------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py39 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 ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/science/py-openbabel XDG_CONFIG_HOME=/construction/science/py-openbabel XDG_CACHE_HOME=/construction/science/py-openbabel/.cache HOME=/construction/science/py-openbabel TMPDIR="/tmp" PATH=/construction/science/py-openbabel/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/py-openbabel/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/science/py-openbabel XDG_CONFIG_HOME=/construction/science/py-openbabel XDG_CACHE_HOME=/construction/science/py-openbabel/.cache HOME=/construction/science/py-openbabel TMPDIR="/tmp" PATH=/construction/science/py-openbabel/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/py-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 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= 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 " 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/py-openbabel/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" 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 ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" 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/pcre2-10.42.pkg Installing /packages/All/swig-4.1.1.pkg Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== 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/py39-setuptools-63.1.0_1.pkg Installing /packages/All/ccache-3.7.12_4.pkg 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) ===== 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 Installing /packages/All/boost-libs-1.82.0_1.pkg ===== 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 Installing /packages/All/coordgenlibs-3.0.2.pkg Installing /packages/All/brotli-1.0.9,1.pkg Installing /packages/All/png-1.6.39.pkg Installing /packages/All/freetype2-2.12.1_2.pkg ===== 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 Running fc-cache to build fontconfig cache... Installing /packages/All/libxml2-2.10.4.pkg Installing /packages/All/libiconv-1.17.pkg Installing /packages/All/glib-2.76.4,2.pkg Generating GIO modules cache Compiling glib schemas No schema files found: doing nothing. Installing /packages/All/libXau-1.0.9.pkg Installing /packages/All/xorgproto-2022.1_1.pkg Installing /packages/All/libXdmcp-1.1.3.pkg Installing /packages/All/libxcb-1.15_1.pkg Installing /packages/All/libX11-1.8.6,1.pkg Installing /packages/All/libXext-1.3.4,1.pkg Installing /packages/All/libglvnd-1.6.0.pkg Installing /packages/All/pixman-0.42.2.pkg Installing /packages/All/libXrender-0.9.10_2.pkg Installing /packages/All/cairo-1.17.4_2,3.pkg Installing /packages/All/graphite2-1.3.14.pkg Installing /packages/All/harfbuzz-7.3.0.pkg Installing /packages/All/libgpg-error-1.47.pkg Installing /packages/All/libgcrypt-1.10.2.pkg Installing /packages/All/libunistring-1.1.pkg Installing /packages/All/libidn2-2.3.4.pkg Installing /packages/All/libpsl-0.21.2_3.pkg UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default Installing /packages/All/libedit-3.1.20221030,1.pkg Installing /packages/All/sqlite3-3.42.0,1.pkg Installing /packages/All/gmp-6.2.1.pkg Installing /packages/All/nettle-3.9.1.pkg Installing /packages/All/libtasn1-4.19.0.pkg Installing /packages/All/p11-kit-0.24.1_2.pkg Installing /packages/All/gnutls-3.7.9.pkg Installing /packages/All/libproxy-0.4.17_1.pkg Installing /packages/All/gsettings-desktop-schemas-42.0.pkg Compiling glib schemas Installing /packages/All/glib-networking-2.76.0.pkg Generating GIO modules cache Installing /packages/All/libsoup-2.74.3.pkg ===== 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 Installing /packages/All/jbigkit-2.1_1.pkg Installing /packages/All/liblz4-1.9.4,1.pkg Installing /packages/All/zstd-1.5.5.pkg Installing /packages/All/jpeg-turbo-2.1.5.1.pkg Installing /packages/All/tiff-4.4.0_1.pkg Installing /packages/All/libmspack-0.11alpha.pkg Installing /packages/All/perl5-5.32.1_3.pkg Installing /packages/All/hunspell-1.7.2.pkg Installing /packages/All/enchant2-2.2.15_3.pkg Installing /packages/All/fribidi-1.0.13.pkg Installing /packages/All/giflib-5.2.1.pkg Installing /packages/All/webp-1.3.0_1.pkg Installing /packages/All/libsecret-0.20.5_2.pkg Installing /packages/All/shared-mime-info-2.2_1.pkg Building the Shared MIME-Info database cache Installing /packages/All/gdk-pixbuf2-2.42.10.pkg Generating gdk-pixbuf modules cache Installing /packages/All/libnotify-0.8.2.pkg Installing /packages/All/hyphen-2.8.8.pkg Installing /packages/All/lcms2-2.15_1.pkg Installing /packages/All/openjpeg-2.5.0.pkg Installing /packages/All/harfbuzz-icu-7.3.0.pkg Installing /packages/All/woff2-1.0.2_4.pkg Installing /packages/All/libepoll-shim-0.0.20230411.pkg Installing /packages/All/wayland-1.22.0.pkg ===== 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 Installing /packages/All/libxkbcommon-1.5.0.pkg ===== 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 Installing /packages/All/libepoxy-1.5.9.pkg Installing /packages/All/wpebackend-fdo-1.12.0.pkg Installing /packages/All/libICE-1.1.0_1,1.pkg Installing /packages/All/libSM-1.2.3,1.pkg Installing /packages/All/dbus-1.14.6,1.pkg ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/libXfixes-6.0.0.pkg Installing /packages/All/libXi-1.8,1.pkg Installing /packages/All/libXtst-1.2.3_2.pkg Installing /packages/All/at-spi2-core-2.48.0.pkg Installing /packages/All/libdaemon-0.14_1.pkg Installing /packages/All/dbus-glib-0.112.pkg Installing /packages/All/gdbm-1.23.pkg Installing /packages/All/libevent-2.1.12.pkg Installing /packages/All/gnome_subr-1.0.pkg Installing /packages/All/avahi-app-0.8_1.pkg ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/libpaper-1.1.28.pkg Installing /packages/All/cups-2.4.6.pkg ===> 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 Installing /packages/All/libthai-0.1.29.pkg ===== 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 Installing /packages/All/mkfontscale-1.2.1.pkg Installing /packages/All/font-bh-ttf-1.0.3_4.pkg Running fc-cache to build fontconfig cache... Installing /packages/All/font-misc-meltho-1.0.3_4.pkg Installing /packages/All/font-misc-ethiopic-1.0.4.pkg Installing /packages/All/encodings-1.0.5,1.pkg Installing /packages/All/dejavu-2.37_1.pkg 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 Installing /packages/All/libXft-2.3.7.pkg Installing /packages/All/pango-1.50.14.pkg Installing /packages/All/hicolor-icon-theme-0.17.pkg Installing /packages/All/gtk-update-icon-cache-3.24.31.pkg Installing /packages/All/adwaita-icon-theme-40.1.1_1.pkg Generating GTK icon cache for /usr/local/share/icons/Adwaita Installing /packages/All/librsvg2-rust-2.56.3.pkg Generating gdk-pixbuf modules cache Installing /packages/All/libXcomposite-0.4.6,1.pkg Installing /packages/All/libXcursor-1.2.0.pkg Installing /packages/All/libXdamage-1.1.6.pkg Installing /packages/All/libXinerama-1.1.4_2,1.pkg Installing /packages/All/libXrandr-1.5.2.pkg Installing /packages/All/gtk3-3.24.34_1.pkg Compiling glib schemas Generating GTK icon cache for /usr/local/share/icons/hicolor Installing /packages/All/libxslt-1.1.37.pkg UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default Installing /packages/All/libunwind-20211201_2.pkg Installing /packages/All/gstreamer1-1.22.5.pkg Installing /packages/All/gobject-introspection-1.76.1,1.pkg Installing /packages/All/json-glib-1.6.6.pkg Installing /packages/All/geoclue-2.5.7.pkg Installing /packages/All/orc-0.4.34_1.pkg Installing /packages/All/libnice-0.1.21_1.pkg Installing /packages/All/iso-codes-4.7.pkg Installing /packages/All/gstreamer1-plugins-1.22.5.pkg Installing /packages/All/gstreamer1-plugins-bad-1.22.5.pkg Installing /packages/All/pygobject3-common-3.42.2.pkg Installing /packages/All/py39-cairo-1.21.0,1.pkg Installing /packages/All/py39-gobject3-3.42.2.pkg Installing /packages/All/graphene-1.10.8.pkg Installing /packages/All/libGLU-9.0.2_2.pkg Installing /packages/All/gstreamer1-plugins-gl-1.22.5.pkg Installing /packages/All/libXt-1.2.1,1.pkg Installing /packages/All/webkit2-gtk3-2.34.6_7.pkg Installing /packages/All/libXxf86vm-1.1.4_3.pkg Installing /packages/All/wx30-gtk3-3.0.5.1_2.pkg Installing /packages/All/openbabel-3.1.1.178.pkg UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default SUCCEEDED 00:00:32 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building => SHA256 Checksum OK for openbabel-3.1.1.1.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building ===> Extracting for py39-openbabel-3.1.1.1 => SHA256 Checksum OK for openbabel-3.1.1.1.tar.gz. Extracted Memory Use: 0.49M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-openbabel-3.1.1.1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-openbabel-3.1.1.1 depends on executable: swig - found ===> py39-openbabel-3.1.1.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/bin/python3.9 - found ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> py39-openbabel-3.1.1.1 depends on shared library: libopenbabel.so - found (/usr/local/lib/libopenbabel.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-openbabel-3.1.1.1 depends on executable: swig - found ===> py39-openbabel-3.1.1.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/bin/python3.9 - found ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/bin/ccache - found ===> py39-openbabel-3.1.1.1 depends on shared library: libopenbabel.so - found (/usr/local/lib/libopenbabel.so) ===> Configuring for py39-openbabel-3.1.1.1 running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-openbabel-3.1.1.1 running build running build_ext Warning: invalid version number '3.1.1.1'. Guessing Open Babel location: - include_dirs: ['/usr/local/include/python3.9', '/usr/local/include/openbabel3'] - library_dirs: ['/usr/local/lib', '/usr/local/lib'] building 'openbabel._openbabel' extension swigging openbabel/openbabel-python.i to openbabel/openbabel-python_wrap.cpp swig -python -c++ -small -O -templatereduce -naturalvar -I/usr/local/include/python3.9 -I/usr/local/include/openbabel3 -o openbabel/openbabel-python_wrap.cpp openbabel/openbabel-python.i /usr/local/include/openbabel3/openbabel/obconversion.h:368: Warning 325: Nested struct not currently supported (StreamState ignored) /usr/local/include/openbabel3/openbabel/isomorphism.h:160: Warning 325: Nested class not currently supported (Functor ignored) /usr/local/include/openbabel3/openbabel/spectrophore.h:571: Warning 312: Nested struct not currently supported (ignored). /usr/local/include/openbabel3/openbabel/spectrophore.h:578: Warning 312: Nested struct not currently supported (ignored). creating build creating build/temp.dragonfly-6.5-x86_64-cpython-39 creating build/temp.dragonfly-6.5-x86_64-cpython-39/openbabel cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -I/usr/local/include/openbabel3 -c openbabel/openbabel-python_wrap.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/openbabel/openbabel-python_wrap.o In file included from openbabel/openbabel-python_wrap.cpp:3403: /usr/local/include/openbabel3/openbabel/math/vector3.h: In member function 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const': /usr/local/include/openbabel3/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 ); ^~~~~ /usr/local/include/openbabel3/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ In file included from /usr/local/include/openbabel3/openbabel/bondtyper.h:22, from openbabel/openbabel-python_wrap.cpp:3420: /usr/local/include/openbabel3/openbabel/parsmart.h: In constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern()': /usr/local/include/openbabel3/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /usr/local/include/openbabel3/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /usr/local/include/openbabel3/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /usr/local/include/openbabel3/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /usr/local/include/openbabel3/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /usr/local/include/openbabel3/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /usr/local/include/openbabel3/openbabel/parsmart.h:183:88: warning: 'OpenBabel::OBSmartsPattern::_growbond' is deprecated [-Wdeprecated-declarations] OBSmartsPattern() : _pat(nullptr), _buffer(nullptr), LexPtr(nullptr), MainPtr(nullptr) { } ^ /usr/local/include/openbabel3/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /usr/local/include/openbabel3/openbabel/parsmart.h: In copy constructor 'OpenBabel::OBSmartsPattern::OBSmartsPattern(const OpenBabel::OBSmartsPattern&)': /usr/local/include/openbabel3/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) ^ /usr/local/include/openbabel3/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /usr/local/include/openbabel3/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) ^ /usr/local/include/openbabel3/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /usr/local/include/openbabel3/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) ^ /usr/local/include/openbabel3/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ /usr/local/include/openbabel3/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) ^ /usr/local/include/openbabel3/openbabel/parsmart.h:158:37: note: declared here OB_DEPRECATED std::vector _growbond; //!< \deprecated (Not used) ^~~~~~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3422: /usr/local/include/openbabel3/openbabel/ring.h: In constructor 'OpenBabel::OBRingSearch::OBRingSearch()': /usr/local/include/openbabel3/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /usr/local/include/openbabel3/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /usr/local/include/openbabel3/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /usr/local/include/openbabel3/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /usr/local/include/openbabel3/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /usr/local/include/openbabel3/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ /usr/local/include/openbabel3/openbabel/ring.h:124:23: warning: 'OpenBabel::OBRingSearch::_bonds' is deprecated [-Wdeprecated-declarations] OBRingSearch() {} ^ /usr/local/include/openbabel3/openbabel/ring.h:121:40: note: declared here OB_DEPRECATED std::vector _bonds; //!< the internal list of closure bonds (deprecated) ^~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBResidueData_LookupBO__SWIG_0(PyObject*, Py_ssize_t, PyObject**)': openbabel/openbabel-python_wrap.cpp:15300:78: warning: 'int OpenBabel::OBResidueData::LookupBO(const string&)' is deprecated: Easier to use the two-argument form [-Wdeprecated-declarations] arg2 = ptr; } result = (int)(arg1)->LookupBO((std::string const &)*arg2); ^ In file included from /usr/local/include/openbabel3/openbabel/bondtyper.h:23, from openbabel/openbabel-python_wrap.cpp:3420: /usr/local/include/openbabel3/openbabel/data.h:257:12: note: declared here int LookupBO(const std::string &); ^~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_vector3___eq__(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:15984:99: warning: 'bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] result = (bool)((OpenBabel::vector3 const *)arg1)->operator ==((OpenBabel::vector3 const &)*arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3403: /usr/local/include/openbabel3/openbabel/math/vector3.h:274:10: note: declared here bool operator== ( const vector3& ) const; ^~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_vector3___ne__(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:15999:99: warning: 'bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const' is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] result = (bool)((OpenBabel::vector3 const *)arg1)->operator !=((OpenBabel::vector3 const &)*arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3403: /usr/local/include/openbabel3/openbabel/math/vector3.h:279:10: note: declared here bool operator!= ( const vector3& other ) const ^~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_matrix3x3_Get(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:16563:104: warning: 'double OpenBabel::matrix3x3::Get(int, int) const' is deprecated: use the constant operator() instead [-Wdeprecated-declarations] arg3 = static_cast< int >(val3); result = (double)((OpenBabel::matrix3x3 const *)arg1)->Get(arg2,arg3); ^ In file included from openbabel/openbabel-python_wrap.cpp:3404: /usr/local/include/openbabel3/openbabel/math/matrix3x3.h:172:14: note: declared here double Get(int row,int column) const ^~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_matrix3x3_Set(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:16578:65: warning: 'void OpenBabel::matrix3x3::Set(int, int, double)' is deprecated: use the non-constant operator() instead [-Wdeprecated-declarations] arg4 = static_cast< double >(val4); (arg1)->Set(arg2,arg3,arg4); resultobj = SWIG_Py_Void(); return resultobj; fail: ^ In file included from openbabel/openbabel-python_wrap.cpp:3404: /usr/local/include/openbabel3/openbabel/math/matrix3x3.h:189:12: note: declared here void Set(int row,int column, double v) ^~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBGridData_GetOriginVector__SWIG_1(PyObject*, Py_ssize_t, PyObject**)': openbabel/openbabel-python_wrap.cpp:21987:108: warning: 'void OpenBabel::OBGridData::GetOriginVector(double*) const' is deprecated: Use GetOriginVector() instead [-Wdeprecated-declarations] arg2 = reinterpret_cast< double * >(argp2); ((OpenBabel::OBGridData const *)arg1)->GetOriginVector(arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3409: /usr/local/include/openbabel3/openbabel/griddata.h:89:10: note: declared here void GetOriginVector(double o[3]) const; ^~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBGridData_SetLimits__SWIG_1(PyObject*, Py_ssize_t, PyObject**)': openbabel/openbabel-python_wrap.cpp:22086:112: warning: 'void OpenBabel::OBGridData::SetLimits(const double*, const double*, const double*, const double*)' is deprecated: Use vector version instead [-Wdeprecated-declarations] (arg1)->SetLimits((double const (*))arg2,(double const (*))arg3,(double const (*))arg4,(double const (*))arg5); ^ In file included from openbabel/openbabel-python_wrap.cpp:3409: /usr/local/include/openbabel3/openbabel/griddata.h:112:10: note: declared here void SetLimits(const double origin[3], const double x[3], const double y[3], ^~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBAtom_SetHybAndGeom(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:27340:79: warning: 'bool OpenBabel::OBAtom::SetHybAndGeom(int)' is deprecated [-Wdeprecated-declarations] arg2 = static_cast< int >(val2); result = (bool)(arg1)->SetHybAndGeom(arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3414: /usr/local/include/openbabel3/openbabel/atom.h:339:26: note: declared here OB_DEPRECATED bool SetHybAndGeom(int); ^~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBBond_Visit_set(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:27745:55: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] arg2 = static_cast< bool >(val2); if (arg1) (arg1)->Visit = arg2; resultobj = SWIG_Py_Void(); return resultobj; fail: ^~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3415: /usr/local/include/openbabel3/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ openbabel/openbabel-python_wrap.cpp:27745:55: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] arg2 = static_cast< bool >(val2); if (arg1) (arg1)->Visit = arg2; resultobj = SWIG_Py_Void(); return resultobj; fail: ^~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3415: /usr/local/include/openbabel3/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ openbabel/openbabel-python_wrap.cpp:27745:55: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] arg2 = static_cast< bool >(val2); if (arg1) (arg1)->Visit = arg2; resultobj = SWIG_Py_Void(); return resultobj; fail: ^~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3415: /usr/local/include/openbabel3/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBBond_Visit_get(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:27752:84: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBBond * >(argp1); result = (bool) ((arg1)->Visit); ^~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3415: /usr/local/include/openbabel3/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ openbabel/openbabel-python_wrap.cpp:27752:84: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBBond * >(argp1); result = (bool) ((arg1)->Visit); ^~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3415: /usr/local/include/openbabel3/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ openbabel/openbabel-python_wrap.cpp:27752:84: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBBond * >(argp1); result = (bool) ((arg1)->Visit); ^~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3415: /usr/local/include/openbabel3/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBMol_GetFirstAtom(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:29280:80: warning: 'OpenBabel::OBAtom* OpenBabel::OBMol::GetFirstAtom() const' is deprecated [-Wdeprecated-declarations] result = (OpenBabel::OBAtom *)((OpenBabel::OBMol const *)arg1)->GetFirstAtom(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3413: /usr/local/include/openbabel3/openbabel/mol.h:280:18: note: declared here OBAtom *GetFirstAtom() const; ^~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRing_PathSize(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:31726:112: warning: 'size_t OpenBabel::OBRing::PathSize() const' is deprecated: Use Size() instead [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRing * >(argp1); result = ((OpenBabel::OBRing const *)arg1)->PathSize(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3422: /usr/local/include/openbabel3/openbabel/ring.h:66:15: note: declared here size_t PathSize() const { return(_path.size()); } ^~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBForceField_UpdateCoordinates(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:35503:104: warning: 'bool OpenBabel::OBForceField::UpdateCoordinates(OpenBabel::OBMol&)' is deprecated: Use GetCooordinates instead. [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); result = (bool)(arg1)->UpdateCoordinates(*arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:714:10: note: declared here bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); } ^~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBForceField_UpdateConformers(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:35529:103: warning: 'bool OpenBabel::OBForceField::UpdateConformers(OpenBabel::OBMol&)' is deprecated: Use GetConformers instead. [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); result = (bool)(arg1)->UpdateConformers(*arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:722:10: note: declared here bool UpdateConformers(OBMol &mol) { return GetConformers(mol); } ^~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBForceField_DistanceGeometry(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:36101:90: warning: 'void OpenBabel::OBForceField::DistanceGeometry()' is deprecated: Use OBDistanceGeometry class instead [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBForceField * >(argp1); (arg1)->DistanceGeometry(); resultobj = SWIG_Py_Void(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1050:10: note: declared here void DistanceGeometry(); ^~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBForceField_LineSearch__SWIG_0(PyObject*, Py_ssize_t, PyObject**)': openbabel/openbabel-python_wrap.cpp:36417:98: warning: 'OpenBabel::vector3 OpenBabel::OBForceField::LineSearch(OpenBabel::OBAtom*, OpenBabel::vector3&)' is deprecated: Current code should use LineSearch(double *, double*) instead. [-Wdeprecated-declarations] arg3 = reinterpret_cast< OpenBabel::vector3 * >(argp3); result = (arg1)->LineSearch(arg2,*arg3); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1223:13: note: declared here vector3 LineSearch(OBAtom *atom, vector3 &direction); ^~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBForceField_VectorLengthDerivative(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:37025:45: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorLengthDerivative(*arg1,*arg2); ^~~~~~~~~~~~~~~~~~~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp:37025:79: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorLengthDerivative(*arg1,*arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp:37025:79: warning: 'static double OpenBabel::OBForceField::VectorLengthDerivative(OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorLengthDerivative(*arg1,*arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1524:19: note: declared here static double VectorLengthDerivative(vector3 &a, vector3 &b); ^~~~~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBForceField_VectorAngleDerivative__SWIG_1(PyObject*, Py_ssize_t, PyObject**)': openbabel/openbabel-python_wrap.cpp:37071:84: warning: 'static double OpenBabel::OBForceField::VectorAngleDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorAngleDerivative(*arg1,*arg2,*arg3); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1540:19: note: declared here static double VectorAngleDerivative(vector3 &a, vector3 &b, vector3 &c); ^~~~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp:37071:84: warning: 'static double OpenBabel::OBForceField::VectorAngleDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorAngleDerivative(*arg1,*arg2,*arg3); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1540:19: note: declared here static double VectorAngleDerivative(vector3 &a, vector3 &b, vector3 &c); ^~~~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBForceField_VectorOOPDerivative__SWIG_1(PyObject*, Py_ssize_t, PyObject**)': openbabel/openbabel-python_wrap.cpp:37141:88: warning: 'static double OpenBabel::OBForceField::VectorOOPDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorOOPDerivative(*arg1,*arg2,*arg3,*arg4); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1557:19: note: declared here static double VectorOOPDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d); ^~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp:37141:88: warning: 'static double OpenBabel::OBForceField::VectorOOPDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorOOPDerivative(*arg1,*arg2,*arg3,*arg4); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1557:19: note: declared here static double VectorOOPDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d); ^~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBForceField_VectorTorsionDerivative__SWIG_1(PyObject*, Py_ssize_t, PyObject**)': openbabel/openbabel-python_wrap.cpp:37211:92: warning: 'static double OpenBabel::OBForceField::VectorTorsionDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorTorsionDerivative(*arg1,*arg2,*arg3,*arg4); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1573:19: note: declared here static double VectorTorsionDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d); ^~~~~~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp:37211:92: warning: 'static double OpenBabel::OBForceField::VectorTorsionDerivative(OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&, OpenBabel::vector3&)' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorTorsionDerivative(*arg1,*arg2,*arg3,*arg4); ^ In file included from openbabel/openbabel-python_wrap.cpp:3431: /usr/local/include/openbabel3/openbabel/forcefield.h:1573:19: note: declared here static double VectorTorsionDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d); ^~~~~~~~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_SetDelta(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40899:60: warning: 'void OpenBabel::OBRotor::SetDelta(double)' is deprecated: Has no effect. [-Wdeprecated-declarations] arg2 = static_cast< double >(val2); (arg1)->SetDelta(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail: return NULL; } ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:429:10: note: declared here void SetDelta(double UNUSED(d)) {} ^~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_GetDelta(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40905:94: warning: 'double OpenBabel::OBRotor::GetDelta()' is deprecated: Has no effect. [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (double)(arg1)->GetDelta(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:432:12: note: declared here double GetDelta() { return 10.0; } ^~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_GetFixedAtoms(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40912:116: warning: 'OpenBabel::OBBitVec& OpenBabel::OBRotor::GetFixedAtoms()' is deprecated [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (OpenBabel::OBBitVec *) &(arg1)->GetFixedAtoms(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:435:15: note: declared here OBBitVec &GetFixedAtoms() { return _fixedatoms; } ^~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_SetFixedAtoms(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40926:88: warning: 'void OpenBabel::OBRotor::SetFixedAtoms(OpenBabel::OBBitVec&)' is deprecated: See SetFixedBonds [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetFixedAtoms(*arg2); resultobj = SWIG_Py_Void(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:438:10: note: declared here void SetFixedAtoms(OBBitVec &bv) { _fixedatoms = bv; } ^~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_GetEvalAtoms(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40933:115: warning: 'OpenBabel::OBBitVec& OpenBabel::OBRotor::GetEvalAtoms()' is deprecated [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (OpenBabel::OBBitVec *) &(arg1)->GetEvalAtoms(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:441:15: note: declared here OBBitVec &GetEvalAtoms() { return _evalatoms; } ^~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_SetEvalAtoms(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40947:87: warning: 'void OpenBabel::OBRotor::SetEvalAtoms(OpenBabel::OBBitVec&)' is deprecated [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetEvalAtoms(*arg2); resultobj = SWIG_Py_Void(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:444:10: note: declared here void SetEvalAtoms(OBBitVec &bv) { _evalatoms = bv; } ^~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_GetRotAtoms(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40954:97: warning: 'void* OpenBabel::OBRotor::GetRotAtoms()' is deprecated [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (void *)(arg1)->GetRotAtoms(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:447:11: note: declared here void* GetRotAtoms() { return &_rotatoms; } ^~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_GetResolution(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40962:86: warning: 'std::vector& OpenBabel::OBRotor::GetResolution()' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] result = (std::vector< double,std::allocator< double > > *) &(arg1)->GetResolution(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:450:26: note: declared here std::vector &GetResolution() { return _torsionAngles; } ^~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotor_SetNumCoords(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:40973:63: warning: 'void OpenBabel::OBRotor::SetNumCoords(int)' is deprecated [-Wdeprecated-declarations] arg2 = static_cast< int >(val2); (arg1)->SetNumCoords(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail: ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:453:10: note: declared here void SetNumCoords(int UNUSED(nc)) {} ^~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotorList_IdentifyEvalAtoms(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:41254:104: warning: 'bool OpenBabel::OBRotorList::IdentifyEvalAtoms(OpenBabel::OBMol&)' is deprecated: Not declared. Use Setup() for top-level functionality [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); result = (bool)(arg1)->IdentifyEvalAtoms(*arg2); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:628:12: note: declared here bool IdentifyEvalAtoms(OBMol &mol) { return SetEvalAtoms(mol); } ^~~~~~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotorList_SetFixAtoms(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:41267:86: warning: 'void OpenBabel::OBRotorList::SetFixAtoms(OpenBabel::OBBitVec&)' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetFixAtoms(*arg2); resultobj = SWIG_Py_Void(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:634:10: note: declared here void SetFixAtoms(OBBitVec &fix) ^~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotorList_HasFixedAtoms(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:41274:101: warning: 'bool OpenBabel::OBRotorList::HasFixedAtoms()' is deprecated: See HasFixedBonds() [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotorList * >(argp1); result = (bool)(arg1)->HasFixedAtoms(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:644:10: note: declared here bool HasFixedAtoms() ^~~~~~~~~~~~~ openbabel/openbabel-python_wrap.cpp: In function 'PyObject* _wrap_OBRotorList_IgnoreSymmetryRemoval(PyObject*, PyObject*)': openbabel/openbabel-python_wrap.cpp:41281:94: warning: 'void OpenBabel::OBRotorList::IgnoreSymmetryRemoval()' is deprecated: Currently has no effect [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotorList * >(argp1); (arg1)->IgnoreSymmetryRemoval(); resultobj = SWIG_Py_Void(); ^ In file included from openbabel/openbabel-python_wrap.cpp:3441: /usr/local/include/openbabel3/openbabel/rotor.h:651:10: note: declared here void IgnoreSymmetryRemoval() { _removesym = false;} ^~~~~~~~~~~~~~~~~~~~~ In file included from openbabel/openbabel-python_wrap.cpp:3415: /usr/local/include/openbabel3/openbabel/bond.h: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBBond; _Args = {const OpenBabel::OBBond&}; _Tp = OpenBabel::OBBond]': /usr/include/c++/8.0/bits/alloc_traits.h:475:4: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBBond; _Args = {const OpenBabel::OBBond&}; _Tp = OpenBabel::OBBond; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/8.0/bits/stl_vector.h:1079:30: required from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OpenBabel::OBBond; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = OpenBabel::OBBond]' openbabel/openbabel-python_wrap.cpp:4443:11: required from 'Sequence* swig::getslice(const Sequence*, Difference, Difference, Py_ssize_t) [with Sequence = std::vector >; Difference = long int; Py_ssize_t = long int]' openbabel/openbabel-python_wrap.cpp:6420:42: required from here /usr/local/include/openbabel3/openbabel/bond.h:58:15: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] class OBAPI OBBond: public OBBase ^~~~~~ /usr/local/include/openbabel3/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ /usr/local/include/openbabel3/openbabel/bond.h:58:15: warning: 'OpenBabel::OBBond::Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] class OBAPI OBBond: public OBBase ^~~~~~ /usr/local/include/openbabel3/openbabel/bond.h:98:12: note: declared here bool Visit; ^~~~~ In file included from /usr/include/c++/8.0/bits/c++allocator.h:33, from /usr/include/c++/8.0/bits/allocator.h:46, from /usr/include/c++/8.0/string:41, from /usr/include/c++/8.0/stdexcept:39, from openbabel/openbabel-python_wrap.cpp:3324: /usr/include/c++/8.0/ext/new_allocator.h:136:4: note: synthesized method 'OpenBabel::OBBond::OBBond(const OpenBabel::OBBond&)' first required here { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ creating build/lib.dragonfly-6.5-x86_64-cpython-39 creating build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel c++ -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/openbabel/openbabel-python_wrap.o -L/usr/local/lib -L/usr/local/lib -lopenbabel -o build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel/_openbabel.cpython-39.so running build_py copying openbabel/pybel.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel copying openbabel/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel copying openbabel/openbabel.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel SUCCEEDED 00:02:15 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py39-openbabel-3.1.1.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/bin/python3.9 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-openbabel-3.1.1.1 ===> py39-openbabel-3.1.1.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/bin/python3.9 - found ===> Generating temporary packing list running install /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build_ext Warning: invalid version number '3.1.1.1'. Guessing Open Babel location: - include_dirs: ['/usr/local/include/python3.9', '/usr/local/include/openbabel3'] - library_dirs: ['/usr/local/lib', '/usr/local/lib'] running build running build_py running install_lib creating /construction/science/py-openbabel/stage/usr/local/lib/python3.9 creating /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages creating /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel copying build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel/_openbabel.cpython-39.so -> /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel copying build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel/pybel.py -> /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel copying build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel/__init__.py -> /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel copying build/lib.dragonfly-6.5-x86_64-cpython-39/openbabel/openbabel.py -> /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel byte-compiling /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel/pybel.py to pybel.cpython-39.pyc byte-compiling /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel/openbabel.py to openbabel.cpython-39.pyc writing byte-compilation script '/tmp/tmpv348j30c.py' /usr/local/bin/python3.9 /tmp/tmpv348j30c.py removing /tmp/tmpv348j30c.py running install_egg_info running egg_info creating openbabel.egg-info writing openbabel.egg-info/PKG-INFO writing dependency_links to openbabel.egg-info/dependency_links.txt writing top-level names to openbabel.egg-info/top_level.txt writing manifest file 'openbabel.egg-info/SOURCES.txt' reading manifest file 'openbabel.egg-info/SOURCES.txt' writing manifest file 'openbabel.egg-info/SOURCES.txt' Copying openbabel.egg-info to /construction/science/py-openbabel/stage/usr/local/lib/python3.9/site-packages/openbabel-3.1.1.1-py3.9.egg-info running install_scripts writing list of installed files to '/construction/science/py-openbabel/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.9/site-packages/openbabel/_openbabel.cpython-39.so is linked to /usr/local/lib/libmaeparser.so.1 from science/maeparser but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libmaeparser.so:science/maeparser Error: /usr/local/lib/python3.9/site-packages/openbabel/_openbabel.cpython-39.so is linked to /usr/local/lib/libcoordgen.so.3 from science/coordgenlibs but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libcoordgen.so:science/coordgenlibs Error: /usr/local/lib/python3.9/site-packages/openbabel/_openbabel.cpython-39.so is linked to /usr/local/lib/libboost_iostreams.so.1.82.0 from devel/boost-libs but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libboost_iostreams.so:devel/boost-libs Error: /usr/local/lib/python3.9/site-packages/openbabel/_openbabel.cpython-39.so is linked to /usr/local/lib/libboost_regex.so.1.82.0 from devel/boost-libs but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libboost_regex.so:devel/boost-libs Error: /usr/local/lib/python3.9/site-packages/openbabel/_openbabel.cpython-39.so 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/python3.9/site-packages/openbabel/_openbabel.cpython-39.so 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/python3.9/site-packages/openbabel/_openbabel.cpython-39.so 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 Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- 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 py39-openbabel-3.1.1.1 file sizes/checksums [15]: 0% file sizes/checksums [15]: 100% Service unavailablepacking files [15]: 0% packing files [15]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:02:57