------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/metis-5.1.0_8.txz ===== Message from metis-5.1.0_8: -- ===> 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/tbb-2020.3.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/binutils-2.33.1_3,1.txz ===== Message from binutils-2.33.1_3,1: -- ===> NOTICE: The binutils 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- 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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.10,1.txz Installing /packages/All/suitesparse-5.8.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.2.20201017.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1h_1,1.txz Installing /packages/All/python37-3.7.9_1.txz ===== Message from python37-3.7.9_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/py37-setuptools-44.0.0.txz Installing /packages/All/py37-numpy-1.16.6,1.txz Installing /packages/All/glm-0.9.8.5_4,1.txz Installing /packages/All/msgpack-3.3.0.txz Installing /packages/All/mmtf-cpp-1.0.0_2.txz Installing /packages/All/xorgproto-2020.1.txz Installing /packages/All/png-1.6.37.txz Installing /packages/All/freetype2-2.10.4.txz ===== Message from freetype2-2.10.4: -- 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/site/index.html, if documentation was installed). Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.58.txz ===== Message from ca_root_nss-3.58: -- 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-7.73.0.txz Installing /packages/All/hdf-szip-2.1.1.txz Installing /packages/All/hdf5-1.10.6,1.txz Installing /packages/All/pkgconf-1.7.3,1.txz Installing /packages/All/netcdf-4.7.3.txz Installing /packages/All/libxml2-2.9.10_1.txz Installing /packages/All/wayland-1.18.0.txz Installing /packages/All/liblz4-1.9.2_1,1.txz Installing /packages/All/zstd-1.4.5_1.txz Installing /packages/All/pciids-20200922.txz Installing /packages/All/libpciaccess-0.16.txz Installing /packages/All/libdrm-2.4.101.txz Installing /packages/All/libunwind-20200331_1.txz Installing /packages/All/libpthread-stubs-0.4.txz Installing /packages/All/libXau-1.0.9.txz Installing /packages/All/libXdmcp-1.1.3.txz Installing /packages/All/libxcb-1.14_1.txz Installing /packages/All/libX11-1.6.12,1.txz Installing /packages/All/libXfixes-5.0.3_2.txz Installing /packages/All/libXdamage-1.1.5.txz Installing /packages/All/libXext-1.3.4,1.txz Installing /packages/All/libxshmfence-1.3.txz Installing /packages/All/libXxf86vm-1.1.4_3.txz Installing /packages/All/libXrender-0.9.10_2.txz Installing /packages/All/libXrandr-1.5.2.txz Installing /packages/All/mesa-libs-20.2.0_1.txz Installing /packages/All/libGLU-9.0.1.txz Installing /packages/All/libXi-1.7.10,1.txz Installing /packages/All/libICE-1.0.10,1.txz Installing /packages/All/libSM-1.2.3,1.txz Installing /packages/All/libXt-1.2.0,1.txz Installing /packages/All/libXmu-1.1.3,1.txz Installing /packages/All/glew-2.2.0.txz Installing /packages/All/freeglut-3.0.0_2.txz ===== Message from freeglut-3.0.0_2: -- 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/py37-msgpack-0.6.2.txz Installing /packages/All/jpeg-turbo-2.0.5.txz Installing /packages/All/fontconfig-2.13.92_2,1.txz Running fc-cache to build fontconfig cache... Font directories: /usr/local/share/fonts /usr/local/lib/X11/fonts /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded Installing /packages/All/tcl86-8.6.10.txz Installing /packages/All/libXft-2.3.3.txz Installing /packages/All/libXScrnSaver-1.2.3_2.txz Installing /packages/All/tk86-8.6.10_1.txz Installing /packages/All/blt-2.5.3_5.txz Installing /packages/All/py37-tkinter-3.7.9_6.txz Installing /packages/All/py37-Pmw-2.0.1_1.txz Installing /packages/All/double-conversion-3.1.5.19.txz Installing /packages/All/icu-67.1,1.txz Installing /packages/All/pcre2-10.35.txz Installing /packages/All/pcre-8.44.txz Installing /packages/All/libiconv-1.16.txz Installing /packages/All/glib-2.66.2,1.txz No schema files found: doing nothing. Installing /packages/All/qtchooser-66_4.txz ===== Message from qtchooser-66_4: -- qtchooser is a wrapper that allows to specify Qt version of binaries for qmake, moc and other tools will be run when invoking the binaries in $PATH. By default, the Qt5 versions are run. It is possible to change the behavior by setting the QT_SELECT environment variable to "qtX", where X is desired Qt version, provided that it is offered by the Ports Collection. See qtchooser(1) for more information. Installing /packages/All/qt5-core-5.15.0_2.txz Installing /packages/All/dbus-1.12.20_3.txz ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/libevdev-1.5.9.txz Installing /packages/All/graphite2-1.3.14.txz Installing /packages/All/harfbuzz-2.7.2_1.txz Installing /packages/All/libudev-devd-0.4.2_1.txz Installing /packages/All/evdev-proto-5.8.txz Installing /packages/All/libmtdev-1.1.6.txz Installing /packages/All/py37-evdev-1.3.0.txz Installing /packages/All/py37-six-1.15.0.txz Installing /packages/All/py37-pyudev-0.22.0.txz Installing /packages/All/libinput-1.12.6_1.txz Installing /packages/All/xcb-util-0.4.0_2,1.txz Installing /packages/All/xcb-util-wm-0.4.1_3.txz Installing /packages/All/xcb-util-image-0.4.0_1.txz Installing /packages/All/xcb-util-keysyms-0.4.0_1.txz Installing /packages/All/xcb-util-renderutil-0.3.9_1.txz Installing /packages/All/xkeyboard-config-2.31.txz Installing /packages/All/libxkbcommon-1.0.1.txz ===== Message from libxkbcommon-1.0.1: -- 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-5.15.0.txz Installing /packages/All/qt5-network-5.15.0.txz Installing /packages/All/vulkan-headers-1.2.135.0.txz Installing /packages/All/hicolor-icon-theme-0.17.txz Installing /packages/All/xprop-1.2.4.txz Installing /packages/All/xset-1.2.4_3.txz Installing /packages/All/xdg-utils-1.1.3_1.txz Installing /packages/All/encodings-1.0.5,1.txz Installing /packages/All/libfontenc-1.1.4.txz Installing /packages/All/mkfontscale-1.2.1.txz Installing /packages/All/font-bh-ttf-1.0.3_4.txz Installing /packages/All/font-misc-meltho-1.0.3_4.txz Installing /packages/All/font-misc-ethiopic-1.0.4.txz Installing /packages/All/dejavu-2.37_1.txz ===== 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.txz Installing /packages/All/qt5-gui-5.15.0_1.txz Installing /packages/All/libdaemon-0.14_1.txz Installing /packages/All/dbus-glib-0.110.txz Installing /packages/All/gdbm-1.18.1_1.txz Installing /packages/All/gobject-introspection-1.66.1,1.txz Installing /packages/All/gnome_subr-1.0.txz Installing /packages/All/avahi-app-0.7_3.txz ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/nettle-3.6.txz Installing /packages/All/libtasn1-4.16.0.txz Installing /packages/All/libunistring-0.9.10_1.txz Installing /packages/All/libidn2-2.3.0_1.txz Installing /packages/All/bash-5.0.18_3.txz Installing /packages/All/bash-completion-2.11,2.txz ===== Message from bash-completion-2.11,2: -- To enable the bash completion library, add the following to your .bashrc file: [[ $PS1 && -f /usr/local/share/bash-completion/bash_completion.sh ]] && \ source /usr/local/share/bash-completion/bash_completion.sh See /usr/local/share/doc/bash-completion/README.md for more information. Installing /packages/All/p11-kit-0.23.21.txz Installing /packages/All/tpm-emulator-0.7.4_2.txz ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. Installing /packages/All/trousers-0.3.14_3.txz ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. ===== Message from trousers-0.3.14_3: -- To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Installing /packages/All/gnutls-3.6.15.txz Installing /packages/All/libpaper-1.1.24.4.txz Installing /packages/All/cups-2.3.3_1.txz ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. Installing /packages/All/qt5-widgets-5.15.0.txz Installing /packages/All/qt5-printsupport-5.15.0.txz Installing /packages/All/qscintilla2-qt5-2.11.5.txz Installing /packages/All/py37-sip-4.19.24,1.txz Installing /packages/All/py37-qt5-core-5.15.0.txz Installing /packages/All/jasper-2.0.22.txz Installing /packages/All/jbigkit-2.1_1.txz Installing /packages/All/tiff-4.1.0.txz Installing /packages/All/lcms-1.19_6,1.txz Installing /packages/All/libmng-1.0.10_3.txz Installing /packages/All/giflib-5.2.1.txz Installing /packages/All/webp-1.1.0.txz Installing /packages/All/qt5-imageformats-5.15.0.txz Installing /packages/All/py37-qt5-gui-5.15.0.txz Installing /packages/All/qt5-opengl-5.15.0.txz Installing /packages/All/py37-qt5-widgets-5.15.0.txz Installing /packages/All/py37-qt5-opengl-5.15.0.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:01:22 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py37-pymol-2.4.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py37-pymol-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-pymol-2.4.0 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py37-pymol-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-pymol-2.4.0 for building => SHA256 Checksum OK for schrodinger-pymol-open-source-v2.4.0_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py37-pymol-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-pymol-2.4.0 for building ===> Extracting for py37-pymol-2.4.0 => SHA256 Checksum OK for schrodinger-pymol-open-source-v2.4.0_GH0.tar.gz. Extracted Memory Use: 41.31M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py37-pymol-2.4.0 ===> Applying ports patches for py37-pymol-2.4.0 from /xports/science/py-pymol/files ===> Applying dragonfly patches for py37-pymol-2.4.0 from /xports/science/py-pymol/dragonfly SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py37-pymol-2.4.0 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> py37-pymol-2.4.0 depends on file: /usr/local/include/glm/glm.hpp - found ===> py37-pymol-2.4.0 depends on file: /usr/local/include/mmtf.hpp - found ===> py37-pymol-2.4.0 depends on package: py37-setuptools>0 - found ===> py37-pymol-2.4.0 depends on file: /usr/local/bin/python3.7 - found ===> py37-pymol-2.4.0 depends on package: xorgproto>=0 - found ===> py37-pymol-2.4.0 depends on package: xorgproto>=0 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> py37-pymol-2.4.0 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so) ===> py37-pymol-2.4.0 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> py37-pymol-2.4.0 depends on shared library: libmsgpackc.so - found (/usr/local/lib/libmsgpackc.so) ===> py37-pymol-2.4.0 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so) ===> py37-pymol-2.4.0 depends on shared library: libGL.so - found (/usr/local/lib/libGL.so) ===> py37-pymol-2.4.0 depends on shared library: libGLEW.so - found (/usr/local/lib/libGLEW.so) ===> py37-pymol-2.4.0 depends on shared library: libGLU.so - found (/usr/local/lib/libGLU.so) ===> py37-pymol-2.4.0 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so) ===> py37-pymol-2.4.0 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py37-pymol-2.4.0 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> py37-pymol-2.4.0 depends on file: /usr/local/include/glm/glm.hpp - found ===> py37-pymol-2.4.0 depends on file: /usr/local/include/mmtf.hpp - found ===> py37-pymol-2.4.0 depends on package: py37-setuptools>0 - found ===> py37-pymol-2.4.0 depends on file: /usr/local/bin/python3.7 - found ===> py37-pymol-2.4.0 depends on package: xorgproto>=0 - found ===> py37-pymol-2.4.0 depends on package: xorgproto>=0 - found ===> py37-pymol-2.4.0 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so) ===> py37-pymol-2.4.0 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> py37-pymol-2.4.0 depends on shared library: libmsgpackc.so - found (/usr/local/lib/libmsgpackc.so) ===> py37-pymol-2.4.0 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so) ===> py37-pymol-2.4.0 depends on shared library: libGL.so - found (/usr/local/lib/libGL.so) ===> py37-pymol-2.4.0 depends on shared library: libGLEW.so - found (/usr/local/lib/libGLEW.so) ===> py37-pymol-2.4.0 depends on shared library: libGLU.so - found (/usr/local/lib/libGLU.so) ===> py37-pymol-2.4.0 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so) ===> py37-pymol-2.4.0 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> Configuring for py37-pymol-2.4.0 running config SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py37-pymol-2.4.0 running build running build_py creating build/lib.dragonfly-5.9-x86_64-3.7 creating build/lib.dragonfly-5.9-x86_64-3.7/pymol2 copying modules/pymol2/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol2 copying modules/pymol2/cmd2.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol2 creating build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/cc1.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/cpv.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/pdb.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/models.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/protein_mmff.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/protein_amber99.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/bond_amber.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/gamess1.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/pkl.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/cif.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/gms.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/bond_mmff.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/io.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/charge.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/bonds.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/protein.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/place.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/mol.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/brick.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/solvate.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/water_amber.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/xyz.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/protein_residues.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/water_residues.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/hetatm.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/neighbor.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/mmd.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/protein_amber.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/dictdb.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/mol2.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/arc.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/map.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/lst.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/mae.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/sdf.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy copying modules/chempy/mass.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy creating build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ creating build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin creating build/lib.dragonfly-5.9-x86_64-3.7/chempy/mmtf copying modules/chempy/mmtf/io.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/mmtf creating build/lib.dragonfly-5.9-x86_64-3.7/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/fast creating build/lib.dragonfly-5.9-x86_64-3.7/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/fragments creating build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker creating build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/TextEditor.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/mimic_tk.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/keymapping.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/builder.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/volume.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/properties_dialog.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt copying modules/pmg_qt/file_dialogs.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt creating build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms creating build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax creating build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/parser.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/parsing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/povray.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/preset.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/pymolhttpd.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/querying.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/rpc.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/selecting.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/selector.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/seqalign.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/setting.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/shortcut.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/util.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/vfont.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/viewing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/wizarding.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/xray.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/xwin.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/api.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/callback.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/cgo.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/checking.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/cmd.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/colorprinting.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/colorramping.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/commanding.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/completing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/computing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/constants.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/constants_palette.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/controlling.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/creating.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/diagnosing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/editing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/editor.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/experimenting.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/exporting.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/externing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/feedingback.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/fitting.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/gui.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/headering.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/helping.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/importing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/internal.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/invocation.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/keyboard.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/keywords.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/lazyio.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/locking.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/menu.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/monitoring.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/morphing.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/movie.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/moving.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/__main__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol copying modules/pymol/_gui.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/stereochemistry creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/command.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/fedora.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/openvr.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/contrib copying modules/pymol/contrib/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/contrib creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl copying modules/pymol/opengl/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/gl copying modules/pymol/opengl/gl/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/gl creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/glu copying modules/pymol/opengl/glu/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/glu creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/glut copying modules/pymol/opengl/glut/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/glut creating build/lib.dragonfly-5.9-x86_64-3.7/pymol/Qt copying modules/pymol/Qt/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/Qt copying modules/pymol/Qt/utils.py -> build/lib.dragonfly-5.9-x86_64-3.7/pymol/Qt creating build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk creating build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/startup copying modules/pmg_tk/startup/apbs_tools.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/startup creating build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins creating build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/demo creating build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/normal copying modules/pmg_qt/forms/render.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/props.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/save_object.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/askpartial.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms running build_ext building 'pymol._cmd' extension creating build/temp.dragonfly-5.9-x86_64-3.7 creating build/temp.dragonfly-5.9-x86_64-3.7/build creating build/temp.dragonfly-5.9-x86_64-3.7/build/generated creating build/temp.dragonfly-5.9-x86_64-3.7/contrib creating build/temp.dragonfly-5.9-x86_64-3.7/contrib/mmtf-c creating build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc creating build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins creating build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin creating build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src creating build/temp.dragonfly-5.9-x86_64-3.7/layer0 creating build/temp.dragonfly-5.9-x86_64-3.7/layer1 creating build/temp.dragonfly-5.9-x86_64-3.7/layer2 creating build/temp.dragonfly-5.9-x86_64-3.7/layer3 creating build/temp.dragonfly-5.9-x86_64-3.7/layer4 creating build/temp.dragonfly-5.9-x86_64-3.7/layer5 creating build/temp.dragonfly-5.9-x86_64-3.7/modules creating build/temp.dragonfly-5.9-x86_64-3.7/modules/cealign creating build/temp.dragonfly-5.9-x86_64-3.7/modules/cealign/src creating build/temp.dragonfly-5.9-x86_64-3.7/ov creating build/temp.dragonfly-5.9-x86_64-3.7/ov/src c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD build/generated/ShaderText.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/build/generated/ShaderText.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/carplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/corplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/mmtf-c/mmtf_parser.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/mmtf-c/mmtf_parser.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 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++) { ^ c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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/namdbinplugin.c: In function 'write_timestep': contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:206:55: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (fwrite(tmp, sizeof(double), 3*n, namdbin->fd) != 3*n) { ^~ 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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; ^~ 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) { ^ 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; ^~ 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Crystal.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Crystal.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Err.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Err.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Field.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Field.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/GenericBuffer.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/GenericBuffer.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Isosurf.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Isosurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Match.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Match.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/MemoryDebug.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/MemoryDebug.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Parse.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Parse.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/PostProcess.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/PostProcess.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/ShaderPrg.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/ShaderPrg.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Tetsurf.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Tetsurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Block.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Block.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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 -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Tracker.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Tracker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Util.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Util.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer0/Vector.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Vector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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; i ExecutiveLoad(PyMOLGlobals*, const ExecutiveLoadArgs&)': layer3/Executive.cpp:3914:15: warning: unused variable 'object_props' [-Wunused-variable] const char* object_props = args.object_props.c_str(); ^~~~~~~~~~~~ layer3/Executive.cpp:3915:15: warning: unused variable 'atom_props' [-Wunused-variable] const char* atom_props = args.atom_props.c_str(); ^~~~~~~~~~ layer3/Executive.cpp:3924:8: warning: unused variable 'mimic' [-Wunused-variable] auto mimic = args.mimic; ^~~~~ c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD ov/src/OVOneToOne.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVOneToOne.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer3/Seeker.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer3/Seeker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD ov/src/ov_utility.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/ov_utility.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD ov/src/OVRandom.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVRandom.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer1/ScenePicking.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer1/ScenePicking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer3/MoleculeExporter.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer3/MoleculeExporter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer5/PyMOL.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer5/PyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer2/RepAngle.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepAngle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD ov/src/OVContext.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVContext.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer5/main.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer5/main.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer2/CoordSet.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer2/CoordSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer1/Rep.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Rep.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer2/RepCylBond.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepCylBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer3/PlugIOManager.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer3/PlugIOManager.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer1/Shaker.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Shaker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer4/Menu.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer2/ObjectMolecule2.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer3/ExecutivePython.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -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 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.7m -c -MMD layer3/SelectorTmp.cpp -o build/temp.dragonfly-5.9-x86_64-3.7/layer3/SelectorTmp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 c++ -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/build/generated/ShaderText.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/mmtf-c/mmtf_parser.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/hash.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/inthash.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Block.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Crystal.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Deferred.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Err.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Feedback.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Field.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/File.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/GenericBuffer.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/GraphicsUtil.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Isosurf.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Map.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Match.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Matrix.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/MemoryDebug.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/MyPNG.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Parse.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Pixmap.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/PostProcess.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/ShaderMgr.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/ShaderPrg.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Sphere.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Tetsurf.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Texture.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Tracker.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Triangle.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Util.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Util2.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Vector.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/Word.o build/temp.dragonfly-5.9-x86_64-3.7/layer0/os_gl.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Basis.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/ButMode.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/CGO.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/COLLADA.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Character.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Color.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Control.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Extrude.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Font.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/FontGLUT.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/FontGLUT8x13.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/FontGLUT9x15.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/FontGLUTHel10.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/FontGLUTHel12.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/FontGLUTHel18.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/FontType.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Movie.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Ortho.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/P.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/PConv.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Picking.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Pop.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/PyMOLObject.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Ray.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Rep.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Scene.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/ScenePicking.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/SceneRay.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/SceneRender.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/ScrollBar.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Seq.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Setting.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Shaker.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Symmetry.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Text.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/TypeFace.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/View.o build/temp.dragonfly-5.9-x86_64-3.7/layer1/Wizard.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/AssemblyHelpers.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/AtomInfo.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/AtomInfoHistory.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/BondTypeHistory.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/CifFile.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/CifMoleculeReader.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/CoordSet.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/DistSet.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/GadgetSet.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/HydrogenAdder.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/MmodTyping.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/MmtfMoleculeReader.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/Mol2Typing.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/MolV3000.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectAlignment.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectCGO.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectCallback.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectDist.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectGadget.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectGadgetRamp.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectGroup.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectMap.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectMesh.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectMolecule.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectMolecule2.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectSlice.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectSurface.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/ObjectVolume.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepAngle.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepCartoon.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepCylBond.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepDihedral.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepDistDash.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepDistLabel.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepDot.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepEllipsoid.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepLabel.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepMesh.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepNonbonded.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepNonbondedSphere.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepRibbon.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepSphere.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepSphereGenerate.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepSphereImmediate.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepSurface.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/RepWireBond.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/Sculpt.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/SculptCache.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/SideChainHelper.o build/temp.dragonfly-5.9-x86_64-3.7/layer2/VFont.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/AtomIterators.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/CifDataValueFormatter.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/Editor.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/Executive.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/ExecutivePython.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/MaeExportHelpers.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/MoleculeExporter.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/MovieScene.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/PlugIOManager.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/RingFinder.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/Seeker.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/Selector.o build/temp.dragonfly-5.9-x86_64-3.7/layer3/SelectorTmp.o build/temp.dragonfly-5.9-x86_64-3.7/layer4/Cmd.o build/temp.dragonfly-5.9-x86_64-3.7/layer4/Menu.o build/temp.dragonfly-5.9-x86_64-3.7/layer4/PopUp.o build/temp.dragonfly-5.9-x86_64-3.7/layer5/PyMOL.o build/temp.dragonfly-5.9-x86_64-3.7/layer5/TestPyMOL.o build/temp.dragonfly-5.9-x86_64-3.7/layer5/main.o build/temp.dragonfly-5.9-x86_64-3.7/modules/cealign/src/ccealignmodule.o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVContext.o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVHeap.o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVHeapArray.o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVLexicon.o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVOneToAny.o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVOneToOne.o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/OVRandom.o build/temp.dragonfly-5.9-x86_64-3.7/ov/src/ov_utility.o -L/usr/local/lib -L/usr/local/lib -lpng -lfreetype -lxml2 -lGL -lGLEW -lnetcdf -lexecinfo -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pymol/_cmd.so building 'chempy.champ._champ' extension creating build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/champ.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/champ.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/feedback2.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/feedback2.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/champ_module.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/champ_module.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/chiral.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/chiral.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/err2.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/err2.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/vla.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/vla.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/os_memory.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/os_memory.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/strblock.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/strblock.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/sort.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/sort.o 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 -Icontrib/champ -I/usr/local/include/python3.7m -c -MMD contrib/champ/list.c -o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/list.o contrib/champ/os_memory.c: In function 'OSMemoryZero': contrib/champ/os_memory.c:55:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] while(count&&(((int)p)&mask)) { ^ contrib/champ/os_memory.c: In function 'OSMemoryHashAdd': contrib/champ/os_memory.c:137:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] hash=(int)rec; ^ contrib/champ/os_memory.c: In function 'OSMemoryHashRemove': contrib/champ/os_memory.c:150:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] hash=(int)rec; ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/champ.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/champ_module.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/chiral.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/err2.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/feedback2.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/list.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/os_memory.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/sort.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/strblock.o build/temp.dragonfly-5.9-x86_64-3.7/contrib/champ/vla.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ/_champ.so SUCCEEDED 00:00:56 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py37-pymol-2.4.0 depends on package: py37-msgpack>0 - found ===> py37-pymol-2.4.0 depends on package: py37-Pmw>0 - found ===> py37-pymol-2.4.0 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> py37-pymol-2.4.0 depends on package: py37-setuptools>0 - found ===> py37-pymol-2.4.0 depends on file: /usr/local/bin/python3.7 - found ===> py37-pymol-2.4.0 depends on package: py37-qt5-core>=5.15.0 - found ===> py37-pymol-2.4.0 depends on package: py37-qt5-gui>=5.15.0 - found ===> py37-pymol-2.4.0 depends on package: py37-qt5-opengl>=5.15.0 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py37-pymol-2.4.0 ===> py37-pymol-2.4.0 depends on package: py37-msgpack>0 - found ===> py37-pymol-2.4.0 depends on package: py37-Pmw>0 - found ===> py37-pymol-2.4.0 depends on package: py37-numpy>=1.16,1<1.20,1 - found ===> py37-pymol-2.4.0 depends on package: py37-setuptools>0 - found ===> py37-pymol-2.4.0 depends on file: /usr/local/bin/python3.7 - found ===> py37-pymol-2.4.0 depends on package: py37-qt5-core>=5.15.0 - found ===> py37-pymol-2.4.0 depends on package: py37-qt5-gui>=5.15.0 - found ===> py37-pymol-2.4.0 depends on package: py37-qt5-opengl>=5.15.0 - 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/python3.7 creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/cmd.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/viewing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/invocation.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/morphing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/shortcut.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/xwin.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/preset.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/povray.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/colorramping.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/menu.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/checking.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/_gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/stereochemistry copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/stereochemistry/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/stereochemistry copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/setting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/computing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/editor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/colorprinting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins/legacysupport.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins/managergui_qt.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins/installation.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins/repository.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins/managergui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/plugins/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/constants.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/constants_palette.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/gl copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/gl/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/gl copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/glu copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/glu/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/glu creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/glut copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/opengl/glut/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/glut copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/lazyio.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/importing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/cleanup.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/mutagenesis.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/box.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/fedora.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/message.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/label.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/annotation.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/pair_fit.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/appearance.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/pseudoatom.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/measurement.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/filter.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/openvr.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/distance.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/stereodemo.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/demo.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/dragging.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/sculpting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/security.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/toggle.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/command.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/renaming.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/benchmark.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/density.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/charge.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizard/nucmutagenesis.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/exporting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/headering.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/xray.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/completing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/querying.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/keyboard.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/api.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/editing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/movie.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/fitting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/keywords.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/__main__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/controlling.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/externing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/diagnosing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/rpc.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/creating.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/helping.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/wizarding.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/cgo.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/feedingback.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/selecting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/monitoring.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/moving.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/parsing.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/parser.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/contrib copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/contrib/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/contrib copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/commanding.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/seqalign.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/selector.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/locking.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/internal.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/experimenting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/callback.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/pymolhttpd.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/util.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/vfont.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/_cmd.so -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/Qt copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/Qt/utils.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/Qt copying build/lib.dragonfly-5.9-x86_64-3.7/pymol/Qt/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/Qt creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/mimic_tk.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/mimic_pmg_tk.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/pymol_gl_widget.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/file_dialogs.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/advanced_settings_gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/pymol_qt_gui.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/volume.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax/pml.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax/pmlparser.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax/python.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/syntax/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/TextEditor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/load_map.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/colors.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/save_object.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/save_molecule.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/png.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/pluginmanager.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/fetch.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/load_mtz.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/load_mae.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/load_aln.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/movieexport.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/props.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/load_traj.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/pluginitem.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/askpartial.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/forms/render.ui -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/keymapping.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/builder.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_qt/properties_dialog.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/protein_amber99.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/lst.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin/realtime.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin/state.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin/commands.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/bmin/util.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/cc1.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/pkl.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/xyz.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/fragments copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/fragments/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/fragments copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/dictdb.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/bonds.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/mol2.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker/realtime.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker/keyword.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker/state.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/tinker/amber.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/fast copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/fast/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/fast copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/mae.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/gms.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/mmd.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/models.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/map.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/mol.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/pdb.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/water_amber.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/place.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mmtf copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/mmtf/io.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mmtf copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/mmtf/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mmtf copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/gamess1.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/mass.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/io.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/protein.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/cif.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/protein_residues.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/bond_amber.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/cpv.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/protein_mmff.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/charge.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/water_residues.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/arc.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/solvate.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ/_champ.so -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ/formal_charges.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ/assign.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/champ/amber99.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/hetatm.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/bond_mmff.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/neighbor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/protein_amber.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/sdf.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy copying build/lib.dragonfly-5.9-x86_64-3.7/chempy/brick.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol2 copying build/lib.dragonfly-5.9-x86_64-3.7/pymol2/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol2 copying build/lib.dragonfly-5.9-x86_64-3.7/pymol2/cmd2.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol2 creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/PyMOLMapLoad.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/normal copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/normal/builder.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/normal copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/normal/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/normal copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/normal/ModalWindow.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/normal creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/demo copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/skins/demo/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/demo copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/Setting.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/Demo.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/ColorEditor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/SetEditor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/TextEditor.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/startup copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/startup/__init__.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/startup copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/startup/apbs_tools.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/startup copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/volume.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk copying build/lib.dragonfly-5.9-x86_64-3.7/pmg_tk/PMGApp.py -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/cmd.py to cmd.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/viewing.py to viewing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/invocation.py to invocation.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/morphing.py to morphing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/shortcut.py to shortcut.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/xwin.py to xwin.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/preset.py to preset.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/povray.py to povray.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/colorramping.py to colorramping.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/menu.py to menu.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/checking.py to checking.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/_gui.py to _gui.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/stereochemistry/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/setting.py to setting.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/computing.py to computing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/editor.py to editor.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/colorprinting.py to colorprinting.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins/legacysupport.py to legacysupport.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins/managergui_qt.py to managergui_qt.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins/installation.py to installation.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins/repository.py to repository.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins/managergui.py to managergui.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/plugins/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/gui.py to gui.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/constants.py to constants.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/constants_palette.py to constants_palette.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/gl/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/glu/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/opengl/glut/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/lazyio.py to lazyio.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/importing.py to importing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/cleanup.py to cleanup.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/mutagenesis.py to mutagenesis.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/box.py to box.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/fedora.py to fedora.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/message.py to message.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/label.py to label.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/annotation.py to annotation.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/pair_fit.py to pair_fit.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/appearance.py to appearance.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/pseudoatom.py to pseudoatom.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/measurement.py to measurement.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/filter.py to filter.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/openvr.py to openvr.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/distance.py to distance.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/stereodemo.py to stereodemo.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/demo.py to demo.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/dragging.py to dragging.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/sculpting.py to sculpting.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/security.py to security.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/toggle.py to toggle.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/command.py to command.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/renaming.py to renaming.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/benchmark.py to benchmark.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/density.py to density.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/charge.py to charge.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizard/nucmutagenesis.py to nucmutagenesis.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/exporting.py to exporting.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/headering.py to headering.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/xray.py to xray.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/completing.py to completing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/querying.py to querying.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/keyboard.py to keyboard.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/api.py to api.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/editing.py to editing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/movie.py to movie.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/fitting.py to fitting.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/keywords.py to keywords.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/__main__.py to __main__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/controlling.py to controlling.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/externing.py to externing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/diagnosing.py to diagnosing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/rpc.py to rpc.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/creating.py to creating.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/helping.py to helping.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/wizarding.py to wizarding.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/cgo.py to cgo.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/feedingback.py to feedingback.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/selecting.py to selecting.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/monitoring.py to monitoring.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/moving.py to moving.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/parsing.py to parsing.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/parser.py to parser.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/contrib/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/commanding.py to commanding.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/seqalign.py to seqalign.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/selector.py to selector.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/locking.py to locking.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/internal.py to internal.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/experimenting.py to experimenting.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/callback.py to callback.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/pymolhttpd.py to pymolhttpd.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/util.py to util.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/vfont.py to vfont.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/Qt/utils.py to utils.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/Qt/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/mimic_tk.py to mimic_tk.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/mimic_pmg_tk.py to mimic_pmg_tk.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/pymol_gl_widget.py to pymol_gl_widget.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/file_dialogs.py to file_dialogs.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/advanced_settings_gui.py to advanced_settings_gui.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/pymol_qt_gui.py to pymol_qt_gui.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/volume.py to volume.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax/pml.py to pml.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax/pmlparser.py to pmlparser.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax/python.py to python.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/syntax/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/TextEditor.py to TextEditor.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/forms/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/keymapping.py to keymapping.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/builder.py to builder.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_qt/properties_dialog.py to properties_dialog.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/protein_amber99.py to protein_amber99.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/lst.py to lst.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin/realtime.py to realtime.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin/state.py to state.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin/commands.py to commands.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bmin/util.py to util.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/cc1.py to cc1.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/pkl.py to pkl.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/xyz.py to xyz.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/fragments/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/dictdb.py to dictdb.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bonds.py to bonds.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mol2.py to mol2.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker/realtime.py to realtime.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker/keyword.py to keyword.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker/state.py to state.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/tinker/amber.py to amber.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/fast/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mae.py to mae.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/gms.py to gms.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mmd.py to mmd.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/models.py to models.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/map.py to map.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mol.py to mol.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/pdb.py to pdb.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/water_amber.py to water_amber.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/place.py to place.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mmtf/io.py to io.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mmtf/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/gamess1.py to gamess1.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/mass.py to mass.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/io.py to io.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/protein.py to protein.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/cif.py to cif.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/protein_residues.py to protein_residues.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bond_amber.py to bond_amber.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/cpv.py to cpv.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/protein_mmff.py to protein_mmff.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/charge.py to charge.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/water_residues.py to water_residues.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/arc.py to arc.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/solvate.py to solvate.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ/formal_charges.py to formal_charges.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ/assign.py to assign.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/champ/amber99.py to amber99.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/hetatm.py to hetatm.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/bond_mmff.py to bond_mmff.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/neighbor.py to neighbor.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/protein_amber.py to protein_amber.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/sdf.py to sdf.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/chempy/brick.py to brick.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol2/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol2/cmd2.py to cmd2.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/PyMOLMapLoad.py to PyMOLMapLoad.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/normal/builder.py to builder.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/normal/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/normal/ModalWindow.py to ModalWindow.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/skins/demo/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/Setting.py to Setting.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/Demo.py to Demo.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/ColorEditor.py to ColorEditor.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/SetEditor.py to SetEditor.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/TextEditor.py to TextEditor.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/startup/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/startup/apbs_tools.py to apbs_tools.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/volume.py to volume.cpython-37.pyc byte-compiling /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pmg_tk/PMGApp.py to PMGApp.cpython-37.pyc writing byte-compilation script '/tmp/tmp6vllmtsg.py' /usr/local/bin/python3.7 /tmp/tmp6vllmtsg.py removing /tmp/tmp6vllmtsg.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' reading manifest file 'pymol.egg-info/SOURCES.txt' writing manifest file 'pymol.egg-info/SOURCES.txt' Copying pymol.egg-info to /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol-2.4.0-py3.7.egg-info writing list of installed files to '/construction/science/py-pymol/.PLIST.pymodtmp' creating /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/pymol_path copying LICENSE -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/pymol_path copying data -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/pymol_path/data copying test -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol/pymol_path/test copying examples -> /construction/science/py-pymol/stage/usr/local/lib/python3.7/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-3.7 Link: @bin/pymol --> bin/pymol-3.7 ====> Compressing man pages (compress-man) if [ -d "/construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol-2.4.0-py3.7.egg-info" ]; then /bin/ls /construction/science/py-pymol/stage/usr/local/lib/python3.7/site-packages/pymol-2.4.0-py3.7.egg-info | while read f; do echo lib/python3.7/site-packages/pymol-2.4.0-py3.7.egg-info/${f} >> /construction/science/py-pymol/.PLIST.mktmp; done; fi; ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.7/site-packages/chempy/champ/_champ.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libdrm.so.2 from graphics/libdrm but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libdrm.so:graphics/libdrm Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.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/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libxcb-glx.so.0 from x11/libxcb but it is not declared as a dependency Warning: you need USE_XORG+=xcb Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.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/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libX11-xcb.so.1 from x11/libX11 but it is not declared as a dependency Warning: you need USE_XORG+=x11 Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libxcb-dri2.so.0 from x11/libxcb but it is not declared as a dependency Warning: you need USE_XORG+=xcb Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libXext.so.6 from x11/libXext but it is not declared as a dependency Warning: you need USE_XORG+=xext Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libXfixes.so.3 from x11/libXfixes but it is not declared as a dependency Warning: you need USE_XORG+=xfixes Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libXdamage.so.1 from x11/libXdamage but it is not declared as a dependency Warning: you need USE_XORG+=xdamage Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libXxf86vm.so.1 from x11/libXxf86vm but it is not declared as a dependency Warning: you need USE_XORG+=xxf86vm Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libexpat.so.1 from textproc/expat2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libexpat.so:textproc/expat2 Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libhdf5_hl.so.100 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/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libhdf5.so.103 from science/hdf5 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libhdf5.so:science/hdf5 Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.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/python3.7/site-packages/pymol/_cmd.so is linked to /usr/local/lib/libsz.so.2 from science/szip but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libsz.so:science/szip Error: /usr/local/lib/python3.7/site-packages/pymol/_cmd.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/python3.7/site-packages/pymol/_cmd.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/python3.7/site-packages/pymol/_cmd.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/python3.7/site-packages/pymol/_cmd.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/python3.7/site-packages/pymol/_cmd.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 Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py37-pymol-2.4.0 file sizes/checksums [1087]: 0% file sizes/checksums [1087]: 9% file sizes/checksums [1087]: 18% file sizes/checksums [1087]: 27% file sizes/checksums [1087]: 36% file sizes/checksums [1087]: 45% file sizes/checksums [1087]: 55% file sizes/checksums [1087]: 64% file sizes/checksums [1087]: 73% file sizes/checksums [1087]: 82% file sizes/checksums [1087]: 91% file sizes/checksums [1087]: 100% packing files [1087]: 0% packing files [1087]: 9% packing files [1087]: 18% packing files [1087]: 27% packing files [1087]: 36% packing files [1087]: 45% packing files [1087]: 55% packing files [1087]: 64% packing files [1087]: 73% packing files [1087]: 82% packing files [1087]: 91% packing files [1087]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:28 TOTAL TIME 00:03:05