------------------------------------------------------------------------------- -- 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 ------------------------------------------------------------------------------- ===> The following configuration options are available for py39-pymol-2.5.0.97_2: ====> GUI (Graphical User Interface) support: you have to select exactly one of them QT5=on: Qt 5 toolkit support TK=off: Tk GUI toolkit support ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/science/py-pymol XDG_CONFIG_HOME=/construction/science/py-pymol XDG_CACHE_HOME=/construction/science/py-pymol/.cache HOME=/construction/science/py-pymol TMPDIR="/tmp" PATH=/construction/science/py-pymol/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/py-pymol/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/science/py-pymol XDG_CONFIG_HOME=/construction/science/py-pymol XDG_CACHE_HOME=/construction/science/py-pymol/.cache HOME=/construction/science/py-pymol TMPDIR="/tmp" PATH=/construction/science/py-pymol/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/py-pymol/.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= 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 -DMSGPACK_NO_BOOST " 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-pymol/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" 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="" PYQT_APIDIR=share/PyQt5/3.9/qsci PYQT_DOCDIR=share/doc/PyQt5/3.9 PYQT_EXAMPLEDIR=share/examples/PyQt5/3.9 PYQT_SIPDIR=/usr/local/lib/python3.9/site-packages/PyQt5/bindings PYQT_DESIGNERDIR=/designer/PyQt5/3.9 PYQT_QMLDIR=/PyQt5/3.9 PYQT_SIPVERSION=6.7.7 PYQT_QSCIVERSION=2.13.3 PYQT_PYQTVERSION=5.15.9 OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/py39-pymol" EXAMPLESDIR="share/examples/py39-pymol" DATADIR="share/py39-pymol" WWWDIR="www/py39-pymol" ETCDIR="etc/py39-pymol" 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/py39-pymol DOCSDIR=/usr/local/share/doc/py39-pymol EXAMPLESDIR=/usr/local/share/examples/py39-pymol WWWDIR=/usr/local/www/py39-pymol ETCDIR=/usr/local/etc/py39-pymol 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/metis-5.1.0_9.pkg ===== Message from metis-5.1.0_9: -- ===> NOTICE: The metis 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/indexinfo-0.3.1.pkg Installing /packages/All/gmp-6.2.1.pkg Installing /packages/All/mpfr-4.2.0_1,1.pkg Installing /packages/All/mpc-1.3.1_1.pkg UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/liblz4-1.9.4,1.pkg Installing /packages/All/zstd-1.5.5.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/binutils-2.40_4,1.pkg Installing /packages/All/gcc12-12.2.0_6.pkg ===== 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/openblas-0.3.20_1,1.pkg Installing /packages/All/suitesparse-config-7.0.1_1.pkg Installing /packages/All/suitesparse-amd-3.0.3_1.pkg Installing /packages/All/suitesparse-camd-3.0.3_1.pkg Installing /packages/All/suitesparse-colamd-3.0.3_1.pkg Installing /packages/All/suitesparse-ccolamd-3.0.3_1.pkg Installing /packages/All/suitesparse-cholmod-4.0.3_1.pkg Installing /packages/All/suitesparse-umfpack-6.1.0_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/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/py39-numpy-1.24.1_4,1.pkg Installing /packages/All/glm-0.9.9.8,1.pkg Installing /packages/All/msgpack-cxx-6.0.0_1.pkg Installing /packages/All/mmtf-cpp-1.1.0_1.pkg Installing /packages/All/xorgproto-2022.1_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) 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/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/msgpack-c-6.0.0.pkg Installing /packages/All/libnghttp2-1.53.0.pkg Installing /packages/All/libssh2-1.11.0,3.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 Installing /packages/All/ca_root_nss-3.89.1.pkg ===== Message from ca_root_nss-3.89.1: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/curl-8.1.2.pkg Installing /packages/All/libaec-1.0.6.pkg Installing /packages/All/hdf5-1.12.2_2,1.pkg Installing /packages/All/pkgconf-1.8.1,1.pkg Installing /packages/All/netcdf-4.9.2.pkg Installing /packages/All/libXau-1.0.9.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/libGLU-9.0.2_2.pkg Installing /packages/All/libICE-1.1.0_1,1.pkg Installing /packages/All/libSM-1.2.3,1.pkg Installing /packages/All/libXt-1.2.1,1.pkg Installing /packages/All/glew-2.2.0_3.pkg Installing /packages/All/libXfixes-6.0.0.pkg Installing /packages/All/libXi-1.8,1.pkg Installing /packages/All/libXrender-0.9.10_2.pkg Installing /packages/All/libXrandr-1.5.2.pkg Installing /packages/All/libXxf86vm-1.1.4_3.pkg Installing /packages/All/freeglut-3.2.1.pkg ===== Message from freeglut-3.2.1: -- Joystick support is untested and it is unknown if it works. Do not hesitate to contact x11@FreeBSD.org if this causes issues. Installing /packages/All/libxml2-2.10.4.pkg Installing /packages/All/py39-msgpack-1.0.5_1.pkg Installing /packages/All/jpeg-turbo-2.1.5.1.pkg Installing /packages/All/fontconfig-2.14.2,1.pkg Running fc-cache to build fontconfig cache... Installing /packages/All/tcl86-8.6.13.pkg Installing /packages/All/libXft-2.3.7.pkg Installing /packages/All/libXScrnSaver-1.2.4.pkg Installing /packages/All/tk86-8.6.13.pkg Installing /packages/All/blt-2.5.3_5.pkg Installing /packages/All/py39-tkinter-3.9.17_6.pkg Installing /packages/All/py39-Pmw-2.0.1_1.pkg Installing /packages/All/double-conversion-3.3.0.pkg Installing /packages/All/icu-73.2,1.pkg Installing /packages/All/pcre2-10.42.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/qt5-core-5.15.8p157_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/libevdev-1.5.9.pkg Installing /packages/All/graphite2-1.3.14.pkg Installing /packages/All/harfbuzz-7.3.0.pkg Installing /packages/All/libepoll-shim-0.0.20230411.pkg Installing /packages/All/libudev-devd-0.5.1.pkg Installing /packages/All/libmtdev-1.1.6_1.pkg Installing /packages/All/libgudev-234.pkg Installing /packages/All/libwacom-1.5.pkg Installing /packages/All/py39-evdev-1.6.0.pkg Installing /packages/All/py39-six-1.16.0.pkg Installing /packages/All/py39-pyudev-0.22.0.pkg Installing /packages/All/libinput-1.23.0.pkg Installing /packages/All/xcb-util-0.4.1,1.pkg Installing /packages/All/xcb-util-wm-0.4.2.pkg Installing /packages/All/xcb-util-image-0.4.1.pkg Installing /packages/All/xcb-util-keysyms-0.4.1.pkg Installing /packages/All/xcb-util-renderutil-0.3.10.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/qt5-dbus-5.15.8p157.pkg Installing /packages/All/qt5-network-5.15.8p157.pkg Installing /packages/All/vulkan-headers-1.3.257.pkg Installing /packages/All/hicolor-icon-theme-0.17.pkg Installing /packages/All/xprop-1.2.6.pkg Installing /packages/All/libXmu-1.1.3,1.pkg Installing /packages/All/xset-1.2.5.pkg Installing /packages/All/xdg-utils-1.1.3_2.pkg Installing /packages/All/encodings-1.0.5,1.pkg 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/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/qt5-gui-5.15.8p157_1.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/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/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/qt5-widgets-5.15.8p157.pkg Installing /packages/All/qt5-printsupport-5.15.8p157.pkg Installing /packages/All/qscintilla2-qt5-2.13.3_1.pkg Installing /packages/All/qt5-concurrent-5.15.8p157.pkg Installing /packages/All/qt5-sql-5.15.8p157.pkg ===== Message from qt5-sql-5.15.8p157: -- To enable Qt database support, install the database plugin ports. The following plugin ports are available: - databases/qt5-sqldrivers-ibase InterBase/Firebird - databases/qt5-sqldrivers-mysql MySQL - databases/qt5-sqldrivers-odbc Open Database Connectivity - databases/qt5-sqldrivers-pgsql PostgreSQL - databases/qt5-sqldrivers-sqlite2 SQLite 2 - databases/qt5-sqldrivers-sqlite3 SQLite 3 - databases/qt5-sqldrivers-tds FreeTDS Installing /packages/All/qt5-declarative-5.15.8p21.pkg Installing /packages/All/qt5-connectivity-5.15.8p5.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/qt5-sqldrivers-sqlite3-5.15.8p157.pkg Installing /packages/All/qt5-help-5.15.8p1.pkg Installing /packages/All/qt5-serialport-5.15.8p0.pkg Installing /packages/All/qt5-location-5.15.8p3.pkg Installing /packages/All/alsa-lib-1.2.2_1.pkg ===== Message from alsa-lib-1.2.2_1: -- ===> NOTICE: The alsa-lib 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/libunwind-20211201_2.pkg Installing /packages/All/gstreamer1-1.22.5.pkg Installing /packages/All/libmysofa-1.3.1.pkg Installing /packages/All/openal-soft-1.21.1_3.pkg Installing /packages/All/qt5-opengl-5.15.8p157.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/libXv-1.0.12,1.pkg Installing /packages/All/qt5-multimedia-5.15.8p1.pkg Installing /packages/All/assimp-5.2.5.pkg Installing /packages/All/qt5-quick3d-5.15.8p1.pkg Installing /packages/All/qt5-remoteobjects-5.15.8p0.pkg Installing /packages/All/qt5-sensors-5.15.8p0.pkg Installing /packages/All/dotconf-1.3_1.pkg Installing /packages/All/libltdl-2.4.7.pkg Installing /packages/All/libogg-1.3.5,4.pkg Installing /packages/All/flac-1.4.3,1.pkg Installing /packages/All/lame-3.100_4.pkg Installing /packages/All/mpg123-1.31.3_1.pkg Installing /packages/All/opus-1.4.pkg Installing /packages/All/libvorbis-1.3.7_2,3.pkg Installing /packages/All/libsndfile-1.2.0_1.pkg Installing /packages/All/libao-1.2.0_5.pkg Installing /packages/All/pcaudiolib-1.2.pkg Installing /packages/All/espeak-ng-1.51.1_4.pkg Installing /packages/All/speech-dispatcher-0.11.2_2.pkg Installing /packages/All/qt5-speech-5.15.8p1_1.pkg Installing /packages/All/qt5-svg-5.15.8p8.pkg Installing /packages/All/qt5-testlib-5.15.8p157.pkg Installing /packages/All/qt5-webchannel-5.15.8p3.pkg Installing /packages/All/perl5-5.32.1_3.pkg Installing /packages/All/hyphen-2.8.8.pkg Installing /packages/All/giflib-5.2.1.pkg Installing /packages/All/libdeflate-1.18.pkg Installing /packages/All/jbigkit-2.1_1.pkg Installing /packages/All/tiff-4.4.0_1.pkg Installing /packages/All/webp-1.3.0_1.pkg Installing /packages/All/woff2-1.0.2_4.pkg Installing /packages/All/libgpg-error-1.47.pkg Installing /packages/All/libgcrypt-1.10.2.pkg Installing /packages/All/libxslt-1.1.37.pkg UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default Installing /packages/All/highway-1.0.4_1.pkg Installing /packages/All/Imath-3.1.9.pkg Installing /packages/All/openexr-3.1.9.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/libjxl-0.8.2.pkg Building the Shared MIME-Info database cache Generating gdk-pixbuf modules cache ===== Message from libjxl-0.8.2: -- Additional packages recommended for new users: - imlib2-jxl (e.g., feh, scrot) - kf5-kimageformats (e.g., nomacs, flameshot, skanlite) - gimp-jxl-plugin Installing /packages/All/vmaf-2.3.1.pkg Installing /packages/All/aom-3.6.1.pkg Installing /packages/All/fribidi-1.0.13.pkg Installing /packages/All/libunibreak-5.1,1.pkg Installing /packages/All/libass-0.17.1_1.pkg Installing /packages/All/dav1d-1.2.1.pkg Installing /packages/All/libpciaccess-0.17.pkg Installing /packages/All/libdrm-2.4.115,1.pkg Installing /packages/All/lcms2-2.15_1.pkg Installing /packages/All/shaderc-2023.4.pkg Installing /packages/All/vulkan-loader-1.3.257.pkg Installing /packages/All/libplacebo-5.264.1.pkg Installing /packages/All/svt-av1-1.6.0.pkg Installing /packages/All/argp-standalone-1.5.0.pkg Installing /packages/All/libv4l-1.23.0.pkg Installing /packages/All/libva-2.18.0.pkg Installing /packages/All/libvdpau-1.5.pkg Installing /packages/All/libvpx-1.13.0.pkg Installing /packages/All/libx264-0.164.3095.pkg Installing /packages/All/x265-3.4_2.pkg Installing /packages/All/ffmpeg-6.0,1.pkg Installing /packages/All/gstreamer1-libav-1.22.5.pkg Installing /packages/All/liba52-0.8.0.pkg Installing /packages/All/gstreamer1-plugins-ugly-1.22.5.pkg Installing /packages/All/gstreamer1-plugins-a52dec-1.22.5.pkg Installing /packages/All/libdca-0.0.7.pkg Installing /packages/All/gstreamer1-plugins-dts-1.22.5.pkg Installing /packages/All/libdvdread-6.1.3.pkg Installing /packages/All/gstreamer1-plugins-dvdread-1.22.5.pkg Installing /packages/All/gstreamer1-plugins-good-1.22.5.pkg Installing /packages/All/gstreamer1-plugins-mpg123-1.22.5.pkg Installing /packages/All/gstreamer1-plugins-ogg-1.22.5.pkg Installing /packages/All/pixman-0.42.2.pkg Installing /packages/All/cairo-1.17.4_2,3.pkg 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/pango-1.50.14.pkg Installing /packages/All/gstreamer1-plugins-pango-1.22.5.pkg Installing /packages/All/gstreamer1-plugins-png-1.22.5.pkg Installing /packages/All/libdvdnav-6.1.1.pkg Installing /packages/All/gstreamer1-plugins-resindvd-1.22.5.pkg Installing /packages/All/libtheora-1.1.1_7.pkg Installing /packages/All/gstreamer1-plugins-theora-1.22.5.pkg Installing /packages/All/gstreamer1-plugins-vorbis-1.22.5.pkg Installing /packages/All/gstreamer1-plugins-core-1.22.5.pkg Installing /packages/All/libXcomposite-0.4.6,1.pkg Installing /packages/All/qt5-webkit-5.212.0.a4_13.pkg Installing /packages/All/qt5-websockets-5.15.8p2.pkg Installing /packages/All/qt5-x11extras-5.15.8p0.pkg Installing /packages/All/qt5-xml-5.15.8p157.pkg Installing /packages/All/qt5-xmlpatterns-5.15.8p0.pkg Installing /packages/All/pydbus-common-1.3.2.pkg Installing /packages/All/py39-dbus-1.3.2.pkg Installing /packages/All/py39-ply-3.11.pkg Installing /packages/All/py39-qt5-sip-12.11.1_1.pkg Installing /packages/All/py39-qtbuilder-1.14.1.pkg Installing /packages/All/py39-toml-0.10.2.pkg Installing /packages/All/py39-packaging-23.1.pkg Installing /packages/All/py39-sip-6.7.7,1.pkg Installing /packages/All/qt5-assistant-5.15.8p1.pkg Installing /packages/All/qt5-uiplugin-5.15.8p1.pkg Installing /packages/All/qt5-designer-5.15.8p1.pkg Installing /packages/All/jasper-4.0.0.pkg Installing /packages/All/lcms-1.19_6,1.pkg Installing /packages/All/libmng-1.0.10_3.pkg Installing /packages/All/qt5-imageformats-5.15.8p6_2.pkg Installing /packages/All/py39-qt5-pyqt-5.15.9_1.pkg UNFLAVORED devel/binutils -> use devel/binutils@native UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default SUCCEEDED 00:01:14 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-pymol-2.5.0.97_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-pymol-2.5.0.97_2 for building => SHA256 Checksum OK for schrodinger-pymol-open-source-v2.5.0-97-gd24468af_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-pymol-2.5.0.97_2 for building ===> Extracting for py39-pymol-2.5.0.97_2 => SHA256 Checksum OK for schrodinger-pymol-open-source-v2.5.0-97-gd24468af_GH0.tar.gz. Extracted Memory Use: 40.46M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-pymol-2.5.0.97_2 ===> Applying ports patches for py39-pymol-2.5.0.97_2 from /xports/science/py-pymol/files ===> Applying dragonfly patches for py39-pymol-2.5.0.97_2 from /xports/science/py-pymol/dragonfly SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-pymol-2.5.0.97_2 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/include/glm/glm.hpp - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/include/mmtf.hpp - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/bin/python3.9 - found ===> py39-pymol-2.5.0.97_2 depends on package: xorgproto>=0 - found ===> py39-pymol-2.5.0.97_2 depends on package: xorgproto>=0 - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> py39-pymol-2.5.0.97_2 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libmsgpackc.so - found (/usr/local/lib/libmsgpackc.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libGL.so - found (/usr/local/lib/libGL.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libGLEW.so - found (/usr/local/lib/libGLEW.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libGLU.so - found (/usr/local/lib/libGLU.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-pymol-2.5.0.97_2 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/include/glm/glm.hpp - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/include/mmtf.hpp - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/bin/python3.9 - found ===> py39-pymol-2.5.0.97_2 depends on package: xorgproto>=0 - found ===> py39-pymol-2.5.0.97_2 depends on package: xorgproto>=0 - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/bin/ccache - found ===> py39-pymol-2.5.0.97_2 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libmsgpackc.so - found (/usr/local/lib/libmsgpackc.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libGL.so - found (/usr/local/lib/libGL.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libGLEW.so - found (/usr/local/lib/libGLEW.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libGLU.so - found (/usr/local/lib/libGLU.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so) ===> py39-pymol-2.5.0.97_2 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> Configuring for py39-pymol-2.5.0.97_2 running config SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-pymol-2.5.0.97_2 running build running build_py creating build/lib.dragonfly-6.5-x86_64-cpython-39 creating build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/arc.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/bond_amber.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/bond_mmff.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/bonds.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/brick.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/cc1.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/charge.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/cif.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/cpv.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/dictdb.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/gamess1.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/gms.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/hetatm.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/io.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/lst.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/mae.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/map.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/mass.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/mmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/models.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/mol.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/mol2.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/neighbor.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/pdb.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/pkl.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/place.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/protein.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/protein_amber.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/protein_amber99.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/protein_mmff.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/protein_residues.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/sdf.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/solvate.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/water_amber.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/water_residues.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy copying modules/chempy/xyz.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy creating build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin creating build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ creating build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/fast creating build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/fragments creating build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mmtf copying modules/chempy/mmtf/io.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mmtf creating build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker creating build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/TextEditor.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/builder.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/file_dialogs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/keymapping.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/mimic_tk.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/properties_dialog.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/scene_bin_gui.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/shortcut_menu_gui.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt copying modules/pmg_qt/volume.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt creating build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms creating build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax creating build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk creating build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins creating build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/demo creating build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/normal creating build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/startup creating build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/__main__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/_gui.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/api.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/callback.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/cgo.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/cgobuilder.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/checking.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/colorprinting.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/colorramping.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/commanding.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/completing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/computing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/constants.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/constants_palette.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/controlling.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/creating.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/diagnosing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/editing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/editor.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/experimenting.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/exporting.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/externing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/feedingback.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/fitting.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/gui.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/headering.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/helping.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/importing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/internal.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/invocation.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/keyboard.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/keywords.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/lazyio.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/locking.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/menu.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/monitoring.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/morphing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/movie.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/moving.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/mpeg_encode.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/parser.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/parsing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/povray.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/preset.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/pymolhttpd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/querying.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/rpc.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/save_shortcut.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/selecting.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/selector.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/seqalign.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/setting.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/shortcut.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/shortcut_dict.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/shortcut_manager.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/util.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/vfont.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/viewing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/wizarding.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/xray.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol copying modules/pymol/xwin.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol creating build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/Qt copying modules/pymol/Qt/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/Qt copying modules/pymol/Qt/utils.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/Qt creating build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins creating build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/stereochemistry creating build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/command.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/openvr.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard creating build/lib.dragonfly-6.5-x86_64-cpython-39/pymol2 copying modules/pymol2/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol2 copying modules/pymol2/cmd2.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pymol2 copying modules/pmg_qt/forms/askpartial.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/change_confirm.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/create_shortcut.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/help_shortcut.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/props.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/render.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/save_object.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms copying modules/pmg_qt/forms/shortcut_menu.ui -> build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms running build_ext building 'pymol._cmd' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39 creating build/temp.dragonfly-6.5-x86_64-cpython-39/build creating build/temp.dragonfly-6.5-x86_64-cpython-39/build/generated creating build/temp.dragonfly-6.5-x86_64-cpython-39/contrib creating build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/mmtf-c creating build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc creating build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins creating build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin creating build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src creating build/temp.dragonfly-6.5-x86_64-cpython-39/layer0 creating build/temp.dragonfly-6.5-x86_64-cpython-39/layer1 creating build/temp.dragonfly-6.5-x86_64-cpython-39/layer2 creating build/temp.dragonfly-6.5-x86_64-cpython-39/layer3 creating build/temp.dragonfly-6.5-x86_64-cpython-39/layer4 creating build/temp.dragonfly-6.5-x86_64-cpython-39/layer5 creating build/temp.dragonfly-6.5-x86_64-cpython-39/ov creating build/temp.dragonfly-6.5-x86_64-cpython-39/ov/src c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD build/generated/ShaderText.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/build/generated/ShaderText.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/carplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/inthash.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/inthash.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/corplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/mmtf-c/mmtf_parser.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/mmtf-c/mmtf_parser.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c: In function 'read_mmtk_cdf_structure': contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:730:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if (len > sizeof(name)) { ^ contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c: In function 'read_mmtk_cdf_timestep': contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:1060:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i=0; i<(3 * mmtk->atom_numberdim); i++) { ^ 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'int getUniqueResID(char*, int)': contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:443:7: warning: unused variable 'i' [-Wunused-variable] int i, uid; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'int parseStructureFaster(molfile_atom_t*, int*, pdbxParser*)': contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:484:47: warning: unused variable 'j' [-Wunused-variable] int i, count, atomdata, pos, idx, xyzcount, j; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable 'oldChain' [-Wunused-variable] char oldChain[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'bool readAngleBonds(molfile_atom_t*, pdbxParser*)': contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable 'bondTable' [-Wunused-variable] int bondTable[32]; ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable 'j' [-Wunused-variable] int i, pos, j, k; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable 'modelNum' [-Wunused-variable] char modelNum[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable 'atom' [-Wunused-variable] molfile_atom_t * atom; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable 'test' [-Wunused-variable] int test = parser->nbonds + bnum; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'bool readRMSDBonds(molfile_atom_t*, pdbxParser*)': contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable 'bondTable' [-Wunused-variable] int bondTable[32]; ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable 'j' [-Wunused-variable] int i, pos, j, k; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable 'modelNum' [-Wunused-variable] char modelNum[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable 'atom' [-Wunused-variable] molfile_atom_t * atom; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'void* open_file_write(const char*, const char*, int)': contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable 'fd' [-Wunused-variable] FILE* fd; ^~ 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/hash.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/hash.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp 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 -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i=0; ifd) != 3*n) { ^~ c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Map.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/Map.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Matrix.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/Matrix.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/MemoryUsage.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/MemoryUsage.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i=0; i fw) { ^ c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdheader': contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:191:57: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ^~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:204:54: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ^~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:222:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (input_integer[0] != dcdcordmagic) { ^~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:399:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ^~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:416:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ^~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdstep': contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:621:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; ^~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:625:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; ^~ c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Word.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/Word.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/PostProcess.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/PostProcess.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Triangle.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/Triangle.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/CGO.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer1/CGO.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/TTT.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/TTT.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/CGORenderer.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer1/CGORenderer.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Texture.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/Texture.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/ShaderPrg.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/ShaderPrg.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Block.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/Block.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Util2.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/Util2.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/marching_cubes.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/marching_cubes.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'void put_element_ply(PlyFile*, void*)': contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:459:7: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'void ascii_get_element(PlyFile*, char*)': contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1407:7: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'void binary_get_element(PlyFile*, char*)': contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1541:7: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Camera.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer1/Camera.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/GenericBuffer.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/GenericBuffer.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer0/Parse.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer0/Parse.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Basis.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer1/Basis.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Color.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer1/Color.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'abinit_readline': contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:279:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i = 0; i < strlen(line); ++i) { ^ c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer1/Extrude.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/layer1/Extrude.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp c++ -pipe -O2 -fno-strict-aliasing -DMSGPACK_NO_BOOST -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp -o build/temp.dragonfly-6.5-x86_64-cpython-39/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i=0; i py39-pymol-2.5.0.97_2 depends on package: py39-msgpack>0 - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-Pmw>0 - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/bin/python3.9 - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-qt5-pyqt>=5.15.9 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-pymol-2.5.0.97_2 ===> py39-pymol-2.5.0.97_2 depends on package: py39-msgpack>0 - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-Pmw>0 - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pymol-2.5.0.97_2 depends on file: /usr/local/bin/python3.9 - found ===> py39-pymol-2.5.0.97_2 depends on package: py39-qt5-pyqt>=5.15.9 - found ===> Generating temporary packing list running install running build running build_py running build_ext running install_lib creating /construction/science/py-pymol/stage/usr/local/lib/python3.9 creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/arc.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bond_amber.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bond_mmff.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bonds.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/brick.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/cc1.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/charge.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/cif.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/cpv.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/dictdb.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/gamess1.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/gms.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/hetatm.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/io.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/lst.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mae.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/map.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mass.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mmd.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/models.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mol.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mol2.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/neighbor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/pdb.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/pkl.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/place.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/protein.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/protein_amber.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/protein_amber99.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/protein_mmff.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/protein_residues.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/sdf.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/solvate.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/water_amber.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/water_residues.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/xyz.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin/commands.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin/realtime.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin/state.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/bmin/util.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ/amber99.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ/assign.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ/formal_charges.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/champ/_champ.cpython-39.so -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/fast copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/fast/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/fast creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/fragments copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/fragments/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/fragments creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mmtf copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mmtf/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mmtf copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/mmtf/io.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mmtf creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker/amber.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker/keyword.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker/realtime.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker copying build/lib.dragonfly-6.5-x86_64-cpython-39/chempy/tinker/state.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/TextEditor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/advanced_settings_gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/builder.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/file_dialogs.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/keymapping.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/mimic_pmg_tk.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/mimic_tk.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/properties_dialog.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/pymol_gl_widget.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/pymol_qt_gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/scene_bin_gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/shortcut_menu_gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/volume.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/askpartial.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/change_confirm.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/colors.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/create_shortcut.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/fetch.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/help_shortcut.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/load_aln.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/load_mae.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/load_map.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/load_mtz.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/load_traj.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/movieexport.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/pluginitem.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/pluginmanager.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/png.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/props.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/render.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/save_molecule.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/save_object.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/forms/shortcut_menu.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax/pml.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax/pmlparser.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_qt/syntax/python.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/ColorEditor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/Demo.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/PMGApp.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/PyMOLMapLoad.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/SetEditor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/Setting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/TextEditor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/volume.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/demo copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/demo/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/demo creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/normal copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/normal/ModalWindow.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/normal copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/normal/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/normal copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/skins/normal/builder.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/normal creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/startup copying build/lib.dragonfly-6.5-x86_64-cpython-39/pmg_tk/startup/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/startup creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/__main__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/_gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/api.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/callback.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/cgo.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/cgobuilder.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/checking.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/cmd.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/colorprinting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/colorramping.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/commanding.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/completing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/computing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/constants.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/constants_palette.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/controlling.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/creating.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/diagnosing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/editing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/editor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/experimenting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/exporting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/externing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/feedingback.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/fitting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/headering.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/helping.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/importing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/internal.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/invocation.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/keyboard.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/keywords.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/lazyio.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/locking.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/menu.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/monitoring.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/morphing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/movie.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/moving.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/mpeg_encode.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/parser.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/parsing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/povray.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/preset.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/pymolhttpd.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/querying.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/rpc.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/save_shortcut.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/selecting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/selector.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/seqalign.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/setting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/shortcut.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/shortcut_dict.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/shortcut_manager.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/util.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/vfont.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/viewing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizarding.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/xray.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/xwin.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/Qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/Qt/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/Qt copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/Qt/utils.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/Qt creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins/installation.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins/legacysupport.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins/managergui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins/managergui_qt.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/plugins/repository.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/stereochemistry copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/stereochemistry/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/stereochemistry creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/annotation.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/appearance.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/benchmark.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/box.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/charge.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/cleanup.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/command.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/demo.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/density.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/distance.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/dragging.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/filter.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/label.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/measurement.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/message.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/mutagenesis.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/nucmutagenesis.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/openvr.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/pair_fit.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/pseudoatom.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/renaming.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/sculpting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/security.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/stereodemo.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/wizard/toggle.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol/_cmd.cpython-39.so -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol2/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/pymol2/cmd2.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol2 byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/arc.py to arc.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bond_amber.py to bond_amber.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bond_mmff.py to bond_mmff.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bonds.py to bonds.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/brick.py to brick.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/cc1.py to cc1.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/charge.py to charge.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/cif.py to cif.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/cpv.py to cpv.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/dictdb.py to dictdb.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/gamess1.py to gamess1.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/gms.py to gms.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/hetatm.py to hetatm.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/io.py to io.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/lst.py to lst.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mae.py to mae.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/map.py to map.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mass.py to mass.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mmd.py to mmd.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/models.py to models.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mol.py to mol.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mol2.py to mol2.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/neighbor.py to neighbor.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/pdb.py to pdb.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/pkl.py to pkl.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/place.py to place.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/protein.py to protein.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/protein_amber.py to protein_amber.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/protein_amber99.py to protein_amber99.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/protein_mmff.py to protein_mmff.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/protein_residues.py to protein_residues.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/sdf.py to sdf.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/solvate.py to solvate.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/water_amber.py to water_amber.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/water_residues.py to water_residues.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/xyz.py to xyz.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin/commands.py to commands.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin/realtime.py to realtime.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin/state.py to state.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/bmin/util.py to util.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ/amber99.py to amber99.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ/assign.py to assign.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/champ/formal_charges.py to formal_charges.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/fast/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/fragments/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mmtf/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/mmtf/io.py to io.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker/amber.py to amber.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker/keyword.py to keyword.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker/realtime.py to realtime.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/chempy/tinker/state.py to state.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/TextEditor.py to TextEditor.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/advanced_settings_gui.py to advanced_settings_gui.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/builder.py to builder.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/file_dialogs.py to file_dialogs.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/keymapping.py to keymapping.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/mimic_pmg_tk.py to mimic_pmg_tk.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/mimic_tk.py to mimic_tk.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/properties_dialog.py to properties_dialog.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/pymol_gl_widget.py to pymol_gl_widget.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/pymol_qt_gui.py to pymol_qt_gui.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/scene_bin_gui.py to scene_bin_gui.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/shortcut_menu_gui.py to shortcut_menu_gui.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/volume.py to volume.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/forms/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax/pml.py to pml.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax/pmlparser.py to pmlparser.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_qt/syntax/python.py to python.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/ColorEditor.py to ColorEditor.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/Demo.py to Demo.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/PMGApp.py to PMGApp.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/PyMOLMapLoad.py to PyMOLMapLoad.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/SetEditor.py to SetEditor.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/Setting.py to Setting.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/TextEditor.py to TextEditor.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/volume.py to volume.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/demo/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/normal/ModalWindow.py to ModalWindow.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/normal/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/skins/normal/builder.py to builder.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pmg_tk/startup/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/__main__.py to __main__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/_gui.py to _gui.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/api.py to api.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/callback.py to callback.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/cgo.py to cgo.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/cgobuilder.py to cgobuilder.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/checking.py to checking.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/cmd.py to cmd.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/colorprinting.py to colorprinting.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/colorramping.py to colorramping.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/commanding.py to commanding.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/completing.py to completing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/computing.py to computing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/constants.py to constants.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/constants_palette.py to constants_palette.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/controlling.py to controlling.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/creating.py to creating.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/diagnosing.py to diagnosing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/editing.py to editing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/editor.py to editor.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/experimenting.py to experimenting.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/exporting.py to exporting.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/externing.py to externing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/feedingback.py to feedingback.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/fitting.py to fitting.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/gui.py to gui.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/headering.py to headering.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/helping.py to helping.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/importing.py to importing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/internal.py to internal.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/invocation.py to invocation.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/keyboard.py to keyboard.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/keywords.py to keywords.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/lazyio.py to lazyio.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/locking.py to locking.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/menu.py to menu.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/monitoring.py to monitoring.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/morphing.py to morphing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/movie.py to movie.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/moving.py to moving.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/mpeg_encode.py to mpeg_encode.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/parser.py to parser.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/parsing.py to parsing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/povray.py to povray.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/preset.py to preset.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/pymolhttpd.py to pymolhttpd.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/querying.py to querying.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/rpc.py to rpc.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/save_shortcut.py to save_shortcut.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/selecting.py to selecting.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/selector.py to selector.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/seqalign.py to seqalign.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/setting.py to setting.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/shortcut.py to shortcut.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/shortcut_dict.py to shortcut_dict.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/shortcut_manager.py to shortcut_manager.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/util.py to util.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/vfont.py to vfont.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/viewing.py to viewing.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizarding.py to wizarding.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/xray.py to xray.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/xwin.py to xwin.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/Qt/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/Qt/utils.py to utils.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins/installation.py to installation.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins/legacysupport.py to legacysupport.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins/managergui.py to managergui.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins/managergui_qt.py to managergui_qt.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/plugins/repository.py to repository.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/stereochemistry/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/annotation.py to annotation.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/appearance.py to appearance.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/benchmark.py to benchmark.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/box.py to box.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/charge.py to charge.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/cleanup.py to cleanup.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/command.py to command.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/demo.py to demo.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/density.py to density.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/distance.py to distance.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/dragging.py to dragging.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/filter.py to filter.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/label.py to label.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/measurement.py to measurement.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/message.py to message.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/mutagenesis.py to mutagenesis.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/nucmutagenesis.py to nucmutagenesis.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/openvr.py to openvr.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/pair_fit.py to pair_fit.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/pseudoatom.py to pseudoatom.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/renaming.py to renaming.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/sculpting.py to sculpting.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/security.py to security.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/stereodemo.py to stereodemo.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/wizard/toggle.py to toggle.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol2/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol2/cmd2.py to cmd2.cpython-39.pyc writing byte-compilation script '/tmp/tmpfrlbp0cf.py' /usr/local/bin/python3.9 /tmp/tmpfrlbp0cf.py removing /tmp/tmpfrlbp0cf.py running install_egg_info running egg_info creating pymol.egg-info writing pymol.egg-info/PKG-INFO writing dependency_links to pymol.egg-info/dependency_links.txt writing top-level names to pymol.egg-info/top_level.txt writing manifest file 'pymol.egg-info/SOURCES.txt' /usr/local/lib/python3.9/site-packages/setuptools/command/egg_info.py:632: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. Please extend command classes from setuptools instead of distutils. warnings.warn( reading manifest file 'pymol.egg-info/SOURCES.txt' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'pymol.egg-info/SOURCES.txt' Copying pymol.egg-info to /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol-2.6.0a0-py3.9.egg-info writing list of installed files to '/construction/science/py-pymol/.PLIST.pymodtmp' creating /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/pymol_path copying LICENSE -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/pymol_path copying data -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/pymol_path/data copying test -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/pymol_path/test copying examples -> /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol/pymol_path/examples ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/pymol --> bin/pymol-3.9 Link: @bin/pymol --> bin/pymol-3.9 ====> Compressing man pages (compress-man) if [ -d "/construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol-2.5.0.97-py3.9.egg-info" ]; then /bin/ls /construction/science/py-pymol/stage/usr/local/lib/python3.9/site-packages/pymol-2.5.0.97-py3.9.egg-info | while read f; do echo lib/python3.9/site-packages/pymol-2.5.0.97-py3.9.egg-info/${f} >> /construction/science/py-pymol/.PLIST.mktmp; done; fi; ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so 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/python3.9/site-packages/pymol/_cmd.cpython-39.so 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/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libhdf5_hl.so.200 from science/hdf5 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libhdf5_hl.so:science/hdf5 Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libhdf5.so.200 from science/hdf5 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libhdf5.so:science/hdf5 Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libzstd.so.1 from archivers/zstd but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libzstd.so:archivers/zstd Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libcurl.so.4 from ftp/curl but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libcurl.so:ftp/curl Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libsz.so.2 from science/libaec but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libsz.so:science/libaec Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so 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 Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so 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/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libnghttp2.so.14 from www/libnghttp2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libnghttp2.so:www/libnghttp2 Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libssh2.so.1 from security/libssh2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libssh2.so:security/libssh2 Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libpsl.so.5 from dns/libpsl but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libpsl.so:dns/libpsl Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libssl.so.11 from security/openssl but it is not declared as a dependency Warning: you need USES=ssl Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libcrypto.so.11 from security/openssl but it is not declared as a dependency Warning: you need USES=ssl Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libaec.so.0 from science/libaec but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libaec.so:science/libaec Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so 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/python3.9/site-packages/pymol/_cmd.cpython-39.so 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/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libidn2.so.0 from dns/libidn2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libidn2.so:dns/libidn2 Error: /usr/local/lib/python3.9/site-packages/pymol/_cmd.cpython-39.so is linked to /usr/local/lib/libunistring.so.5 from devel/libunistring but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libunistring.so:devel/libunistring Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:12 ------------------------------------------------------------------------------- -- 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 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-pymol-2.5.0.97_2 file sizes/checksums [907]: 0% file sizes/checksums [907]: 11% file sizes/checksums [907]: 22% file sizes/checksums [907]: 33% file sizes/checksums [907]: 44% file sizes/checksums [907]: 55% file sizes/checksums [907]: 66% file sizes/checksums [907]: 77% file sizes/checksums [907]: 88% file sizes/checksums [907]: 99% file sizes/checksums [907]: 100% Service unavailablepacking files [907]: 0% packing files [907]: 11% packing files [907]: 22% packing files [907]: 33% packing files [907]: 44% packing files [907]: 55% packing files [907]: 66% packing files [907]: 77% packing files [907]: 88% packing files [907]: 99% packing files [907]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:04 TOTAL TIME 00:03:46