --- src/formats/CMakeFiles/mpdformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/mpdformat.dir/build.make src/formats/CMakeFiles/mpdformat.dir/depend --- src/formats/CMakeFiles/mpdformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/mpdformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/mpdformat.dir/build.make src/formats/CMakeFiles/mpdformat.dir/build --- src/formats/CMakeFiles/mpdformat.dir/mpdformat.cpp.o --- [ 68%] Building CXX object src/formats/CMakeFiles/mpdformat.dir/mpdformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmpdformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/mpdformat.dir/mpdformat.cpp.o -MF CMakeFiles/mpdformat.dir/mpdformat.cpp.o.d -o CMakeFiles/mpdformat.dir/mpdformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mpdformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/conformer.cpp:35: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/conformersearch.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/conformer.cpp:37: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/formats/CMakeFiles/groformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/groformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o --- [ 68%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o cd /construction/science/openbabel/.build/src && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opconfab.cpp --- src/formats/CMakeFiles/groformat.dir/all --- --- lib/groformat.so --- [ 68%] Linking CXX shared module ../../lib/groformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/groformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/groformat.so CMakeFiles/groformat.dir/groformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/cifformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/cifformat.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/cifformat.so --- [ 68%] Linking CXX shared module ../../lib/cifformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cifformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cifformat.so CMakeFiles/cifformat.dir/cifformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/groformat.dir/all --- [ 68%] Built target groformat --- src/formats/CMakeFiles/mpqcformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/mpqcformat.dir/build.make src/formats/CMakeFiles/mpqcformat.dir/depend --- src/formats/CMakeFiles/mpqcformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/mpqcformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/mpqcformat.dir/build.make src/formats/CMakeFiles/mpqcformat.dir/build --- src/formats/CMakeFiles/mpqcformat.dir/mpqcformat.cpp.o --- --- src/formats/CMakeFiles/cifformat.dir/all --- [ 68%] Built target cifformat --- src/formats/CMakeFiles/msiformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/msiformat.dir/build.make src/formats/CMakeFiles/msiformat.dir/depend --- src/formats/CMakeFiles/msiformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/msiformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/mpqcformat.dir/all --- [ 68%] Building CXX object src/formats/CMakeFiles/mpqcformat.dir/mpqcformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmpqcformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/mpqcformat.dir/mpqcformat.cpp.o -MF CMakeFiles/mpqcformat.dir/mpqcformat.cpp.o.d -o CMakeFiles/mpqcformat.dir/mpqcformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mpqcformat.cpp --- src/formats/CMakeFiles/msiformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/msiformat.dir/build.make src/formats/CMakeFiles/msiformat.dir/build --- src/formats/CMakeFiles/msiformat.dir/msiformat.cpp.o --- [ 68%] Building CXX object src/formats/CMakeFiles/msiformat.dir/msiformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmsiformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/msiformat.dir/msiformat.cpp.o -MF CMakeFiles/msiformat.dir/msiformat.cpp.o.d -o CMakeFiles/msiformat.dir/msiformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/msiformat.cpp --- src/formats/CMakeFiles/mpdformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mpdformat.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/mpdformat.so --- [ 68%] Linking CXX shared module ../../lib/mpdformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mpdformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/mpdformat.so CMakeFiles/mpdformat.dir/mpdformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/lpmdformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/lpmdformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/mpdformat.dir/all --- [ 68%] Built target mpdformat --- src/formats/CMakeFiles/msmsformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/msmsformat.dir/build.make src/formats/CMakeFiles/msmsformat.dir/depend --- src/formats/CMakeFiles/msmsformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/msmsformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/msmsformat.dir/build.make src/formats/CMakeFiles/msmsformat.dir/build --- src/formats/CMakeFiles/msmsformat.dir/msmsformat.cpp.o --- [ 68%] Building CXX object src/formats/CMakeFiles/msmsformat.dir/msmsformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmsmsformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/msmsformat.dir/msmsformat.cpp.o -MF CMakeFiles/msmsformat.dir/msmsformat.cpp.o.d -o CMakeFiles/msmsformat.dir/msmsformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/msmsformat.cpp --- src/formats/CMakeFiles/lpmdformat.dir/all --- --- lib/lpmdformat.so --- [ 68%] Linking CXX shared module ../../lib/lpmdformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/lpmdformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/lpmdformat.so CMakeFiles/lpmdformat.dir/lpmdformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/mmodformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mmodformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/lpmdformat.dir/all --- [ 68%] Built target lpmdformat --- src/formats/CMakeFiles/opendxformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/opendxformat.dir/build.make src/formats/CMakeFiles/opendxformat.dir/depend --- src/formats/CMakeFiles/opendxformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/opendxformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/opendxformat.dir/build.make src/formats/CMakeFiles/opendxformat.dir/build --- src/formats/CMakeFiles/opendxformat.dir/opendxformat.cpp.o --- [ 69%] Building CXX object src/formats/CMakeFiles/opendxformat.dir/opendxformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dopendxformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/opendxformat.dir/opendxformat.cpp.o -MF CMakeFiles/opendxformat.dir/opendxformat.cpp.o.d -o CMakeFiles/opendxformat.dir/opendxformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/opendxformat.cpp --- src/formats/CMakeFiles/mmodformat.dir/all --- --- lib/mmodformat.so --- [ 69%] Linking CXX shared module ../../lib/mmodformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mmodformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/mmodformat.so CMakeFiles/mmodformat.dir/mmodformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 69%] Built target mmodformat --- src/formats/CMakeFiles/outformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/outformat.dir/build.make src/formats/CMakeFiles/outformat.dir/depend --- src/formats/CMakeFiles/outformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/outformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/outformat.dir/build.make src/formats/CMakeFiles/outformat.dir/build --- src/formats/CMakeFiles/outformat.dir/outformat.cpp.o --- [ 69%] Building CXX object src/formats/CMakeFiles/outformat.dir/outformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Doutformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/outformat.dir/outformat.cpp.o -MF CMakeFiles/outformat.dir/outformat.cpp.o.d -o CMakeFiles/outformat.dir/outformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/outformat.cpp --- src/formats/CMakeFiles/moldenformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/moldenformat.cpp:38: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/moldenformat.so --- [ 69%] Linking CXX shared module ../../lib/moldenformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/moldenformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/moldenformat.so CMakeFiles/moldenformat.dir/moldenformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 69%] Built target moldenformat --- src/formats/CMakeFiles/pcmodelformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pcmodelformat.dir/build.make src/formats/CMakeFiles/pcmodelformat.dir/depend --- src/formats/CMakeFiles/pcmodelformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/pcmodelformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/pcmodelformat.dir/build.make src/formats/CMakeFiles/pcmodelformat.dir/build --- src/formats/CMakeFiles/pcmodelformat.dir/pcmodelformat.cpp.o --- [ 70%] Building CXX object src/formats/CMakeFiles/pcmodelformat.dir/pcmodelformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpcmodelformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pcmodelformat.dir/pcmodelformat.cpp.o -MF CMakeFiles/pcmodelformat.dir/pcmodelformat.cpp.o.d -o CMakeFiles/pcmodelformat.dir/pcmodelformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pcmodelformat.cpp --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/align.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opalign.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opalign.cpp:24: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- src/formats/CMakeFiles/pdbqtformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pdbqtformat.dir/build.make src/formats/CMakeFiles/pdbqtformat.dir/depend --- src/formats/CMakeFiles/pdbqtformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/pdbqtformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/pdbqtformat.dir/build.make src/formats/CMakeFiles/pdbqtformat.dir/build --- src/formats/CMakeFiles/pdbqtformat.dir/pdbqtformat.cpp.o --- [ 71%] Building CXX object src/formats/CMakeFiles/pdbqtformat.dir/pdbqtformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpdbqtformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pdbqtformat.dir/pdbqtformat.cpp.o -MF CMakeFiles/pdbqtformat.dir/pdbqtformat.cpp.o.d -o CMakeFiles/pdbqtformat.dir/pdbqtformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pdbqtformat.cpp --- src/formats/CMakeFiles/mdffformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mdffformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/mdffformat.so --- [ 71%] Linking CXX shared module ../../lib/mdffformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mdffformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/mdffformat.so CMakeFiles/mdffformat.dir/mdffformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 71%] Built target mdffformat --- src/formats/CMakeFiles/pointcloudformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pointcloudformat.dir/build.make src/formats/CMakeFiles/pointcloudformat.dir/depend --- src/formats/CMakeFiles/pointcloudformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/pointcloudformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/pointcloudformat.dir/build.make src/formats/CMakeFiles/pointcloudformat.dir/build --- src/formats/CMakeFiles/pointcloudformat.dir/pointcloudformat.cpp.o --- [ 71%] Building CXX object src/formats/CMakeFiles/pointcloudformat.dir/pointcloudformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpointcloudformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pointcloudformat.dir/pointcloudformat.cpp.o -MF CMakeFiles/pointcloudformat.dir/pointcloudformat.cpp.o.d -o CMakeFiles/pointcloudformat.dir/pointcloudformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pointcloudformat.cpp --- src/formats/CMakeFiles/mmcifformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mmcifformat.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/mmcifformat.so --- [ 72%] Linking CXX shared module ../../lib/mmcifformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mmcifformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/mmcifformat.so CMakeFiles/mmcifformat.dir/mmcifformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/mpqcformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/mpqcformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/CMakeFiles/plugin_ops.dir/all --- --- src/CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/ops/opconfab.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/mpqcformat.dir/all --- --- lib/mpqcformat.so --- --- src/CMakeFiles/plugin_ops.dir/all --- --- lib/plugin_ops.so --- --- src/formats/CMakeFiles/mpqcformat.dir/all --- [ 72%] Linking CXX shared module ../../lib/mpqcformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mpqcformat.dir/link.txt --verbose=1 --- src/CMakeFiles/plugin_ops.dir/all --- [ 72%] Linking CXX shared module ../lib/plugin_ops.so cd /construction/science/openbabel/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/plugin_ops.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 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CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o CMakeFiles/plugin_ops.dir/ops/xout.cpp.o CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz ../lib/libopenbabel.so.7.0.0 --- src/formats/CMakeFiles/mpqcformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/mpqcformat.so CMakeFiles/mpqcformat.dir/mpqcformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/mmcifformat.dir/all --- [ 72%] Built target mmcifformat --- src/formats/CMakeFiles/posformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/posformat.dir/build.make src/formats/CMakeFiles/posformat.dir/depend --- src/formats/CMakeFiles/posformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/posformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/posformat.dir/build.make src/formats/CMakeFiles/posformat.dir/build --- src/formats/CMakeFiles/posformat.dir/posformat.cpp.o --- [ 72%] Building CXX object src/formats/CMakeFiles/posformat.dir/posformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dposformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/posformat.dir/posformat.cpp.o -MF CMakeFiles/posformat.dir/posformat.cpp.o.d -o CMakeFiles/posformat.dir/posformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/posformat.cpp --- src/formats/CMakeFiles/mpqcformat.dir/all --- [ 73%] Built target mpqcformat --- src/formats/CMakeFiles/pqrformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pqrformat.dir/build.make src/formats/CMakeFiles/pqrformat.dir/depend --- src/formats/CMakeFiles/pqrformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats 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[-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/pqrformat.dir/all --- --- src/formats/CMakeFiles/pqrformat.dir/pqrformat.cpp.o --- --- src/formats/CMakeFiles/lmpdatformat.dir/all --- --- lib/lmpdatformat.so --- --- src/CMakeFiles/plugin_ops.dir/all --- [ 73%] Built target plugin_ops --- src/formats/CMakeFiles/rinchiformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/rinchiformat.dir/build.make src/formats/CMakeFiles/rinchiformat.dir/depend --- src/formats/CMakeFiles/pqrformat.dir/all --- [ 73%] Building CXX object src/formats/CMakeFiles/pqrformat.dir/pqrformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpqrformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pqrformat.dir/pqrformat.cpp.o -MF CMakeFiles/pqrformat.dir/pqrformat.cpp.o.d -o CMakeFiles/pqrformat.dir/pqrformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pqrformat.cpp --- src/formats/CMakeFiles/rinchiformat.dir/all --- --- src/formats/CMakeFiles/rinchiformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/rinchiformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/lmpdatformat.dir/all --- [ 73%] Linking CXX shared module ../../lib/lmpdatformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/lmpdatformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/rinchiformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/rinchiformat.dir/build.make src/formats/CMakeFiles/rinchiformat.dir/build --- src/formats/CMakeFiles/lmpdatformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/lmpdatformat.so CMakeFiles/lmpdatformat.dir/lmpdatformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/rinchiformat.dir/all --- --- src/formats/CMakeFiles/rinchiformat.dir/rinchiformat.cpp.o --- [ 73%] Building CXX object src/formats/CMakeFiles/rinchiformat.dir/rinchiformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS 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Building CXX object src/formats/CMakeFiles/rsmiformat.dir/rsmiformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Drsmiformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG 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[-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/msmsformat.so --- [ 73%] Linking CXX shared module ../../lib/msmsformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/msmsformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/msmsformat.so CMakeFiles/msmsformat.dir/msmsformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 74%] Built target msmsformat --- src/formats/CMakeFiles/rxnformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/rxnformat.dir/build.make src/formats/CMakeFiles/rxnformat.dir/depend --- src/formats/CMakeFiles/rxnformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/rxnformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/rxnformat.dir/build.make src/formats/CMakeFiles/rxnformat.dir/build --- src/formats/CMakeFiles/rxnformat.dir/rxnformat.cpp.o --- [ 74%] Building CXX object src/formats/CMakeFiles/rxnformat.dir/rxnformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Drxnformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/rxnformat.dir/rxnformat.cpp.o -MF CMakeFiles/rxnformat.dir/rxnformat.cpp.o.d -o CMakeFiles/rxnformat.dir/rxnformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rxnformat.cpp --- src/formats/CMakeFiles/outformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/outformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/outformat.so --- [ 75%] Linking CXX shared module ../../lib/outformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/outformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/outformat.so CMakeFiles/outformat.dir/outformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 75%] Built target outformat --- src/formats/CMakeFiles/shelxformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/shelxformat.dir/build.make src/formats/CMakeFiles/shelxformat.dir/depend --- src/formats/CMakeFiles/shelxformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/shelxformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/shelxformat.dir/build.make src/formats/CMakeFiles/shelxformat.dir/build --- src/formats/CMakeFiles/shelxformat.dir/shelxformat.cpp.o --- [ 75%] Building CXX object src/formats/CMakeFiles/shelxformat.dir/shelxformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dshelxformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/shelxformat.dir/shelxformat.cpp.o -MF CMakeFiles/shelxformat.dir/shelxformat.cpp.o.d -o CMakeFiles/shelxformat.dir/shelxformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/shelxformat.cpp --- src/formats/CMakeFiles/opendxformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/opendxformat.cpp:26: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/opendxformat.cpp: In member function 'virtual bool OpenBabel::OBOpenDXCubeFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/opendxformat.cpp:275:31: warning: 'void OpenBabel::OBGridData::GetOriginVector(double*) const' is deprecated: Use GetOriginVector() instead [-Wdeprecated-declarations] gd->GetOriginVector(origin); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/opendxformat.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/griddata.h:89:10: note: declared here void GetOriginVector(double o[3]) const; ^~~~~~~~~~~~~~~ --- lib/opendxformat.so --- [ 75%] Linking CXX shared module ../../lib/opendxformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/opendxformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/opendxformat.so CMakeFiles/opendxformat.dir/opendxformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 75%] Built target opendxformat --- src/formats/CMakeFiles/smileyformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/smileyformat.dir/build.make src/formats/CMakeFiles/smileyformat.dir/depend --- src/formats/CMakeFiles/smileyformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/smileyformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/smileyformat.dir/build.make src/formats/CMakeFiles/smileyformat.dir/build --- src/formats/CMakeFiles/smileyformat.dir/smileyformat.cpp.o --- [ 75%] Building CXX object src/formats/CMakeFiles/smileyformat.dir/smileyformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dsmileyformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/smileyformat.dir/smileyformat.cpp.o -MF CMakeFiles/smileyformat.dir/smileyformat.cpp.o.d -o CMakeFiles/smileyformat.dir/smileyformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/smileyformat.cpp --- src/formats/CMakeFiles/pcmodelformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pcmodelformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/pcmodelformat.so --- [ 75%] Linking CXX shared module ../../lib/pcmodelformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pcmodelformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pcmodelformat.so CMakeFiles/pcmodelformat.dir/pcmodelformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 75%] Built target pcmodelformat --- src/formats/CMakeFiles/stlformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/stlformat.dir/build.make src/formats/CMakeFiles/stlformat.dir/depend --- src/formats/CMakeFiles/stlformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/stlformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/stlformat.dir/build.make src/formats/CMakeFiles/stlformat.dir/build --- src/formats/CMakeFiles/stlformat.dir/stlformat.cpp.o --- [ 75%] Building CXX object src/formats/CMakeFiles/stlformat.dir/stlformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dstlformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/stlformat.dir/stlformat.cpp.o -MF CMakeFiles/stlformat.dir/stlformat.cpp.o.d -o CMakeFiles/stlformat.dir/stlformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/stlformat.cpp --- src/formats/CMakeFiles/msiformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/msiformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/msiformat.so --- [ 75%] Linking CXX shared module ../../lib/msiformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/msiformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/msiformat.so CMakeFiles/msiformat.dir/msiformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 75%] Built target msiformat --- src/formats/CMakeFiles/thermoformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/thermoformat.dir/build.make src/formats/CMakeFiles/thermoformat.dir/depend --- src/formats/CMakeFiles/thermoformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/thermoformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/thermoformat.dir/build.make src/formats/CMakeFiles/thermoformat.dir/build --- src/formats/CMakeFiles/thermoformat.dir/thermoformat.cpp.o --- [ 76%] Building CXX object src/formats/CMakeFiles/thermoformat.dir/thermoformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dthermoformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/thermoformat.dir/thermoformat.cpp.o -MF CMakeFiles/thermoformat.dir/thermoformat.cpp.o.d -o CMakeFiles/thermoformat.dir/thermoformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/thermoformat.cpp --- src/formats/CMakeFiles/pointcloudformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pointcloudformat.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/pointcloudformat.so --- [ 76%] Linking CXX shared module ../../lib/pointcloudformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pointcloudformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pointcloudformat.so CMakeFiles/pointcloudformat.dir/pointcloudformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 77%] Built target pointcloudformat --- src/formats/CMakeFiles/tinkerformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/tinkerformat.dir/build.make src/formats/CMakeFiles/tinkerformat.dir/depend --- src/formats/CMakeFiles/tinkerformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/tinkerformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/tinkerformat.dir/build.make src/formats/CMakeFiles/tinkerformat.dir/build --- src/formats/CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o --- [ 77%] Building CXX object src/formats/CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dtinkerformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o -MF CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o.d -o CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/tinkerformat.cpp --- src/formats/CMakeFiles/posformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/posformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/posformat.so --- [ 77%] Linking CXX shared module ../../lib/posformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/posformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/posformat.so CMakeFiles/posformat.dir/posformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 77%] Built target posformat --- src/formats/CMakeFiles/unichemformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/unichemformat.dir/build.make src/formats/CMakeFiles/unichemformat.dir/depend --- src/formats/CMakeFiles/unichemformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/unichemformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/unichemformat.dir/build.make src/formats/CMakeFiles/unichemformat.dir/build --- src/formats/CMakeFiles/unichemformat.dir/unichemformat.cpp.o --- [ 78%] Building CXX object src/formats/CMakeFiles/unichemformat.dir/unichemformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dunichemformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/unichemformat.dir/unichemformat.cpp.o -MF CMakeFiles/unichemformat.dir/unichemformat.cpp.o.d -o CMakeFiles/unichemformat.dir/unichemformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/unichemformat.cpp --- src/formats/CMakeFiles/rinchiformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rinchiformat.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rinchiformat.cpp: In member function 'virtual bool OpenBabel::ReactionInChIFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rinchiformat.cpp:147:53: warning: 'OpenBabel::OBAtom* OpenBabel::OBMol::GetFirstAtom() const' is deprecated [-Wdeprecated-declarations] if (mol.NumAtoms() == 1 && mol.GetFirstAtom()->GetAtomicNum() == 0) { ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rinchiformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/mol.h:280:18: note: declared here OBAtom *GetFirstAtom() const; ^~~~~~~~~~~~ --- lib/rinchiformat.so --- [ 78%] Linking CXX shared module ../../lib/rinchiformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rinchiformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/rinchiformat.so CMakeFiles/rinchiformat.dir/rinchiformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 78%] Built target rinchiformat --- src/formats/CMakeFiles/viewmolformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/viewmolformat.dir/build.make src/formats/CMakeFiles/viewmolformat.dir/depend --- src/formats/CMakeFiles/viewmolformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/viewmolformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/viewmolformat.dir/build.make src/formats/CMakeFiles/viewmolformat.dir/build --- src/formats/CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o --- [ 78%] Building CXX object src/formats/CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dviewmolformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o -MF CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o.d -o CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/viewmolformat.cpp --- src/formats/CMakeFiles/stlformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/stlformat.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/stlformat.so --- [ 78%] Linking CXX shared module ../../lib/stlformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/stlformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/stlformat.so CMakeFiles/stlformat.dir/stlformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 78%] Built target stlformat --- src/formats/CMakeFiles/wlnformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/wlnformat.dir/build.make src/formats/CMakeFiles/wlnformat.dir/depend --- src/formats/CMakeFiles/wlnformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/wlnformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/wlnformat.dir/build.make src/formats/CMakeFiles/wlnformat.dir/build --- src/formats/CMakeFiles/wlnformat.dir/wlnformat.cpp.o --- [ 78%] Building CXX object src/formats/CMakeFiles/wlnformat.dir/wlnformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dwlnformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/wlnformat.dir/wlnformat.cpp.o -MF CMakeFiles/wlnformat.dir/wlnformat.cpp.o.d -o CMakeFiles/wlnformat.dir/wlnformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/wlnformat.cpp --- src/formats/CMakeFiles/rsmiformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rsmiformat.cpp:20: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/rsmiformat.so --- [ 78%] Linking CXX shared module ../../lib/rsmiformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rsmiformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/rsmiformat.so CMakeFiles/rsmiformat.dir/rsmiformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/shelxformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/shelxformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/shelxformat.so --- [ 78%] Linking CXX shared module ../../lib/shelxformat.so --- src/formats/CMakeFiles/rsmiformat.dir/all --- [ 79%] Built target rsmiformat --- src/formats/CMakeFiles/shelxformat.dir/all --- cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/shelxformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/xedformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/xedformat.dir/build.make src/formats/CMakeFiles/xedformat.dir/depend --- src/formats/CMakeFiles/shelxformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/shelxformat.so CMakeFiles/shelxformat.dir/shelxformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/xedformat.dir/all --- --- src/formats/CMakeFiles/xedformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/xedformat.dir/DependInfo.cmake --- src/formats/CMakeFiles/rxnformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rxnformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rxnformat.cpp: In function 'void OpenBabel::WriteMolFile(OpenBabel::OBMol*, OpenBabel::OBConversion*, OpenBabel::OBFormat*)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rxnformat.cpp:262:38: warning: 'OpenBabel::OBAtom* OpenBabel::OBMol::GetFirstAtom() const' is deprecated [-Wdeprecated-declarations] OBAtom *atm = pmol->GetFirstAtom(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/rxnformat.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/mol.h:280:18: note: declared here OBAtom *GetFirstAtom() const; ^~~~~~~~~~~~ --- src/formats/CMakeFiles/xedformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/xedformat.dir/build.make src/formats/CMakeFiles/xedformat.dir/build --- src/formats/CMakeFiles/rxnformat.dir/all --- --- lib/rxnformat.so --- --- src/formats/CMakeFiles/xedformat.dir/all --- --- src/formats/CMakeFiles/xedformat.dir/xedformat.cpp.o --- --- src/formats/CMakeFiles/rxnformat.dir/all --- [ 79%] Linking CXX shared module ../../lib/rxnformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rxnformat.dir/link.txt --verbose=1 --- src/formats/CMakeFiles/xedformat.dir/all --- [ 80%] Building CXX object src/formats/CMakeFiles/xedformat.dir/xedformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dxedformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xedformat.dir/xedformat.cpp.o -MF CMakeFiles/xedformat.dir/xedformat.cpp.o.d -o CMakeFiles/xedformat.dir/xedformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xedformat.cpp --- src/formats/CMakeFiles/rxnformat.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/rxnformat.so CMakeFiles/rxnformat.dir/rxnformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/shelxformat.dir/all --- [ 81%] Built target shelxformat --- src/formats/CMakeFiles/xyzformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/xyzformat.dir/build.make src/formats/CMakeFiles/xyzformat.dir/depend --- src/formats/CMakeFiles/xyzformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/xyzformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/xyzformat.dir/build.make src/formats/CMakeFiles/xyzformat.dir/build --- src/formats/CMakeFiles/xyzformat.dir/xyzformat.cpp.o --- --- src/formats/CMakeFiles/rxnformat.dir/all --- [ 81%] Built target rxnformat --- src/formats/CMakeFiles/yasaraformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/yasaraformat.dir/build.make src/formats/CMakeFiles/yasaraformat.dir/depend --- src/formats/CMakeFiles/xyzformat.dir/all --- [ 81%] Building CXX object src/formats/CMakeFiles/xyzformat.dir/xyzformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dxyzformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xyzformat.dir/xyzformat.cpp.o -MF CMakeFiles/xyzformat.dir/xyzformat.cpp.o.d -o CMakeFiles/xyzformat.dir/xyzformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xyzformat.cpp --- src/formats/CMakeFiles/yasaraformat.dir/all --- --- src/formats/CMakeFiles/yasaraformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/yasaraformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/yasaraformat.dir/build.make src/formats/CMakeFiles/yasaraformat.dir/build --- src/formats/CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o --- [ 81%] Building CXX object src/formats/CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dyasaraformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -MF CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o.d -o CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/yasaraformat.cpp --- src/formats/CMakeFiles/pqrformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pqrformat.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/pqrformat.so --- [ 81%] Linking CXX shared module ../../lib/pqrformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pqrformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pqrformat.so CMakeFiles/pqrformat.dir/pqrformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 81%] Built target pqrformat --- src/formats/CMakeFiles/png2format.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/png2format.dir/build.make src/formats/CMakeFiles/png2format.dir/depend --- src/formats/CMakeFiles/png2format.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/png2format.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/png2format.dir/build.make src/formats/CMakeFiles/png2format.dir/build --- src/formats/CMakeFiles/png2format.dir/png2format.cpp.o --- [ 81%] Building CXX object src/formats/CMakeFiles/png2format.dir/png2format.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpng2format_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/png2format.dir/png2format.cpp.o -MF CMakeFiles/png2format.dir/png2format.cpp.o.d -o CMakeFiles/png2format.dir/png2format.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/png2format.cpp --- src/formats/CMakeFiles/tinkerformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/tinkerformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/tinkerformat.so --- [ 81%] Linking CXX shared module ../../lib/tinkerformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/tinkerformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/tinkerformat.so CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 81%] Built target tinkerformat --- src/formats/CMakeFiles/cdxmlformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cdxmlformat.dir/build.make src/formats/CMakeFiles/cdxmlformat.dir/depend --- src/formats/CMakeFiles/cdxmlformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cdxmlformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cdxmlformat.dir/build.make src/formats/CMakeFiles/cdxmlformat.dir/build --- src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o --- [ 81%] Building CXX object src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcdxmlformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o -MF CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o.d -o CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/cdxmlformat.cpp --- src/formats/CMakeFiles/viewmolformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/viewmolformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/viewmolformat.so --- [ 82%] Linking CXX shared module ../../lib/viewmolformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/viewmolformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/viewmolformat.so CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 82%] Built target viewmolformat --- src/formats/CMakeFiles/png2format.dir/all --- --- src/formats/CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o --- [ 82%] Building CXX object src/formats/CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpng2format_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o -MF CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o.d -o CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/depict/cairopainter.cpp --- src/formats/CMakeFiles/unichemformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/unichemformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/unichemformat.so --- [ 82%] Linking CXX shared module ../../lib/unichemformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/unichemformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/unichemformat.so CMakeFiles/unichemformat.dir/unichemformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- src/formats/CMakeFiles/wlnformat.dir/all --- --- src/formats/CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o --- [ 82%] Building CXX object src/formats/CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dwlnformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o -MF CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o.d -o CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/wln-nextmove.cpp --- src/formats/CMakeFiles/unichemformat.dir/all --- [ 82%] Built target unichemformat --- src/formats/CMakeFiles/cmlformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cmlformat.dir/build.make src/formats/CMakeFiles/cmlformat.dir/depend --- src/formats/CMakeFiles/cmlformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cmlformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cmlformat.dir/build.make src/formats/CMakeFiles/cmlformat.dir/build --- src/formats/CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o --- [ 82%] Building CXX object src/formats/CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcmlformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o -MF CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o.d -o CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/cmlformat.cpp --- src/formats/CMakeFiles/thermoformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/thermoformat.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/thermoformat.so --- [ 82%] Linking CXX shared module ../../lib/thermoformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/thermoformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/thermoformat.so CMakeFiles/thermoformat.dir/thermoformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 82%] Built target thermoformat --- src/formats/CMakeFiles/cdxmlformat.dir/all --- --- src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o --- [ 82%] Building CXX object src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcdxmlformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o -MF CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o.d -o CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/xml.cpp --- src/formats/CMakeFiles/xedformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xedformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/xedformat.so --- [ 82%] Linking CXX shared module ../../lib/xedformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/xedformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/xedformat.so CMakeFiles/xedformat.dir/xedformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 82%] Built target xedformat --- src/formats/CMakeFiles/cmlreactformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/cmlreactformat.dir/build.make src/formats/CMakeFiles/cmlreactformat.dir/depend --- src/formats/CMakeFiles/cmlreactformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cmlreactformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cmlreactformat.dir/build.make src/formats/CMakeFiles/cmlreactformat.dir/build --- src/formats/CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o --- [ 82%] Building CXX object src/formats/CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcmlreactformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o -MF CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o.d -o CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/cmlreactformat.cpp --- src/formats/CMakeFiles/cmlreactformat.dir/xml/xml.cpp.o --- [ 82%] Building CXX object src/formats/CMakeFiles/cmlreactformat.dir/xml/xml.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcmlreactformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cmlreactformat.dir/xml/xml.cpp.o -MF CMakeFiles/cmlreactformat.dir/xml/xml.cpp.o.d -o CMakeFiles/cmlreactformat.dir/xml/xml.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/xml.cpp --- src/formats/CMakeFiles/yasaraformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/yasaraformat.cpp:36: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/yasaraformat.so --- [ 82%] Linking CXX shared module ../../lib/yasaraformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/yasaraformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/yasaraformat.so CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 82%] Built target yasaraformat --- src/formats/CMakeFiles/pubchem.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pubchem.dir/build.make src/formats/CMakeFiles/pubchem.dir/depend --- src/formats/CMakeFiles/pubchem.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/pubchem.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/pubchem.dir/build.make src/formats/CMakeFiles/pubchem.dir/build --- src/formats/CMakeFiles/pubchem.dir/xml/pubchem.cpp.o --- [ 82%] Building CXX object src/formats/CMakeFiles/pubchem.dir/xml/pubchem.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpubchem_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pubchem.dir/xml/pubchem.cpp.o -MF CMakeFiles/pubchem.dir/xml/pubchem.cpp.o.d -o CMakeFiles/pubchem.dir/xml/pubchem.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/pubchem.cpp --- src/formats/CMakeFiles/png2format.dir/all --- --- src/formats/CMakeFiles/png2format.dir/png2format.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/depict/depict.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/png2format.cpp:18: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/png2format.so --- [ 83%] Linking CXX shared module ../../lib/png2format.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/png2format.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/png2format.so CMakeFiles/png2format.dir/png2format.cpp.o CMakeFiles/png2format.dir/__/depict/cairopainter.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 83%] Built target png2format --- src/formats/CMakeFiles/xmlformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/xmlformat.dir/build.make src/formats/CMakeFiles/xmlformat.dir/depend --- src/formats/CMakeFiles/xmlformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/xmlformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/xmlformat.dir/build.make src/formats/CMakeFiles/xmlformat.dir/build --- src/formats/CMakeFiles/xmlformat.dir/xml/xmlformat.cpp.o --- [ 83%] Building CXX object src/formats/CMakeFiles/xmlformat.dir/xml/xmlformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dxmlformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xmlformat.dir/xml/xmlformat.cpp.o -MF CMakeFiles/xmlformat.dir/xml/xmlformat.cpp.o.d -o CMakeFiles/xmlformat.dir/xml/xmlformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/xmlformat.cpp --- src/formats/CMakeFiles/cdxmlformat.dir/all --- --- src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/cdxmlformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/xmlformat.dir/all --- --- src/formats/CMakeFiles/xmlformat.dir/xml/xml.cpp.o --- --- src/formats/CMakeFiles/xyzformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xyzformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/xyzformat.so --- --- src/formats/CMakeFiles/xmlformat.dir/all --- [ 83%] Building CXX object src/formats/CMakeFiles/xmlformat.dir/xml/xml.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dxmlformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xmlformat.dir/xml/xml.cpp.o -MF CMakeFiles/xmlformat.dir/xml/xml.cpp.o.d -o CMakeFiles/xmlformat.dir/xml/xml.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/xml.cpp --- src/formats/CMakeFiles/xyzformat.dir/all --- [ 83%] Linking CXX shared module ../../lib/xyzformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/xyzformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/xyzformat.so CMakeFiles/xyzformat.dir/xyzformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 84%] Built target xyzformat --- src/formats/CMakeFiles/chemdoodlejsonformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/chemdoodlejsonformat.dir/build.make src/formats/CMakeFiles/chemdoodlejsonformat.dir/depend --- src/formats/CMakeFiles/chemdoodlejsonformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/chemdoodlejsonformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/chemdoodlejsonformat.dir/build.make src/formats/CMakeFiles/chemdoodlejsonformat.dir/build --- src/formats/CMakeFiles/chemdoodlejsonformat.dir/json/chemdoodlejsonformat.cpp.o --- [ 84%] Building CXX object src/formats/CMakeFiles/chemdoodlejsonformat.dir/json/chemdoodlejsonformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchemdoodlejsonformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chemdoodlejsonformat.dir/json/chemdoodlejsonformat.cpp.o -MF CMakeFiles/chemdoodlejsonformat.dir/json/chemdoodlejsonformat.cpp.o.d -o CMakeFiles/chemdoodlejsonformat.dir/json/chemdoodlejsonformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/json/chemdoodlejsonformat.cpp --- src/formats/CMakeFiles/smileyformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/smileyformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/smileyformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- lib/smileyformat.so --- [ 84%] Linking CXX shared module ../../lib/smileyformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/smileyformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/smileyformat.so CMakeFiles/smileyformat.dir/smileyformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 84%] Built target smileyformat --- src/formats/CMakeFiles/chemicaljsonformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/chemicaljsonformat.dir/build.make src/formats/CMakeFiles/chemicaljsonformat.dir/depend --- src/formats/CMakeFiles/chemicaljsonformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/chemicaljsonformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/chemicaljsonformat.dir/build.make src/formats/CMakeFiles/chemicaljsonformat.dir/build --- src/formats/CMakeFiles/chemicaljsonformat.dir/json/chemicaljsonformat.cpp.o --- [ 84%] Building CXX object src/formats/CMakeFiles/chemicaljsonformat.dir/json/chemicaljsonformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchemicaljsonformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chemicaljsonformat.dir/json/chemicaljsonformat.cpp.o -MF CMakeFiles/chemicaljsonformat.dir/json/chemicaljsonformat.cpp.o.d -o CMakeFiles/chemicaljsonformat.dir/json/chemicaljsonformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/json/chemicaljsonformat.cpp --- src/formats/CMakeFiles/cdxmlformat.dir/all --- --- lib/cdxmlformat.so --- [ 84%] Linking CXX shared module ../../lib/cdxmlformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cdxmlformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cdxmlformat.so CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.cpp.o CMakeFiles/cdxmlformat.dir/xml/xml.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm /usr/local/lib/libxml2.so ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 84%] Built target cdxmlformat --- src/formats/CMakeFiles/pubchemjsonformat.dir/all --- /usr/bin/make -f src/formats/CMakeFiles/pubchemjsonformat.dir/build.make src/formats/CMakeFiles/pubchemjsonformat.dir/depend --- src/formats/CMakeFiles/pubchemjsonformat.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/pubchemjsonformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/pubchemjsonformat.dir/build.make src/formats/CMakeFiles/pubchemjsonformat.dir/build --- tools/CMakeFiles/obabel.dir/all --- /usr/bin/make -f tools/CMakeFiles/obabel.dir/build.make tools/CMakeFiles/obabel.dir/depend --- src/formats/CMakeFiles/pubchemjsonformat.dir/all --- --- src/formats/CMakeFiles/pubchemjsonformat.dir/json/pubchemjsonformat.cpp.o --- --- tools/CMakeFiles/obabel.dir/all --- --- tools/CMakeFiles/obabel.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obabel.dir/DependInfo.cmake --- src/formats/CMakeFiles/pubchemjsonformat.dir/all --- [ 84%] Building CXX object src/formats/CMakeFiles/pubchemjsonformat.dir/json/pubchemjsonformat.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpubchemjsonformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pubchemjsonformat.dir/json/pubchemjsonformat.cpp.o -MF CMakeFiles/pubchemjsonformat.dir/json/pubchemjsonformat.cpp.o.d -o CMakeFiles/pubchemjsonformat.dir/json/pubchemjsonformat.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/json/pubchemjsonformat.cpp --- tools/CMakeFiles/obabel.dir/all --- /usr/bin/make -f tools/CMakeFiles/obabel.dir/build.make tools/CMakeFiles/obabel.dir/build --- tools/CMakeFiles/obabel.dir/obabel.cpp.o --- [ 84%] Building CXX object tools/CMakeFiles/obabel.dir/obabel.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obabel.dir/obabel.cpp.o -MF CMakeFiles/obabel.dir/obabel.cpp.o.d -o CMakeFiles/obabel.dir/obabel.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obabel.cpp --- src/formats/CMakeFiles/pdbqtformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/obfunctions.h:22, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pdbqtformat.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/typer.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/pdbqtformat.cpp:33: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- lib/pdbqtformat.so --- [ 84%] Linking CXX shared module ../../lib/pdbqtformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pdbqtformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pdbqtformat.so CMakeFiles/pdbqtformat.dir/pdbqtformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 84%] Built target pdbqtformat --- tools/CMakeFiles/obconformer.dir/all --- /usr/bin/make -f tools/CMakeFiles/obconformer.dir/build.make tools/CMakeFiles/obconformer.dir/depend --- tools/CMakeFiles/obconformer.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obconformer.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obconformer.dir/build.make tools/CMakeFiles/obconformer.dir/build --- tools/CMakeFiles/obconformer.dir/obconformer.cpp.o --- [ 84%] Building CXX object tools/CMakeFiles/obconformer.dir/obconformer.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obconformer.dir/obconformer.cpp.o -MF CMakeFiles/obconformer.dir/obconformer.cpp.o.d -o CMakeFiles/obconformer.dir/obconformer.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obconformer.cpp --- src/formats/CMakeFiles/pubchem.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/pubchem.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- src/formats/CMakeFiles/pubchem.dir/xml/xml.cpp.o --- [ 84%] Building CXX object src/formats/CMakeFiles/pubchem.dir/xml/xml.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpubchem_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pubchem.dir/xml/xml.cpp.o -MF CMakeFiles/pubchem.dir/xml/xml.cpp.o.d -o CMakeFiles/pubchem.dir/xml/xml.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/xml.cpp --- src/formats/CMakeFiles/cmlformat.dir/all --- --- src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o --- [ 85%] Building CXX object src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o cd /construction/science/openbabel/.build/src/formats && /usr/local/libexec/ccache/c++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcmlformat_EXPORTS -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/usr/local/include/cairo -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/inchi -I/usr/local/include/libxml2 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cmlformat.dir/xml/xml.cpp.o -MF CMakeFiles/cmlformat.dir/xml/xml.cpp.o.d -o CMakeFiles/cmlformat.dir/xml/xml.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/xml.cpp --- src/formats/CMakeFiles/xmlformat.dir/all --- --- lib/xmlformat.so --- [ 85%] Linking CXX shared module ../../lib/xmlformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/xmlformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/xmlformat.so CMakeFiles/xmlformat.dir/xml/xmlformat.cpp.o CMakeFiles/xmlformat.dir/xml/xml.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm /usr/local/lib/libxml2.so ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- tools/CMakeFiles/obenergy.dir/all --- --- src/CMakeFiles/plugin_charges.dir/all --- --- src/CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/chargemodel.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/qeq.h:22, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/qeq.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- tools/CMakeFiles/obenergy.dir/all --- /usr/bin/make -f tools/CMakeFiles/obenergy.dir/build.make tools/CMakeFiles/obenergy.dir/depend --- tools/CMakeFiles/obenergy.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obenergy.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obenergy.dir/build.make tools/CMakeFiles/obenergy.dir/build --- src/formats/CMakeFiles/xmlformat.dir/all --- [ 86%] Built target xmlformat --- tools/CMakeFiles/obfit.dir/all --- /usr/bin/make -f tools/CMakeFiles/obfit.dir/build.make tools/CMakeFiles/obfit.dir/depend --- tools/CMakeFiles/obfit.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obfit.dir/DependInfo.cmake --- tools/CMakeFiles/obenergy.dir/all --- --- tools/CMakeFiles/obenergy.dir/obenergy.cpp.o --- [ 86%] Building CXX object tools/CMakeFiles/obenergy.dir/obenergy.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obenergy.dir/obenergy.cpp.o -MF CMakeFiles/obenergy.dir/obenergy.cpp.o.d -o CMakeFiles/obenergy.dir/obenergy.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obenergy.cpp --- tools/CMakeFiles/obfit.dir/all --- /usr/bin/make -f tools/CMakeFiles/obfit.dir/build.make tools/CMakeFiles/obfit.dir/build --- tools/CMakeFiles/obfit.dir/obfit.cpp.o --- [ 86%] Building CXX object tools/CMakeFiles/obfit.dir/obfit.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obfit.dir/obfit.cpp.o -MF CMakeFiles/obfit.dir/obfit.cpp.o.d -o CMakeFiles/obfit.dir/obfit.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obfit.cpp --- src/CMakeFiles/plugin_charges.dir/all --- --- src/CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/chargemodel.h:25, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/qtpie.h:22, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/charges/qtpie.cpp:21: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/plugin_charges.so --- [ 86%] Linking CXX shared module ../lib/plugin_charges.so cd /construction/science/openbabel/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/plugin_charges.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../lib/plugin_charges.so CMakeFiles/plugin_charges.dir/charges/eem.cpp.o CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o CMakeFiles/plugin_charges.dir/charges/none.cpp.o CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o CMakeFiles/plugin_charges.dir/charges/qtpie.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz ../lib/libopenbabel.so.7.0.0 [ 87%] Built target plugin_charges --- tools/CMakeFiles/obfitall.dir/all --- /usr/bin/make -f tools/CMakeFiles/obfitall.dir/build.make tools/CMakeFiles/obfitall.dir/depend --- tools/CMakeFiles/obfitall.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obfitall.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obfitall.dir/build.make tools/CMakeFiles/obfitall.dir/build --- tools/CMakeFiles/obfitall.dir/obfitall.cpp.o --- [ 87%] Building CXX object tools/CMakeFiles/obfitall.dir/obfitall.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obfitall.dir/obfitall.cpp.o -MF 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/usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obgen.dir/obgen.cpp.o -MF CMakeFiles/obgen.dir/obgen.cpp.o.d -o CMakeFiles/obgen.dir/obgen.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obgen.cpp --- tools/CMakeFiles/obabel.dir/all --- --- bin/obabel --- [ 88%] Linking CXX executable ../bin/obabel cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obabel.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obabel.dir/obabel.cpp.o -o ../bin/obabel -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 88%] Built target obabel --- tools/CMakeFiles/obminimize.dir/all --- /usr/bin/make -f tools/CMakeFiles/obminimize.dir/build.make tools/CMakeFiles/obminimize.dir/depend --- tools/CMakeFiles/obminimize.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obminimize.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obminimize.dir/build.make tools/CMakeFiles/obminimize.dir/build --- tools/CMakeFiles/obminimize.dir/obminimize.cpp.o --- [ 88%] Building CXX object tools/CMakeFiles/obminimize.dir/obminimize.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obminimize.dir/obminimize.cpp.o -MF CMakeFiles/obminimize.dir/obminimize.cpp.o.d -o CMakeFiles/obminimize.dir/obminimize.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obminimize.cpp --- tools/CMakeFiles/obfit.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obfit.cpp:36: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obfit.cpp:38: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- bin/obfit --- [ 88%] Linking CXX executable ../bin/obfit cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obfit.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obfit.dir/obfit.cpp.o -o ../bin/obfit -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 88%] Built target obfit --- tools/CMakeFiles/obmm.dir/all --- /usr/bin/make -f tools/CMakeFiles/obmm.dir/build.make tools/CMakeFiles/obmm.dir/depend --- tools/CMakeFiles/obmm.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obmm.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obmm.dir/build.make tools/CMakeFiles/obmm.dir/build --- tools/CMakeFiles/obmm.dir/obmm.cpp.o --- [ 88%] Building CXX object tools/CMakeFiles/obmm.dir/obmm.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obmm.dir/obmm.cpp.o -MF CMakeFiles/obmm.dir/obmm.cpp.o.d -o CMakeFiles/obmm.dir/obmm.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp --- src/formats/CMakeFiles/pubchem.dir/all --- --- lib/pubchem.so --- [ 89%] Linking CXX shared module ../../lib/pubchem.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pubchem.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pubchem.so CMakeFiles/pubchem.dir/xml/pubchem.cpp.o CMakeFiles/pubchem.dir/xml/xml.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm /usr/local/lib/libxml2.so ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 89%] Built target pubchem --- tools/CMakeFiles/obconformer.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obconformer.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obconformer.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obconformer.cpp: In function 'int main(int, char**)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obconformer.cpp:90:33: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(mol); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obconformer.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obconformer.cpp:106:33: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(mol); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obconformer.cpp:25: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ --- tools/CMakeFiles/obprobe.dir/all --- /usr/bin/make -f tools/CMakeFiles/obprobe.dir/build.make tools/CMakeFiles/obprobe.dir/depend --- tools/CMakeFiles/obconformer.dir/all --- --- bin/obconformer --- [ 89%] Linking CXX executable ../bin/obconformer cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obconformer.dir/link.txt --verbose=1 --- tools/CMakeFiles/obprobe.dir/all --- --- tools/CMakeFiles/obprobe.dir/depend --- --- tools/CMakeFiles/obconformer.dir/all --- /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obconformer.dir/obconformer.cpp.o -o ../bin/obconformer -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 --- tools/CMakeFiles/obprobe.dir/all --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obprobe.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obprobe.dir/build.make tools/CMakeFiles/obprobe.dir/build --- tools/CMakeFiles/obprobe.dir/obprobe.cpp.o --- [ 89%] Building CXX object tools/CMakeFiles/obprobe.dir/obprobe.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obprobe.dir/obprobe.cpp.o -MF CMakeFiles/obprobe.dir/obprobe.cpp.o.d -o CMakeFiles/obprobe.dir/obprobe.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obprobe.cpp --- tools/CMakeFiles/obconformer.dir/all --- [ 90%] Built target obconformer --- tools/CMakeFiles/obprop.dir/all --- /usr/bin/make -f tools/CMakeFiles/obprop.dir/build.make tools/CMakeFiles/obprop.dir/depend --- tools/CMakeFiles/obprop.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obprop.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obprop.dir/build.make tools/CMakeFiles/obprop.dir/build --- tools/CMakeFiles/obprop.dir/obprop.cpp.o --- [ 90%] Building CXX object tools/CMakeFiles/obprop.dir/obprop.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obprop.dir/obprop.cpp.o -MF CMakeFiles/obprop.dir/obprop.cpp.o.d -o CMakeFiles/obprop.dir/obprop.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obprop.cpp --- tools/CMakeFiles/obenergy.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obenergy.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- bin/obenergy --- [ 90%] Linking CXX executable ../bin/obenergy cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obenergy.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obenergy.dir/obenergy.cpp.o -o ../bin/obenergy -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 91%] Built target obenergy --- tools/CMakeFiles/obrotamer.dir/all --- /usr/bin/make -f tools/CMakeFiles/obrotamer.dir/build.make tools/CMakeFiles/obrotamer.dir/depend --- tools/CMakeFiles/obrotamer.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obrotamer.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obrotamer.dir/build.make tools/CMakeFiles/obrotamer.dir/build --- tools/CMakeFiles/obrotamer.dir/obrotamer.cpp.o --- [ 91%] Building CXX object tools/CMakeFiles/obrotamer.dir/obrotamer.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obrotamer.dir/obrotamer.cpp.o -MF CMakeFiles/obrotamer.dir/obrotamer.cpp.o.d -o CMakeFiles/obrotamer.dir/obrotamer.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotamer.cpp --- src/formats/CMakeFiles/cmlreactformat.dir/all --- --- src/formats/CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/cmlreactformat.cpp:16: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/cmlreactformat.so --- [ 91%] Linking CXX shared module ../../lib/cmlreactformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmlreactformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cmlreactformat.so CMakeFiles/cmlreactformat.dir/xml/cmlreactformat.cpp.o CMakeFiles/cmlreactformat.dir/xml/xml.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm /usr/local/lib/libxml2.so ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 92%] Built target cmlreactformat --- tools/CMakeFiles/obrotate.dir/all --- /usr/bin/make -f tools/CMakeFiles/obrotate.dir/build.make tools/CMakeFiles/obrotate.dir/depend --- tools/CMakeFiles/obrotate.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obrotate.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obrotate.dir/build.make tools/CMakeFiles/obrotate.dir/build --- tools/CMakeFiles/obrotate.dir/obrotate.cpp.o --- [ 92%] Building CXX object tools/CMakeFiles/obrotate.dir/obrotate.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obrotate.dir/obrotate.cpp.o -MF CMakeFiles/obrotate.dir/obrotate.cpp.o.d -o CMakeFiles/obrotate.dir/obrotate.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotate.cpp --- tools/CMakeFiles/obminimize.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obminimize.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- bin/obminimize --- [ 93%] Linking CXX executable ../bin/obminimize cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obminimize.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obminimize.dir/obminimize.cpp.o -o ../bin/obminimize -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 93%] Built target obminimize --- tools/CMakeFiles/obsym.dir/all --- /usr/bin/make -f tools/CMakeFiles/obsym.dir/build.make tools/CMakeFiles/obsym.dir/depend --- tools/CMakeFiles/obsym.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obsym.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obsym.dir/build.make tools/CMakeFiles/obsym.dir/build --- tools/CMakeFiles/obsym.dir/obsym.cpp.o --- [ 93%] Building CXX object tools/CMakeFiles/obsym.dir/obsym.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obsym.dir/obsym.cpp.o -MF CMakeFiles/obsym.dir/obsym.cpp.o.d -o CMakeFiles/obsym.dir/obsym.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obsym.cpp --- tools/CMakeFiles/obfitall.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obfitall.cpp:36: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obfitall.cpp:37: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- bin/obfitall --- [ 93%] Linking CXX executable ../bin/obfitall cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obfitall.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obfitall.dir/obfitall.cpp.o -o ../bin/obfitall -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 93%] Built target obfitall --- tools/CMakeFiles/obtautomer.dir/all --- /usr/bin/make -f tools/CMakeFiles/obtautomer.dir/build.make tools/CMakeFiles/obtautomer.dir/depend --- tools/CMakeFiles/obtautomer.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obtautomer.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obtautomer.dir/build.make tools/CMakeFiles/obtautomer.dir/build --- tools/CMakeFiles/obtautomer.dir/obtautomer.cpp.o --- [ 93%] Building CXX object tools/CMakeFiles/obtautomer.dir/obtautomer.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obtautomer.dir/obtautomer.cpp.o -MF CMakeFiles/obtautomer.dir/obtautomer.cpp.o.d -o CMakeFiles/obtautomer.dir/obtautomer.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obtautomer.cpp --- tools/CMakeFiles/obrotamer.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotamer.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/transform3d.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/spacegroup.h:23, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/generic.h:29, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotamer.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotamer.cpp: In function 'int main(int, char**)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotamer.cpp:99:61: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] rotorKey[i] = rand.NextInt() % rotor->GetResolution().size(); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotamer.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotamer.cpp:28: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ --- bin/obrotamer --- [ 93%] Linking CXX executable ../bin/obrotamer cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obrotamer.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obrotamer.dir/obrotamer.cpp.o -o ../bin/obrotamer -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 93%] Built target obrotamer --- tools/CMakeFiles/obthermo.dir/all --- /usr/bin/make -f tools/CMakeFiles/obthermo.dir/build.make tools/CMakeFiles/obthermo.dir/depend --- tools/CMakeFiles/obthermo.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obthermo.dir/DependInfo.cmake --- src/formats/CMakeFiles/wlnformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/wln-nextmove.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/wlnformat.so --- --- tools/CMakeFiles/obthermo.dir/all --- /usr/bin/make -f tools/CMakeFiles/obthermo.dir/build.make tools/CMakeFiles/obthermo.dir/build --- tools/CMakeFiles/obthermo.dir/obthermo.cpp.o --- --- src/formats/CMakeFiles/wlnformat.dir/all --- [ 93%] Linking CXX shared module ../../lib/wlnformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/wlnformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/wlnformat.so CMakeFiles/wlnformat.dir/wlnformat.cpp.o "CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o" -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm --- tools/CMakeFiles/obthermo.dir/all --- [ 93%] Building CXX object tools/CMakeFiles/obthermo.dir/obthermo.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obthermo.dir/obthermo.cpp.o -MF CMakeFiles/obthermo.dir/obthermo.cpp.o.d -o CMakeFiles/obthermo.dir/obthermo.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obthermo.cpp --- src/formats/CMakeFiles/wlnformat.dir/all --- [ 93%] Built target wlnformat --- tools/CMakeFiles/obdistgen.dir/all --- /usr/bin/make -f tools/CMakeFiles/obdistgen.dir/build.make tools/CMakeFiles/obdistgen.dir/depend --- tools/CMakeFiles/obdistgen.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obdistgen.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obdistgen.dir/build.make tools/CMakeFiles/obdistgen.dir/build --- tools/CMakeFiles/obdistgen.dir/obdistgen.cpp.o --- [ 93%] Building CXX object tools/CMakeFiles/obdistgen.dir/obdistgen.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obdistgen.dir/obdistgen.cpp.o -MF CMakeFiles/obdistgen.dir/obdistgen.cpp.o.d -o CMakeFiles/obdistgen.dir/obdistgen.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obdistgen.cpp --- tools/CMakeFiles/obgen.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obgen.cpp:33: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obgen.cpp: In function 'int main(int, char**)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obgen.cpp:138:33: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(mol); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obgen.cpp:33: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ --- bin/obgen --- [ 93%] Linking CXX executable ../bin/obgen cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obgen.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obgen.dir/obgen.cpp.o -o ../bin/obgen -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 --- tools/CMakeFiles/obmm.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:56: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp: In function 'int main(int, char**)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:274:33: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(mol); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:59: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:280:33: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(mol); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:59: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:402:33: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(mol); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:59: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:415:33: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] pFF->UpdateCoordinates(mol); ^ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obmm.cpp:59: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ --- bin/obmm --- [ 93%] Linking CXX executable ../bin/obmm cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obmm.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obmm.dir/obmm.cpp.o -o ../bin/obmm -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 93%] Built target obmm --- tools/CMakeFiles/obgrep.dir/all --- /usr/bin/make -f tools/CMakeFiles/obgrep.dir/build.make tools/CMakeFiles/obgrep.dir/depend --- tools/CMakeFiles/obgen.dir/all --- [ 93%] Built target obgen --- tools/CMakeFiles/obspectrophore.dir/all --- /usr/bin/make -f tools/CMakeFiles/obspectrophore.dir/build.make tools/CMakeFiles/obspectrophore.dir/depend --- tools/CMakeFiles/obgrep.dir/all --- --- tools/CMakeFiles/obgrep.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obgrep.dir/DependInfo.cmake --- tools/CMakeFiles/obspectrophore.dir/all --- --- tools/CMakeFiles/obspectrophore.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obspectrophore.dir/DependInfo.cmake --- tools/CMakeFiles/obgrep.dir/all --- /usr/bin/make -f tools/CMakeFiles/obgrep.dir/build.make tools/CMakeFiles/obgrep.dir/build --- tools/CMakeFiles/obspectrophore.dir/all --- /usr/bin/make -f tools/CMakeFiles/obspectrophore.dir/build.make tools/CMakeFiles/obspectrophore.dir/build --- tools/CMakeFiles/obgrep.dir/all --- --- tools/CMakeFiles/obgrep.dir/obgrep.cpp.o --- [ 93%] Building CXX object tools/CMakeFiles/obgrep.dir/obgrep.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obgrep.dir/obgrep.cpp.o -MF CMakeFiles/obgrep.dir/obgrep.cpp.o.d -o CMakeFiles/obgrep.dir/obgrep.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obgrep.cpp --- tools/CMakeFiles/obspectrophore.dir/all --- --- tools/CMakeFiles/obspectrophore.dir/obspectrophore.cpp.o --- [ 93%] Building CXX object tools/CMakeFiles/obspectrophore.dir/obspectrophore.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obspectrophore.dir/obspectrophore.cpp.o -MF CMakeFiles/obspectrophore.dir/obspectrophore.cpp.o.d -o CMakeFiles/obspectrophore.dir/obspectrophore.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obspectrophore.cpp --- tools/CMakeFiles/obprop.dir/all --- --- bin/obprop --- [ 93%] Linking CXX executable ../bin/obprop cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obprop.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obprop.dir/obprop.cpp.o -o ../bin/obprop -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 93%] Built target obprop --- tools/CMakeFiles/obrms.dir/all --- /usr/bin/make -f tools/CMakeFiles/obrms.dir/build.make tools/CMakeFiles/obrms.dir/depend --- tools/CMakeFiles/obrms.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obrms.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obrms.dir/build.make tools/CMakeFiles/obrms.dir/build --- tools/CMakeFiles/obrms.dir/obrms.cpp.o --- [ 93%] Building CXX object tools/CMakeFiles/obrms.dir/obrms.cpp.o cd /construction/science/openbabel/.build/tools && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT tools/CMakeFiles/obrms.dir/obrms.cpp.o -MF CMakeFiles/obrms.dir/obrms.cpp.o.d -o CMakeFiles/obrms.dir/obrms.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrms.cpp --- tools/CMakeFiles/obsym.dir/all --- --- bin/obsym --- [ 93%] Linking CXX executable ../bin/obsym cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obsym.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obsym.dir/obsym.cpp.o -o ../bin/obsym -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 94%] Built target obsym --- src/GUI/CMakeFiles/obgui.dir/all --- /usr/bin/make -f src/GUI/CMakeFiles/obgui.dir/build.make src/GUI/CMakeFiles/obgui.dir/depend --- src/GUI/CMakeFiles/obgui.dir/depend --- cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/GUI /construction/science/openbabel/.build /construction/science/openbabel/.build/src/GUI /construction/science/openbabel/.build/src/GUI/CMakeFiles/obgui.dir/DependInfo.cmake /usr/bin/make -f src/GUI/CMakeFiles/obgui.dir/build.make src/GUI/CMakeFiles/obgui.dir/build --- src/GUI/CMakeFiles/obgui.dir/OBGUI.cpp.o --- [ 95%] Building CXX object src/GUI/CMakeFiles/obgui.dir/OBGUI.cpp.o cd /construction/science/openbabel/.build/src/GUI && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/GUI/. -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT src/GUI/CMakeFiles/obgui.dir/OBGUI.cpp.o -MF CMakeFiles/obgui.dir/OBGUI.cpp.o.d -o CMakeFiles/obgui.dir/OBGUI.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/GUI/OBGUI.cpp --- tools/CMakeFiles/obrotate.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotate.cpp:39: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrotate.cpp:40: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- bin/obrotate --- [ 95%] Linking CXX executable ../bin/obrotate cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obrotate.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obrotate.dir/obrotate.cpp.o -o ../bin/obrotate -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 96%] Built target obrotate --- src/GUI/CMakeFiles/obgui.dir/all --- --- src/GUI/CMakeFiles/obgui.dir/stdwx.cpp.o --- [ 96%] Building CXX object src/GUI/CMakeFiles/obgui.dir/stdwx.cpp.o cd /construction/science/openbabel/.build/src/GUI && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/GUI/. -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT src/GUI/CMakeFiles/obgui.dir/stdwx.cpp.o -MF CMakeFiles/obgui.dir/stdwx.cpp.o.d -o CMakeFiles/obgui.dir/stdwx.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/GUI/stdwx.cpp --- tools/CMakeFiles/obtautomer.dir/all --- --- bin/obtautomer --- [ 96%] Linking CXX executable ../bin/obtautomer cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obtautomer.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obtautomer.dir/obtautomer.cpp.o -o ../bin/obtautomer -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 --- tools/CMakeFiles/obthermo.dir/all --- --- bin/obthermo --- --- tools/CMakeFiles/obtautomer.dir/all --- [ 96%] Built target obtautomer --- src/GUI/CMakeFiles/obgui.dir/all --- --- src/GUI/CMakeFiles/obgui.dir/optswx.cpp.o --- --- tools/CMakeFiles/obthermo.dir/all --- [ 96%] Linking CXX executable ../bin/obthermo cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obthermo.dir/link.txt --verbose=1 --- src/GUI/CMakeFiles/obgui.dir/all --- [ 96%] Building CXX object src/GUI/CMakeFiles/obgui.dir/optswx.cpp.o cd /construction/science/openbabel/.build/src/GUI && /usr/local/libexec/ccache/c++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RAPIDJSON -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/usr/local/include -I/construction/science/openbabel/.build/include -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data -I/construction/science/openbabel/.build/data -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include -I/usr/local/include/eigen3 -I/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/GUI/. -isystem /usr/local/lib/wx/include/gtk3-unicode-3.0 -isystem /usr/local/include/wx-3.0 -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIE -MD -MT src/GUI/CMakeFiles/obgui.dir/optswx.cpp.o -MF CMakeFiles/obgui.dir/optswx.cpp.o.d -o CMakeFiles/obgui.dir/optswx.cpp.o -c /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/GUI/optswx.cpp --- tools/CMakeFiles/obthermo.dir/all --- /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obthermo.dir/obthermo.cpp.o -o ../bin/obthermo -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 97%] Built target obthermo --- tools/CMakeFiles/obprobe.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/griddata.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obprobe.cpp:31: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- bin/obprobe --- [ 98%] Linking CXX executable ../bin/obprobe cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obprobe.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obprobe.dir/obprobe.cpp.o -o ../bin/obprobe -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 --- tools/CMakeFiles/obgrep.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obgrep.cpp:29: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ --- bin/obgrep --- [ 98%] Linking CXX executable ../bin/obgrep cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obgrep.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obgrep.dir/obgrep.cpp.o -o ../bin/obgrep -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 --- tools/CMakeFiles/obprobe.dir/all --- [ 98%] Built target obprobe --- tools/CMakeFiles/obgrep.dir/all --- [ 98%] Built target obgrep --- src/formats/CMakeFiles/chemdoodlejsonformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/json/chemdoodlejsonformat.cpp:22: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/chemdoodlejsonformat.so --- [ 98%] Linking CXX shared module ../../lib/chemdoodlejsonformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/chemdoodlejsonformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/chemdoodlejsonformat.so CMakeFiles/chemdoodlejsonformat.dir/json/chemdoodlejsonformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 98%] Built target chemdoodlejsonformat --- src/formats/CMakeFiles/chemicaljsonformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/json/chemicaljsonformat.cpp:17: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/chemicaljsonformat.so --- [ 99%] Linking CXX shared module ../../lib/chemicaljsonformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/chemicaljsonformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/chemicaljsonformat.so CMakeFiles/chemicaljsonformat.dir/json/chemicaljsonformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [ 99%] Built target chemicaljsonformat --- tools/CMakeFiles/obdistgen.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/forcefield.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obdistgen.cpp:30: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- bin/obdistgen --- [ 99%] Linking CXX executable ../bin/obdistgen cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obdistgen.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obdistgen.dir/obdistgen.cpp.o -o ../bin/obdistgen -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [ 99%] Built target obdistgen --- tools/CMakeFiles/obrms.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrms.cpp:33: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:186:112: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern(const OBSmartsPattern& cp): _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) ^ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/bond.h:32, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/query.h:27, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools/obrms.cpp:35: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- bin/obrms --- [ 99%] Linking CXX executable ../bin/obrms cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obrms.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obrms.dir/obrms.cpp.o -o ../bin/obrms -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [100%] Built target obrms --- src/formats/CMakeFiles/cmlformat.dir/all --- --- src/formats/CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/matrix3x3.h:26, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/xml/cmlformat.cpp:19: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/cmlformat.so --- [100%] Linking CXX shared module ../../lib/cmlformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmlformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/cmlformat.so CMakeFiles/cmlformat.dir/xml/cmlformat.cpp.o CMakeFiles/cmlformat.dir/xml/xml.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm /usr/local/lib/libxml2.so ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [100%] Built target cmlformat --- src/formats/CMakeFiles/pubchemjsonformat.dir/all --- In file included from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/atom.h:35, from /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats/json/pubchemjsonformat.cpp:23: /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:281:29: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] return ! ( (*this) == other ); ^~~~~ /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/include/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ --- lib/pubchemjsonformat.so --- [100%] Linking CXX shared module ../../lib/pubchemjsonformat.so cd /construction/science/openbabel/.build/src/formats && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pubchemjsonformat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -fPIC -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG -shared -o ../../lib/pubchemjsonformat.so CMakeFiles/pubchemjsonformat.dir/json/pubchemjsonformat.cpp.o -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so ../../lib/libinchi.so.0.4.1 -lm ../../lib/libopenbabel.so.7.0.0 /usr/local/lib/libmaeparser.so /usr/local/lib/libcoordgen.so -lm -ldl -lz /usr/local/lib/libcairo.so -lc -lm [100%] Built target pubchemjsonformat --- tools/CMakeFiles/obspectrophore.dir/all --- --- bin/obspectrophore --- [100%] Linking CXX executable ../bin/obspectrophore cd /construction/science/openbabel/.build/tools && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obspectrophore.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obspectrophore.dir/obspectrophore.cpp.o -o ../bin/obspectrophore -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../lib/libopenbabel.so.7.0.0 [100%] Built target obspectrophore --- src/GUI/CMakeFiles/obgui.dir/all --- --- bin/obgui --- [100%] Linking CXX executable ../../bin/obgui cd /construction/science/openbabel/.build/src/GUI && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/obgui.dir/link.txt --verbose=1 /usr/local/libexec/ccache/c++ -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -pthread -pipe -O2 -fno-strict-aliasing -Wno-narrowing -std=c++11 -DNDEBUG -O3 -DNDEBUG CMakeFiles/obgui.dir/OBGUI.cpp.o CMakeFiles/obgui.dir/stdwx.cpp.o CMakeFiles/obgui.dir/optswx.cpp.o -o ../../bin/obgui -L/usr/local/lib -Wl,-z,origin,-rpath,/usr/local/lib:/construction/science/openbabel/.build/lib ../../lib/libopenbabel.so.7.0.0 -L/usr/local/lib -pthread -lwx_baseu-3.0 -lwx_gtk3u_core-3.0 -lwx_gtk3u_adv-3.0 [100%] Built target obgui /usr/local/bin/cmake -E cmake_progress_start /construction/science/openbabel/.build/CMakeFiles 0 SUCCEEDED 00:03:23 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for openbabel-3.1.1.178 ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac -B/construction/science/openbabel/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/openbabel/.build/CMakeFiles /construction/science/openbabel/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f data/CMakeFiles/data_headers.dir/build.make data/CMakeFiles/data_headers.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/data 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src/CMakeFiles/plugin_descriptors.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src /construction/science/openbabel/.build /construction/science/openbabel/.build/src /construction/science/openbabel/.build/src/CMakeFiles/plugin_descriptors.dir/DependInfo.cmake /usr/bin/make -f src/CMakeFiles/plugin_descriptors.dir/build.make src/CMakeFiles/plugin_descriptors.dir/build [ 13%] Built target plugin_descriptors /usr/bin/make -f src/CMakeFiles/plugin_fingerprints.dir/build.make src/CMakeFiles/plugin_fingerprints.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src /construction/science/openbabel/.build 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src/formats/CMakeFiles/smilesformat.dir/build.make src/formats/CMakeFiles/smilesformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/smilesformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/smilesformat.dir/build.make src/formats/CMakeFiles/smilesformat.dir/build [ 29%] Built target smilesformat /usr/bin/make -f src/formats/CMakeFiles/mdlformat.dir/build.make src/formats/CMakeFiles/mdlformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac 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/construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/inchiformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/inchiformat.dir/build.make src/formats/CMakeFiles/inchiformat.dir/build [ 30%] Built target inchiformat /usr/bin/make -f src/formats/CMakeFiles/asciiformat.dir/build.make src/formats/CMakeFiles/asciiformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats 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src/formats/CMakeFiles/MNAformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/MNAformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/MNAformat.dir/build.make src/formats/CMakeFiles/MNAformat.dir/build [ 32%] Built target MNAformat /usr/bin/make -f src/formats/CMakeFiles/molreport.dir/build.make src/formats/CMakeFiles/molreport.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build 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src/formats/CMakeFiles/pngformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/pngformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/pngformat.dir/build.make src/formats/CMakeFiles/pngformat.dir/build [ 36%] Built target pngformat /usr/bin/make -f src/formats/CMakeFiles/acesformat.dir/build.make src/formats/CMakeFiles/acesformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build 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src/formats/CMakeFiles/vaspformat.dir/build.make src/formats/CMakeFiles/vaspformat.dir/build [ 50%] Built target vaspformat /usr/bin/make -f src/formats/CMakeFiles/xsfformat.dir/build.make src/formats/CMakeFiles/xsfformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/xsfformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/xsfformat.dir/build.make src/formats/CMakeFiles/xsfformat.dir/build [ 50%] Built target xsfformat /usr/bin/make -f src/formats/CMakeFiles/zindoformat.dir/build.make src/formats/CMakeFiles/zindoformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix 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/construction/science/openbabel/.build/src/formats/CMakeFiles/maeformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/maeformat.dir/build.make src/formats/CMakeFiles/maeformat.dir/build [ 51%] Built target maeformat /usr/bin/make -f src/formats/CMakeFiles/gamessukformat.dir/build.make src/formats/CMakeFiles/gamessukformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/gamessukformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/gamessukformat.dir/build.make src/formats/CMakeFiles/gamessukformat.dir/build [ 51%] Built target gamessukformat /usr/bin/make -f src/formats/CMakeFiles/orcaformat.dir/build.make src/formats/CMakeFiles/orcaformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/orcaformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/orcaformat.dir/build.make src/formats/CMakeFiles/orcaformat.dir/build [ 51%] Built target orcaformat /usr/bin/make -f src/formats/CMakeFiles/APIInterface.dir/build.make src/formats/CMakeFiles/APIInterface.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build 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src/formats/CMakeFiles/PQSformat.dir/build.make src/formats/CMakeFiles/PQSformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/PQSformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/PQSformat.dir/build.make src/formats/CMakeFiles/PQSformat.dir/build [ 52%] Built target PQSformat /usr/bin/make -f src/formats/CMakeFiles/MCDLformat.dir/build.make src/formats/CMakeFiles/MCDLformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats 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src/formats/CMakeFiles/cssrformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/cssrformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/cssrformat.dir/build.make src/formats/CMakeFiles/cssrformat.dir/build [ 61%] Built target cssrformat /usr/bin/make -f src/formats/CMakeFiles/dlpolyformat.dir/build.make src/formats/CMakeFiles/dlpolyformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build 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src/formats/CMakeFiles/fastsearchformat.dir/build.make src/formats/CMakeFiles/fastsearchformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fastsearchformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/fastsearchformat.dir/build.make src/formats/CMakeFiles/fastsearchformat.dir/build [ 64%] Built target fastsearchformat /usr/bin/make -f src/formats/CMakeFiles/fastaformat.dir/build.make src/formats/CMakeFiles/fastaformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac 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src/formats/CMakeFiles/featformat.dir/build.make src/formats/CMakeFiles/featformat.dir/build [ 65%] Built target featformat /usr/bin/make -f src/formats/CMakeFiles/fhformat.dir/build.make src/formats/CMakeFiles/fhformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/fhformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/fhformat.dir/build.make src/formats/CMakeFiles/fhformat.dir/build [ 65%] Built target fhformat /usr/bin/make -f src/formats/CMakeFiles/fingerprintformat.dir/build.make src/formats/CMakeFiles/fingerprintformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix 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src/formats/CMakeFiles/ghemicalformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/ghemicalformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/ghemicalformat.dir/build.make src/formats/CMakeFiles/ghemicalformat.dir/build [ 66%] Built target ghemicalformat /usr/bin/make -f src/formats/CMakeFiles/gromos96format.dir/build.make src/formats/CMakeFiles/gromos96format.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats 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groformat /usr/bin/make -f src/formats/CMakeFiles/lmpdatformat.dir/build.make src/formats/CMakeFiles/lmpdatformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/lmpdatformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/lmpdatformat.dir/build.make src/formats/CMakeFiles/lmpdatformat.dir/build [ 67%] Built target lmpdatformat /usr/bin/make -f src/formats/CMakeFiles/lpmdformat.dir/build.make src/formats/CMakeFiles/lpmdformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac 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src/formats/CMakeFiles/mpqcformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build /construction/science/openbabel/.build/src/formats /construction/science/openbabel/.build/src/formats/CMakeFiles/mpqcformat.dir/DependInfo.cmake /usr/bin/make -f src/formats/CMakeFiles/mpqcformat.dir/build.make src/formats/CMakeFiles/mpqcformat.dir/build [ 71%] Built target mpqcformat /usr/bin/make -f src/formats/CMakeFiles/msiformat.dir/build.make src/formats/CMakeFiles/msiformat.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/src/formats /construction/science/openbabel/.build 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tools/CMakeFiles/obthermo.dir/build.make tools/CMakeFiles/obthermo.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build /construction/science/openbabel/.build/tools /construction/science/openbabel/.build/tools/CMakeFiles/obthermo.dir/DependInfo.cmake /usr/bin/make -f tools/CMakeFiles/obthermo.dir/build.make tools/CMakeFiles/obthermo.dir/build [ 98%] Built target obthermo /usr/bin/make -f tools/CMakeFiles/obdistgen.dir/build.make tools/CMakeFiles/obdistgen.dir/depend cd /construction/science/openbabel/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac /construction/science/openbabel/openbabel-3-1-1-178-g2b211d6ac/tools /construction/science/openbabel/.build 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/construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/xyzformat.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/yasaraformat.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/png2format.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/cdxmlformat.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/cmlformat.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/cmlreactformat.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/pubchem.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/xmlformat.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/chemdoodlejsonformat.so -- Installing: /construction/science/openbabel/stage/usr/local/lib/openbabel/3.1.1/chemicaljsonformat.so -- Installing: 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/construction/science/openbabel/stage/usr/local/bin/obprobe -- Installing: /construction/science/openbabel/stage/usr/local/bin/obprop -- Installing: /construction/science/openbabel/stage/usr/local/bin/obrotamer -- Installing: /construction/science/openbabel/stage/usr/local/bin/obrotate -- Installing: /construction/science/openbabel/stage/usr/local/bin/obsym -- Installing: /construction/science/openbabel/stage/usr/local/bin/obtautomer -- Installing: /construction/science/openbabel/stage/usr/local/bin/obthermo -- Installing: /construction/science/openbabel/stage/usr/local/bin/obdistgen -- Installing: /construction/science/openbabel/stage/usr/local/bin/obgrep -- Installing: /construction/science/openbabel/stage/usr/local/bin/obspectrophore -- Installing: /construction/science/openbabel/stage/usr/local/bin/obrms -- Installing: /construction/science/openbabel/stage/usr/local/bin/obgui ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libpixman-1.so.0 from x11/pixman but it is not declared as a dependency Warning: you need USE_XORG+=pixman Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libfontconfig.so.1 from x11-fonts/fontconfig but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libfontconfig.so:x11-fonts/fontconfig Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libfreetype.so.6 from print/freetype2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libfreetype.so:print/freetype2 Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libEGL.so.1 from graphics/libglvnd but it is not declared as a dependency Warning: you need USE_GL+=egl Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libpng16.so.16 from graphics/png but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libpng16.so:graphics/png Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libxcb-shm.so.0 from x11/libxcb but it is not declared as a dependency Warning: you need USE_XORG+=xcb Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libxcb.so.1 from x11/libxcb but it is not declared as a dependency Warning: you need USE_XORG+=xcb Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libxcb-render.so.0 from x11/libxcb but it is not declared as a dependency Warning: you need USE_XORG+=xcb Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libXrender.so.1 from x11/libXrender but it is not declared as a dependency Warning: you need USE_XORG+=xrender Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libX11.so.6 from x11/libX11 but it is not declared as a dependency Warning: you need USE_XORG+=x11 Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libXext.so.6 from x11/libXext but it is not declared as a dependency Warning: you need USE_XORG+=xext Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libGL.so.1 from graphics/libglvnd but it is not declared as a dependency Warning: you need USE_GL+=gl Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libicudata.so.73 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicudata.so:devel/icu Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libicui18n.so.73 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicui18n.so:devel/icu Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libicuuc.so.73 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicuuc.so:devel/icu Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libexpat.so.1 from textproc/expat2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libexpat.so:textproc/expat2 Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libbrotlidec.so.1 from archivers/brotli but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libbrotlidec.so:archivers/brotli Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libGLdispatch.so.0 from graphics/libglvnd but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libGLdispatch.so:graphics/libglvnd Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libXau.so.6 from x11/libXau but it is not declared as a dependency Warning: you need USE_XORG+=xau Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libXdmcp.so.6 from x11/libXdmcp but it is not declared as a dependency Warning: you need USE_XORG+=xdmcp Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libGLX.so.0 from graphics/libglvnd but it is not declared as a dependency Warning: you need USE_GL+=gl Error: /usr/local/lib/libinchi.so.0.4.1 is linked to /usr/local/lib/libbrotlicommon.so.1 from archivers/brotli but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libbrotlicommon.so:archivers/brotli Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:39 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for openbabel-3.1.1.178 file sizes/checksums [324]: 0% file sizes/checksums [324]: 30% file sizes/checksums [324]: 61% file sizes/checksums [324]: 92% file sizes/checksums [324]: 100% Service unavailablepacking files [324]: 0% packing files [324]: 30% packing files [324]: 61% packing files [324]: 92% packing files [324]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:05 TOTAL TIME 00:06:01