=>> Building science/py-pymol build started at Sat Jun 6 15:02:23 JST 2026 port directory: /usr/ports/science/py-pymol package name: py311-pymol-3.0.0_3 building for: FreeBSD curamd64-setuptools-job-01 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2114 May 2 10:23 /usr/ports/science/py-pymol/Makefile Ports top last git commit: a8b187544 Ports top unclean checkout: yes Port dir last git commit: a8b187544 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1600018 Jail OSVERSION: 1600018 Job Id: 01 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600018 UNAME_v=FreeBSD 16.0-CURRENT 1600018 UNAME_r=16.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.4 MASTERMNT=/usr/local/poudriere/data/.m/curamd64-setuptools/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/curamd64-setuptools/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=curamd64-setuptools SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/curamd64-setuptools/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for py311-pymol-3.0.0_3: ====> GUI (Graphical User Interface) support: you have to select exactly one of them QT5=on: Qt 5 toolkit support TK=off: Tk GUI toolkit support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-pymol/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pymol/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-pymol/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-pymol/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pymol/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-pymol/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DMSGPACK_NO_BOOST " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd16 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PYQT_APIDIR=share/PyQt5/3.11/qsci PYQT_DOCDIR=share/doc/PyQt5/3.11 PYQT_EXAMPLEDIR=share/examples/PyQt5/3.11 PYQT_SIPDIR=/usr/local/lib/python3.11/site-packages/PyQt5/bindings PYQT_DESIGNERDIR=/designer/PyQt5/3.11 PYQT_QMLDIR=/PyQt5/3.11 PYQT_SIPVERSION=6.15.1 PYQT_QSCIVERSION=2.14.1 PYQT_PYQTVERSION=5.15.11 OSREL=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py311-pymol" EXAMPLESDIR="share/examples/py311-pymol" DATADIR="share/py311-pymol" WWWDIR="www/py311-pymol" ETCDIR="etc/py311-pymol" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd16 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py311-pymol DOCSDIR=/usr/local/share/doc/py311-pymol EXAMPLESDIR=/usr/local/share/examples/py311-pymol WWWDIR=/usr/local/www/py311-pymol ETCDIR=/usr/local/etc/py311-pymol --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+= magick=7-x11 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5_mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= GAMMA INPUTMETHOD LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+= magick=7-x11 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5_mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= GAMMA INPUTMETHOD LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 12099 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License PyMOL accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pymol-3.0.0_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [curamd64-setuptools-job-01] Installing pkg-2.7.5... [curamd64-setuptools-job-01] Extracting pkg-2.7.5: .......... done ===> py311-pymol-3.0.0_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-pymol-3.0.0_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License PyMOL accepted by the user => schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://codeload.github.com/schrodinger/pymol-open-source/tar.gz/v3.0.0?dummy=/schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz fetch: https://codeload.github.com/schrodinger/pymol-open-source/tar.gz/v3.0.0?dummy=/schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz: size unknown fetch: https://codeload.github.com/schrodinger/pymol-open-source/tar.gz/v3.0.0?dummy=/schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz: size of remote file is not known schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz 28 MB 9 MBps 02s ===> Fetching all distfiles required by py311-pymol-3.0.0_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License PyMOL accepted by the user ===> Fetching all distfiles required by py311-pymol-3.0.0_3 for building => SHA256 Checksum OK for schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License PyMOL accepted by the user ===> Fetching all distfiles required by py311-pymol-3.0.0_3 for building ===> Extracting for py311-pymol-3.0.0_3 => SHA256 Checksum OK for schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for py311-pymol-3.0.0_3 ===> Applying FreeBSD patches for py311-pymol-3.0.0_3 from /usr/ports/science/py-pymol/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pymol-3.0.0_3 depends on package: py311-numpy1>=1.16 - not found ===> Installing existing package /packages/All/py311-numpy1-1.26.4_3.pkg [curamd64-setuptools-job-01] Installing py311-numpy1-1.26.4_3... [curamd64-setuptools-job-01] `-- Installing gcc14-14.2.0_4... [curamd64-setuptools-job-01] | `-- Installing binutils-2.44,1... [curamd64-setuptools-job-01] | | `-- Installing indexinfo-0.3.1_1... [curamd64-setuptools-job-01] | | `-- Extracting indexinfo-0.3.1_1: .... done [curamd64-setuptools-job-01] | | `-- Installing zstd-1.5.7_1... [curamd64-setuptools-job-01] | | `-- Extracting zstd-1.5.7_1: .......... done [curamd64-setuptools-job-01] | `-- Extracting binutils-2.44,1: .......... done [curamd64-setuptools-job-01] | `-- Installing gmp-6.3.0... [curamd64-setuptools-job-01] | `-- Extracting gmp-6.3.0: .......... done [curamd64-setuptools-job-01] | `-- Installing mpc-1.4.1... [curamd64-setuptools-job-01] | | `-- Installing mpfr-4.2.2,1... [curamd64-setuptools-job-01] | | `-- Extracting mpfr-4.2.2,1: .......... done [curamd64-setuptools-job-01] | `-- Extracting mpc-1.4.1: .......... done [curamd64-setuptools-job-01] `-- Extracting gcc14-14.2.0_4: .......... done [curamd64-setuptools-job-01] `-- Installing openblas-0.3.30,2... [curamd64-setuptools-job-01] `-- Extracting openblas-0.3.30,2: .......... done [curamd64-setuptools-job-01] `-- Installing python311-3.11.15_2... [curamd64-setuptools-job-01] | `-- Installing gettext-runtime-1.0... [curamd64-setuptools-job-01] | `-- Extracting gettext-runtime-1.0: .......... done [curamd64-setuptools-job-01] | `-- Installing libffi-3.5.1... [curamd64-setuptools-job-01] | `-- Extracting libffi-3.5.1: .......... done [curamd64-setuptools-job-01] | `-- Installing mpdecimal-4.0.1... [curamd64-setuptools-job-01] | `-- Extracting mpdecimal-4.0.1: .......... done [curamd64-setuptools-job-01] | `-- Installing openssl-3.0.20,1... [curamd64-setuptools-job-01] | `-- Extracting openssl-3.0.20,1: .......... done [curamd64-setuptools-job-01] | `-- Installing readline-8.3.3... [curamd64-setuptools-job-01] | `-- Extracting readline-8.3.3: .......... done [curamd64-setuptools-job-01] `-- Extracting python311-3.11.15_2: .......... done [curamd64-setuptools-job-01] Extracting py311-numpy1-1.26.4_3: .......... done ===== Message from gcc14-14.2.0_4: -- 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/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python311-3.11.15_2: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> py311-pymol-3.0.0_3 depends on package: py311-numpy1>=1.16 - found ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on file: /usr/local/include/glm/glm.hpp - not found ===> Installing existing package /packages/All/glm-1.0.3,1.pkg [curamd64-setuptools-job-01] Installing glm-1.0.3,1... [curamd64-setuptools-job-01] Extracting glm-1.0.3,1: .......... done ===> py311-pymol-3.0.0_3 depends on file: /usr/local/include/glm/glm.hpp - found ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on file: /usr/local/include/mmtf.hpp - not found ===> Installing existing package /packages/All/mmtf-cpp-1.1.0_1.pkg [curamd64-setuptools-job-01] Installing mmtf-cpp-1.1.0_1... [curamd64-setuptools-job-01] `-- Installing msgpack-cxx-6.1.1... [curamd64-setuptools-job-01] `-- Extracting msgpack-cxx-6.1.1: .......... done [curamd64-setuptools-job-01] Extracting mmtf-cpp-1.1.0_1: .......... done ===> py311-pymol-3.0.0_3 depends on file: /usr/local/include/mmtf.hpp - found ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-81.0.0.pkg [curamd64-setuptools-job-01] Installing py311-setuptools-81.0.0... [curamd64-setuptools-job-01] `-- Installing py311-more-itertools-10.6.0... [curamd64-setuptools-job-01] `-- Extracting py311-more-itertools-10.6.0: .......... done [curamd64-setuptools-job-01] `-- Installing py311-packaging-26.2... [curamd64-setuptools-job-01] `-- Extracting py311-packaging-26.2: .......... done [curamd64-setuptools-job-01] `-- Installing py311-wheel-0.47.0... [curamd64-setuptools-job-01] `-- Extracting py311-wheel-0.47.0: .......... done [curamd64-setuptools-job-01] Extracting py311-setuptools-81.0.0: .......... done ===> py311-pymol-3.0.0_3 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on file: /usr/local/bin/python3.11 - found ===> py311-pymol-3.0.0_3 depends on package: xorgproto>=0 - not found ===> Installing existing package /packages/All/xorgproto-2024.1.pkg [curamd64-setuptools-job-01] Installing xorgproto-2024.1... [curamd64-setuptools-job-01] Extracting xorgproto-2024.1: .......... done ===> py311-pymol-3.0.0_3 depends on package: xorgproto>=0 - found ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on package: xorgproto>=0 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pymol-3.0.0_3 depends on shared library: libfreetype.so - not found ===> Installing existing package /packages/All/freetype2-2.14.3.pkg [curamd64-setuptools-job-01] Installing freetype2-2.14.3... [curamd64-setuptools-job-01] `-- Installing brotli-1.2.0,1... [curamd64-setuptools-job-01] `-- Extracting brotli-1.2.0,1: .......... done [curamd64-setuptools-job-01] `-- Installing png-1.6.58... [curamd64-setuptools-job-01] `-- Extracting png-1.6.58: .......... done [curamd64-setuptools-job-01] Extracting freetype2-2.14.3: .......... done ===== Message from freetype2-2.14.3: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===> py311-pymol-3.0.0_3 depends on shared library: libfreetype.so - found (/usr/local/lib/libfreetype.so) ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on shared library: libnetcdf.so - not found ===> Installing existing package /packages/All/netcdf-4.10.0.pkg [curamd64-setuptools-job-01] Installing netcdf-4.10.0... [curamd64-setuptools-job-01] `-- Installing curl-8.19.0_2... [curamd64-setuptools-job-01] | `-- Installing libidn2-2.3.8... [curamd64-setuptools-job-01] | | `-- Installing libunistring-1.4.2... [curamd64-setuptools-job-01] | | `-- Extracting libunistring-1.4.2: .......... done [curamd64-setuptools-job-01] | `-- Extracting libidn2-2.3.8: .......... done [curamd64-setuptools-job-01] | `-- Installing libnghttp2-1.69.0... [curamd64-setuptools-job-01] | `-- Extracting libnghttp2-1.69.0: .......... done [curamd64-setuptools-job-01] | `-- Installing libpsl-0.21.5_2... [curamd64-setuptools-job-01] | `-- Extracting libpsl-0.21.5_2: .......... done [curamd64-setuptools-job-01] | `-- Installing libssh2-1.11.1,3... [curamd64-setuptools-job-01] | `-- Extracting libssh2-1.11.1,3: .......... done [curamd64-setuptools-job-01] `-- Extracting curl-8.19.0_2: .......... done [curamd64-setuptools-job-01] `-- Installing hdf5-1.12.2_2,1... [curamd64-setuptools-job-01] | `-- Installing libaec-1.1.6... [curamd64-setuptools-job-01] | `-- Extracting libaec-1.1.6: .......... done [curamd64-setuptools-job-01] `-- Extracting hdf5-1.12.2_2,1: .......... done [curamd64-setuptools-job-01] `-- Installing pkgconf-2.4.3,1... [curamd64-setuptools-job-01] `-- Extracting pkgconf-2.4.3,1: .......... done [curamd64-setuptools-job-01] Extracting netcdf-4.10.0: .......... done ===> py311-pymol-3.0.0_3 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so) ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on shared library: libpng16.so - found (/usr/local/lib/libpng16.so) ===> py311-pymol-3.0.0_3 depends on shared library: libGL.so - not found ===> Installing existing package /packages/All/libglvnd-1.7.0.pkg [curamd64-setuptools-job-01] Installing libglvnd-1.7.0... [curamd64-setuptools-job-01] `-- Installing libX11-1.8.13_1,1... [curamd64-setuptools-job-01] | `-- Installing libxcb-1.17.0... [curamd64-setuptools-job-01] | | `-- Installing libXau-1.0.12... [curamd64-setuptools-job-01] | | `-- Extracting libXau-1.0.12: .......... done [curamd64-setuptools-job-01] | | `-- Installing libXdmcp-1.1.5... [curamd64-setuptools-job-01] | | `-- Extracting libXdmcp-1.1.5: ......... done [curamd64-setuptools-job-01] | `-- Extracting libxcb-1.17.0: .......... done [curamd64-setuptools-job-01] `-- Extracting libX11-1.8.13_1,1: .......... done [curamd64-setuptools-job-01] `-- Installing libXext-1.3.6,1... [curamd64-setuptools-job-01] `-- Extracting libXext-1.3.6,1: .......... done [curamd64-setuptools-job-01] Extracting libglvnd-1.7.0: .......... done ===> py311-pymol-3.0.0_3 depends on shared library: libGL.so - found (/usr/local/lib/libGL.so) ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on shared library: libGLEW.so - not found ===> Installing existing package /packages/All/glew-2.2.0_3.pkg [curamd64-setuptools-job-01] Installing glew-2.2.0_3... [curamd64-setuptools-job-01] `-- Installing libGLU-9.0.3... [curamd64-setuptools-job-01] `-- Extracting libGLU-9.0.3: ..... done [curamd64-setuptools-job-01] Extracting glew-2.2.0_3: .......... done ===> py311-pymol-3.0.0_3 depends on shared library: libGLEW.so - found (/usr/local/lib/libGLEW.so) ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on shared library: libGLU.so - found (/usr/local/lib/libGLU.so) ===> py311-pymol-3.0.0_3 depends on shared library: libxml2.so - not found ===> Installing existing package /packages/All/libxml2-2.15.3.pkg [curamd64-setuptools-job-01] Installing libxml2-2.15.3... [curamd64-setuptools-job-01] Extracting libxml2-2.15.3: .......... done ===> py311-pymol-3.0.0_3 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> Returning to build of py311-pymol-3.0.0_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for py311-pymol-3.0.0_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py311-pymol-3.0.0_3 In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:459:7: warning: unused variable 'i' [-Wunused-variable] 459 | int i,j,k; | ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1407:7: warning: unused variable 'i' [-Wunused-variable] 1407 | int i,j,k; | ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1541:7: warning: unused variable 'i' [-Wunused-variable] 1541 | int i,j,k; | ^ 3 warnings generated. contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:443:7: warning: unused variable 'i' [-Wunused-variable] 443 | int i, uid; | ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:484:47: warning: unused variable 'j' [-Wunused-variable] 484 | int i, count, atomdata, pos, idx, xyzcount, j; | ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable 'oldChain' [-Wunused-variable] 503 | char oldChain[8]; | ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable 'bondTable' [-Wunused-variable] 803 | int bondTable[32]; | ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable 'j' [-Wunused-variable] 807 | int i, pos, j, k; | ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable 'modelNum' [-Wunused-variable] 811 | char modelNum[8]; | ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable 'atom' [-Wunused-variable] 822 | molfile_atom_t * atom; | ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable 'test' [-Wunused-variable] 884 | int test = parser->nbonds + bnum; | ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable 'bondTable' [-Wunused-variable] 984 | int bondTable[32]; | ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable 'j' [-Wunused-variable] 988 | int i, pos, j, k; | ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable 'modelNum' [-Wunused-variable] 991 | char modelNum[8]; | ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable 'atom' [-Wunused-variable] 1002 | molfile_atom_t * atom; | ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable 'fd' [-Wunused-variable] 1409 | FILE* fd; | ^~ 13 warnings generated. contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:392:29: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 392 | if (sscanf(s, " %255s%n", aid_specifier, &n) < 1) { | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:414:32: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 414 | while (sscanf(s, " %255s%n", keyword, &n) == 1) { | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:797:31: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 797 | sscanf(line, " %255s%n", s, &n); | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:819:32: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 819 | sscanf(line, " %255s%n", s, &n); | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:829:32: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 829 | sscanf(line, " %255s%n", s, &n); | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:839:32: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 839 | sscanf(line, " %255s%n", s, &n); | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:1048:34: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 1048 | sscanf(line, " %255s%n", s, &n); | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:1104:34: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 1104 | sscanf(line, " %255s%n", s, &n); | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:1114:34: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 1114 | sscanf(line, " %255s%n", s, &n); | ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:1128:34: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 1128 | sscanf(line, " %255s%n", s, &n); | ^ 10 warnings generated. contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1904:9: warning: unused variable 'last_ctnumber' [-Wunused-variable] 1904 | int last_ctnumber = -1; | ^~~~~~~~~~~~~ 1 warning generated. layer0/Texture.cpp:130:9: warning: unused variable 'use_shader' [-Wunused-variable] 130 | short use_shader = (short) SettingGetGlobal_b(G, cSetting_use_shaders); | ^~~~~~~~~~ 1 warning generated. contrib/champ/os_memory.c:55:18: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] 55 | while(count&&(((int)p)&mask)) { | ^~~~~~ contrib/champ/os_memory.c:137:8: warning: cast to smaller integer type 'int' from 'DebugRec *' (aka 'struct DebugRec *') [-Wpointer-to-int-cast] 137 | hash=(int)rec; | ^~~~~~~~ contrib/champ/os_memory.c:150:8: warning: cast to smaller integer type 'int' from 'DebugRec *' (aka 'struct DebugRec *') [-Wpointer-to-int-cast] 150 | hash=(int)rec; | ^~~~~~~~ 3 warnings generated. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-pymol-3.0.0_3 depends on package: py311-msgpack>0 - not found ===> Installing existing package /packages/All/py311-msgpack-1.1.2.pkg [curamd64-setuptools-job-01] Installing py311-msgpack-1.1.2... [curamd64-setuptools-job-01] Extracting py311-msgpack-1.1.2: .......... done ===> py311-pymol-3.0.0_3 depends on package: py311-msgpack>0 - found ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on package: py311-Pmw>0 - not found ===> Installing existing package /packages/All/py311-Pmw-2.0.1_2.pkg [curamd64-setuptools-job-01] Installing py311-Pmw-2.0.1_2... [curamd64-setuptools-job-01] `-- Installing blt-2.5.3_7... [curamd64-setuptools-job-01] | `-- Installing jpeg-turbo-3.1.4.1... [curamd64-setuptools-job-01] | `-- Extracting jpeg-turbo-3.1.4.1: .......... done [curamd64-setuptools-job-01] | `-- Installing tcl86-8.6.17... [curamd64-setuptools-job-01] | `-- Extracting tcl86-8.6.17: .......... done [curamd64-setuptools-job-01] | `-- Installing tk86-8.6.17... [curamd64-setuptools-job-01] | | `-- Installing fontconfig-2.17.1,1... [curamd64-setuptools-job-01] | | `-- Installing expat-2.8.0... [curamd64-setuptools-job-01] | | `-- Extracting expat-2.8.0: .......... done [curamd64-setuptools-job-01] | | `-- Extracting fontconfig-2.17.1,1: .......... done [curamd64-setuptools-job-01] | | `-- Installing libXScrnSaver-1.2.4_1... [curamd64-setuptools-job-01] | | `-- Extracting libXScrnSaver-1.2.4_1: .......... done [curamd64-setuptools-job-01] | | `-- Installing libXft-2.3.8... [curamd64-setuptools-job-01] | | `-- Installing libXrender-0.9.12... [curamd64-setuptools-job-01] | | `-- Extracting libXrender-0.9.12: .......... done [curamd64-setuptools-job-01] | | `-- Extracting libXft-2.3.8: .......... done [curamd64-setuptools-job-01] | `-- Extracting tk86-8.6.17: .......... done [curamd64-setuptools-job-01] `-- Extracting blt-2.5.3_7: .......... done [curamd64-setuptools-job-01] `-- Installing py311-tkinter-3.11.15_11... [curamd64-setuptools-job-01] `-- Extracting py311-tkinter-3.11.15_11: ......... done [curamd64-setuptools-job-01] Extracting py311-Pmw-2.0.1_2: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===> py311-pymol-3.0.0_3 depends on package: py311-Pmw>0 - found ===> Returning to build of py311-pymol-3.0.0_3 ===> py311-pymol-3.0.0_3 depends on package: py311-numpy1>=1.16 - found ===> py311-pymol-3.0.0_3 depends on file: /usr/local/bin/python3.11 - found ===> py311-pymol-3.0.0_3 depends on package: py311-qt5-pyqt>=5.15.11 - not found ===> Installing existing package /packages/All/py311-qt5-pyqt-5.15.11_2.pkg [curamd64-setuptools-job-01] Installing py311-qt5-pyqt-5.15.11_2... [curamd64-setuptools-job-01] `-- Installing dbus-1.16.2_4,1... [curamd64-setuptools-job-01] | `-- Installing libICE-1.1.2,1... [curamd64-setuptools-job-01] | `-- Extracting libICE-1.1.2,1: .......... done [curamd64-setuptools-job-01] | `-- Installing libSM-1.2.6,1... [curamd64-setuptools-job-01] | `-- Extracting libSM-1.2.6,1: .......... done ===> Creating groups Creating group 'messagebus' with gid '556' ===> Creating users Creating user 'messagebus' with uid '556' [curamd64-setuptools-job-01] `-- Extracting dbus-1.16.2_4,1: ......... done [curamd64-setuptools-job-01] `-- Installing py311-PyQt5-sip-12.18.0... [curamd64-setuptools-job-01] `-- Extracting py311-PyQt5-sip-12.18.0: ......... done [curamd64-setuptools-job-01] `-- Installing py311-dbus-1.4.0... [curamd64-setuptools-job-01] | `-- Installing glib-2.84.4,2... [curamd64-setuptools-job-01] | | `-- Installing libiconv-1.18_1... [curamd64-setuptools-job-01] | | `-- Extracting libiconv-1.18_1: .......... done [curamd64-setuptools-job-01] | | `-- Installing pcre2-10.47_1... 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[curamd64-setuptools-job-01] | | | `-- Installing xcb-util-0.4.1,1... [curamd64-setuptools-job-01] | | | `-- Extracting xcb-util-0.4.1,1: .......... done [curamd64-setuptools-job-01] | | `-- Extracting xcb-util-image-0.4.1: .......... done [curamd64-setuptools-job-01] | | `-- Installing xcb-util-keysyms-0.4.1... [curamd64-setuptools-job-01] | | `-- Extracting xcb-util-keysyms-0.4.1: ......... done [curamd64-setuptools-job-01] | | `-- Installing xcb-util-renderutil-0.3.10... [curamd64-setuptools-job-01] | | `-- Extracting xcb-util-renderutil-0.3.10: ......... done [curamd64-setuptools-job-01] | | `-- Installing xcb-util-wm-0.4.2... [curamd64-setuptools-job-01] | | `-- Extracting xcb-util-wm-0.4.2: .......... done [curamd64-setuptools-job-01] | | `-- Installing xdg-utils-1.2.1... [curamd64-setuptools-job-01] | | | `-- Installing hicolor-icon-theme-0.18... 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[curamd64-setuptools-job-01] | | | | `-- Installing libfontenc-1.1.9... [curamd64-setuptools-job-01] | | | | `-- Extracting libfontenc-1.1.9: ......... done [curamd64-setuptools-job-01] | | | `-- Extracting mkfontscale-1.2.3: ....... done [curamd64-setuptools-job-01] | | | `-- Extracting dejavu-2.37_4: .......... done [curamd64-setuptools-job-01] | | | `-- Installing font-bh-ttf-1.0.3_5... [curamd64-setuptools-job-01] | | | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [curamd64-setuptools-job-01] | | | `-- Installing font-misc-ethiopic-1.0.4... [curamd64-setuptools-job-01] | | | `-- Extracting font-misc-ethiopic-1.0.4: ...... done [curamd64-setuptools-job-01] | | | `-- Installing font-misc-meltho-1.0.3_5... [curamd64-setuptools-job-01] | | | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [curamd64-setuptools-job-01] | | `-- Extracting xorg-fonts-truetype-7.7_1: ... done [curamd64-setuptools-job-01] | | `-- Extracting qt5-gui-5.15.18p109: .......... done [curamd64-setuptools-job-01] | | `-- Installing qt5-sql-5.15.18p109... [curamd64-setuptools-job-01] | | `-- Extracting qt5-sql-5.15.18p109: .......... done [curamd64-setuptools-job-01] | | `-- Installing qt5-widgets-5.15.18p109... [curamd64-setuptools-job-01] | | `-- Extracting qt5-widgets-5.15.18p109: .......... done [curamd64-setuptools-job-01] | `-- Extracting qt5-declarative-5.15.18p22: .......... done [curamd64-setuptools-job-01] `-- Extracting qt5-connectivity-5.15.18p1: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-designer-5.15.18p3... [curamd64-setuptools-job-01] | `-- Installing qt5-assistant-5.15.18p3... [curamd64-setuptools-job-01] | | `-- Installing qt5-help-5.15.18p3... [curamd64-setuptools-job-01] | | `-- Installing qt5-sqldrivers-sqlite3-5.15.18p109... [curamd64-setuptools-job-01] | | | `-- Installing sqlite3-3.50.4_2,1... [curamd64-setuptools-job-01] | | | `-- Installing libedit-3.1.20251016_1,1... [curamd64-setuptools-job-01] | | | `-- Extracting libedit-3.1.20251016_1,1: .......... done [curamd64-setuptools-job-01] | | | `-- Extracting sqlite3-3.50.4_2,1: .......... done [curamd64-setuptools-job-01] | | `-- Extracting qt5-sqldrivers-sqlite3-5.15.18p109: ..... done [curamd64-setuptools-job-01] | | `-- Extracting qt5-help-5.15.18p3: .......... done [curamd64-setuptools-job-01] | | `-- Installing qt5-printsupport-5.15.18p109... [curamd64-setuptools-job-01] | | `-- Installing cups-2.4.19... [curamd64-setuptools-job-01] | | | `-- Installing avahi-app-0.8_6... [curamd64-setuptools-job-01] | | | `-- Installing dbus-glib-0.114... [curamd64-setuptools-job-01] | | | `-- Extracting dbus-glib-0.114: .......... done [curamd64-setuptools-job-01] | | | `-- Installing gdbm-1.26... [curamd64-setuptools-job-01] | | | `-- Extracting gdbm-1.26: .......... done [curamd64-setuptools-job-01] | | | `-- Installing gnome_subr-1.0... [curamd64-setuptools-job-01] | | | `-- Extracting gnome_subr-1.0: .... done [curamd64-setuptools-job-01] | | | `-- Installing libdaemon-0.14_1... [curamd64-setuptools-job-01] | | | `-- Extracting libdaemon-0.14_1: .......... done [curamd64-setuptools-job-01] | | | `-- Installing libevent-2.1.12... [curamd64-setuptools-job-01] | | | `-- Extracting libevent-2.1.12: .......... done ===> Creating groups Creating group 'avahi' with gid '558' ===> Creating users Creating user 'avahi' with uid '558' [curamd64-setuptools-job-01] | | | `-- Extracting avahi-app-0.8_6: .......... done [curamd64-setuptools-job-01] | | | `-- Installing gnutls-3.8.13... [curamd64-setuptools-job-01] | | | `-- Installing libtasn1-4.21.0... [curamd64-setuptools-job-01] | | | `-- Extracting libtasn1-4.21.0: .......... done [curamd64-setuptools-job-01] | | | `-- Installing nettle-3.10.2... [curamd64-setuptools-job-01] | | | `-- Extracting nettle-3.10.2: .......... done [curamd64-setuptools-job-01] | | | `-- Installing p11-kit-0.26.2... [curamd64-setuptools-job-01] | | | `-- Extracting p11-kit-0.26.2: .......... done [curamd64-setuptools-job-01] | | | `-- Extracting gnutls-3.8.13: .......... done [curamd64-setuptools-job-01] | | | `-- Installing libpaper-1.1.28_1... [curamd64-setuptools-job-01] | | | `-- Extracting libpaper-1.1.28_1: .......... done ===> Creating groups Creating group 'cups' with gid '193' ===> Creating users Creating user 'cups' with uid '193' [curamd64-setuptools-job-01] | | `-- Extracting cups-2.4.19: .......... done [curamd64-setuptools-job-01] | | `-- Extracting qt5-printsupport-5.15.18p109: .......... done [curamd64-setuptools-job-01] | `-- Extracting qt5-assistant-5.15.18p3: ...... done [curamd64-setuptools-job-01] | `-- Installing qt5-uiplugin-5.15.18p3... [curamd64-setuptools-job-01] | `-- Extracting qt5-uiplugin-5.15.18p3: .......... done [curamd64-setuptools-job-01] | `-- Installing qt5-xml-5.15.18p109... [curamd64-setuptools-job-01] | `-- Extracting qt5-xml-5.15.18p109: .......... done [curamd64-setuptools-job-01] `-- Extracting qt5-designer-5.15.18p3: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-imageformats-5.15.18p2... [curamd64-setuptools-job-01] | `-- Installing jasper-4.2.9... [curamd64-setuptools-job-01] | `-- Extracting jasper-4.2.9: .......... done [curamd64-setuptools-job-01] | `-- Installing libmng-2.0.3_3... [curamd64-setuptools-job-01] | | `-- Installing lcms2-2.19... [curamd64-setuptools-job-01] | | `-- Installing tiff-4.7.1_1... [curamd64-setuptools-job-01] | | | `-- Installing jbigkit-2.1_3... [curamd64-setuptools-job-01] | | | `-- Extracting jbigkit-2.1_3: .......... done [curamd64-setuptools-job-01] | | | `-- Installing lerc-4.1.0... [curamd64-setuptools-job-01] | | | `-- Extracting lerc-4.1.0: ........ done [curamd64-setuptools-job-01] | | | `-- Installing libdeflate-1.25... [curamd64-setuptools-job-01] | | | `-- Extracting libdeflate-1.25: .......... done [curamd64-setuptools-job-01] | | `-- Extracting tiff-4.7.1_1: .......... done [curamd64-setuptools-job-01] | | `-- Extracting lcms2-2.19: .......... done [curamd64-setuptools-job-01] | `-- Extracting libmng-2.0.3_3: ......... done [curamd64-setuptools-job-01] | `-- Installing webp-1.6.0... [curamd64-setuptools-job-01] | | `-- Installing giflib-5.2.2... [curamd64-setuptools-job-01] | | `-- Extracting giflib-5.2.2: .......... done [curamd64-setuptools-job-01] | `-- Extracting webp-1.6.0: .......... done [curamd64-setuptools-job-01] `-- Extracting qt5-imageformats-5.15.18p2: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-location-5.15.18p7... [curamd64-setuptools-job-01] | `-- Installing qt5-serialport-5.15.18p0... [curamd64-setuptools-job-01] | `-- Extracting qt5-serialport-5.15.18p0: .......... done [curamd64-setuptools-job-01] `-- Extracting qt5-location-5.15.18p7: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-multimedia-5.15.18p2... [curamd64-setuptools-job-01] | `-- Installing alsa-lib-1.2.15.3... [curamd64-setuptools-job-01] | `-- Extracting alsa-lib-1.2.15.3: .......... done [curamd64-setuptools-job-01] | `-- Installing alsa-plugins-1.2.12_2... [curamd64-setuptools-job-01] | `-- Extracting alsa-plugins-1.2.12_2: .......... done [curamd64-setuptools-job-01] | `-- Installing gstreamer1-1.28.1_2... [curamd64-setuptools-job-01] | | `-- Installing libunwind-20250904... [curamd64-setuptools-job-01] | | `-- Extracting libunwind-20250904: .......... done [curamd64-setuptools-job-01] | `-- Extracting gstreamer1-1.28.1_2: .......... done [curamd64-setuptools-job-01] | `-- Installing gstreamer1-plugins-1.28.1... [curamd64-setuptools-job-01] | | `-- Installing iso-codes-4.20.1... [curamd64-setuptools-job-01] | | `-- Extracting iso-codes-4.20.1: .......... done [curamd64-setuptools-job-01] | | `-- Installing libdrm-2.4.131,1... [curamd64-setuptools-job-01] | | `-- Installing libpciaccess-0.19... [curamd64-setuptools-job-01] | | | `-- Installing hwdata-0.406,1... [curamd64-setuptools-job-01] | | | `-- Extracting hwdata-0.406,1: .......... done [curamd64-setuptools-job-01] | | `-- Extracting libpciaccess-0.19: ........ done [curamd64-setuptools-job-01] | | `-- Extracting libdrm-2.4.131,1: .......... done [curamd64-setuptools-job-01] | | `-- Installing orc-0.4.42... [curamd64-setuptools-job-01] | | `-- Extracting orc-0.4.42: .......... done [curamd64-setuptools-job-01] | `-- Extracting gstreamer1-plugins-1.28.1: .......... done [curamd64-setuptools-job-01] | `-- Installing gstreamer1-plugins-bad-1.28.1... [curamd64-setuptools-job-01] | | `-- Installing json-glib-1.10.8... [curamd64-setuptools-job-01] | | `-- Extracting json-glib-1.10.8: .......... done [curamd64-setuptools-job-01] | | `-- Installing pango-1.56.4_1... [curamd64-setuptools-job-01] | | `-- Installing fribidi-1.0.16... [curamd64-setuptools-job-01] | | `-- Extracting fribidi-1.0.16: .......... done [curamd64-setuptools-job-01] | | `-- Installing libthai-0.1.30... [curamd64-setuptools-job-01] | | | `-- Installing libdatrie-0.2.14_1... [curamd64-setuptools-job-01] | | | `-- Extracting libdatrie-0.2.14_1: .......... done [curamd64-setuptools-job-01] | | `-- Extracting libthai-0.1.30: .......... done [curamd64-setuptools-job-01] | | `-- Extracting pango-1.56.4_1: .......... done [curamd64-setuptools-job-01] | `-- Extracting gstreamer1-plugins-bad-1.28.1: .......... done [curamd64-setuptools-job-01] | `-- Installing libXv-1.0.13,1... [curamd64-setuptools-job-01] | `-- Extracting libXv-1.0.13,1: .......... done [curamd64-setuptools-job-01] | `-- Installing openal-soft-1.25.1... [curamd64-setuptools-job-01] | | `-- Installing libmysofa-1.3.3... [curamd64-setuptools-job-01] | | `-- Extracting libmysofa-1.3.3: .......... done [curamd64-setuptools-job-01] | `-- Extracting openal-soft-1.25.1: .......... done [curamd64-setuptools-job-01] | `-- Installing qt5-opengl-5.15.18p109... [curamd64-setuptools-job-01] | `-- Extracting qt5-opengl-5.15.18p109: .......... done [curamd64-setuptools-job-01] `-- Extracting qt5-multimedia-5.15.18p2: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-quick3d-5.15.18p1... [curamd64-setuptools-job-01] | `-- Installing assimp-6.0.5... [curamd64-setuptools-job-01] | `-- Extracting assimp-6.0.5: .......... done [curamd64-setuptools-job-01] `-- Extracting qt5-quick3d-5.15.18p1: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-remoteobjects-5.15.18p0... [curamd64-setuptools-job-01] `-- Extracting qt5-remoteobjects-5.15.18p0: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-sensors-5.15.18p0... [curamd64-setuptools-job-01] `-- Extracting qt5-sensors-5.15.18p0: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-speech-5.15.18p1... [curamd64-setuptools-job-01] | `-- Installing speech-dispatcher-0.12.1_1... [curamd64-setuptools-job-01] | | `-- Installing dotconf-1.4.1_1... [curamd64-setuptools-job-01] | | `-- Extracting dotconf-1.4.1_1: .......... done [curamd64-setuptools-job-01] | | `-- Installing espeak-ng-1.52.0_1... [curamd64-setuptools-job-01] | | `-- Installing pcaudiolib-1.2_2... [curamd64-setuptools-job-01] | | `-- Extracting pcaudiolib-1.2_2: ........ done [curamd64-setuptools-job-01] | | `-- Extracting espeak-ng-1.52.0_1: .......... done [curamd64-setuptools-job-01] | | `-- Installing libsndfile-1.2.2.20251216... [curamd64-setuptools-job-01] | | `-- Installing flac-1.5.0,1... [curamd64-setuptools-job-01] | | | `-- Installing libogg-1.3.6,4... [curamd64-setuptools-job-01] | | | `-- Extracting libogg-1.3.6,4: .......... done [curamd64-setuptools-job-01] | | `-- Extracting flac-1.5.0,1: .......... done [curamd64-setuptools-job-01] | | `-- Installing lame-3.100_5... [curamd64-setuptools-job-01] | | `-- Extracting lame-3.100_5: .......... done [curamd64-setuptools-job-01] | | `-- Installing libvorbis-1.3.7_2,3... [curamd64-setuptools-job-01] | | `-- Extracting libvorbis-1.3.7_2,3: .......... done [curamd64-setuptools-job-01] | | `-- Installing mpg123-1.33.5... [curamd64-setuptools-job-01] | | `-- Extracting mpg123-1.33.5: .......... done [curamd64-setuptools-job-01] | | `-- Installing opus-1.6.1... [curamd64-setuptools-job-01] | | `-- Extracting opus-1.6.1: .......... done [curamd64-setuptools-job-01] | | `-- Extracting libsndfile-1.2.2.20251216: .......... done [curamd64-setuptools-job-01] | | `-- Installing pulseaudio-17.0_4... [curamd64-setuptools-job-01] | | `-- Installing consolekit2-1.2.6_6... [curamd64-setuptools-job-01] | | | `-- Installing libxslt-1.1.45... [curamd64-setuptools-job-01] | | | `-- Installing libgcrypt-1.12.2... [curamd64-setuptools-job-01] | | | | `-- Installing libgpg-error-1.60... [curamd64-setuptools-job-01] | | | | `-- Extracting libgpg-error-1.60: .......... done [curamd64-setuptools-job-01] | | | `-- Extracting libgcrypt-1.12.2: .......... done [curamd64-setuptools-job-01] | | | `-- Extracting libxslt-1.1.45: .......... done [curamd64-setuptools-job-01] | | | `-- Installing polkit-127... [curamd64-setuptools-job-01] | | | `-- Installing duktape-lib-2.7.0_1... [curamd64-setuptools-job-01] | | | `-- Extracting duktape-lib-2.7.0_1: ......... done ===> Creating groups Creating group 'polkitd' with gid '565' ===> Creating users Creating user 'polkitd' with uid '565' [curamd64-setuptools-job-01] | | | `-- Extracting polkit-127: ......... done [curamd64-setuptools-job-01] | | `-- Extracting consolekit2-1.2.6_6: .......... done [curamd64-setuptools-job-01] | | `-- Installing fftw3-3.3.10_5... [curamd64-setuptools-job-01] | | `-- Extracting fftw3-3.3.10_5: .......... done [curamd64-setuptools-job-01] | | `-- Installing fftw3-float-3.3.10_5... [curamd64-setuptools-job-01] | | `-- Extracting fftw3-float-3.3.10_5: .......... done [curamd64-setuptools-job-01] | | `-- Installing libXtst-1.2.5... [curamd64-setuptools-job-01] | | `-- Extracting libXtst-1.2.5: .......... done [curamd64-setuptools-job-01] | | `-- Installing libltdl-2.5.4... [curamd64-setuptools-job-01] | | `-- Extracting libltdl-2.5.4: .......... done [curamd64-setuptools-job-01] | | `-- Installing libsoxr-0.1.3_3... [curamd64-setuptools-job-01] | | `-- Extracting libsoxr-0.1.3_3: .......... done [curamd64-setuptools-job-01] | | `-- Installing speexdsp-1.2.1... [curamd64-setuptools-job-01] | | `-- Extracting speexdsp-1.2.1: .......... done [curamd64-setuptools-job-01] | | `-- Installing webrtc-audio-processing-1.3_1... [curamd64-setuptools-job-01] | | | `-- Installing abseil-20250127.1_1... [curamd64-setuptools-job-01] | | | `-- Extracting abseil-20250127.1_1: .......... done [curamd64-setuptools-job-01] | | `-- Extracting webrtc-audio-processing-1.3_1: .......... done ===> Creating groups Creating group 'pulse' with gid '563' Creating group 'pulse-access' with gid '564' Creating group 'pulse-rt' with gid '557' ===> Creating users Creating user 'pulse' with uid '563' [curamd64-setuptools-job-01] | | `-- Extracting pulseaudio-17.0_4: .......... done [curamd64-setuptools-job-01] | `-- Extracting speech-dispatcher-0.12.1_1: .......... done [curamd64-setuptools-job-01] `-- Extracting qt5-speech-5.15.18p1: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-svg-5.15.18p5... [curamd64-setuptools-job-01] `-- Extracting qt5-svg-5.15.18p5: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-testlib-5.15.18p109... [curamd64-setuptools-job-01] `-- Extracting qt5-testlib-5.15.18p109: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-webchannel-5.15.18p3... [curamd64-setuptools-job-01] `-- Extracting qt5-webchannel-5.15.18p3: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-websockets-5.15.18p2... [curamd64-setuptools-job-01] `-- Extracting qt5-websockets-5.15.18p2: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-x11extras-5.15.18p0... [curamd64-setuptools-job-01] `-- Extracting qt5-x11extras-5.15.18p0: .......... done [curamd64-setuptools-job-01] `-- Installing qt5-xmlpatterns-5.15.18p0... [curamd64-setuptools-job-01] `-- Extracting qt5-xmlpatterns-5.15.18p0: .......... done [curamd64-setuptools-job-01] Extracting py311-qt5-pyqt-5.15.11_2: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ==> Running trigger: gio-modules.ucl Generating GIO modules cache ===== Message from wayland-1.24.0_2: -- Wayland requires XDG_RUNTIME_DIR to be defined to a path that will contain "wayland-%d" unix(4) sockets. This is usually handled by consolekit2 (via ck-launch-session) or pam_xdg (via login). ===== Message from libxkbcommon-1.13.1: -- 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 ===== Message from qt5-sql-5.15.18p109: -- To enable Qt database support, install the database plugin ports. The following plugin ports are available: - databases/qt5-sqldrivers-mysql MySQL - databases/qt5-sqldrivers-odbc Open Database Connectivity - databases/qt5-sqldrivers-pgsql PostgreSQL - databases/qt5-sqldrivers-sqlite2 SQLite 2 - databases/qt5-sqldrivers-sqlite3 SQLite 3 - databases/qt5-sqldrivers-tds FreeTDS ===== Message from alsa-plugins-1.2.12_2: -- ===> NOTICE: The alsa-plugins port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from pulseaudio-17.0_4: -- Pulseaudio tries to determine default values for FreeBSD OSS driver at first start, based on /dev/sndstat output. The hw.snd.default_unit sysctl may affect these values, but restart of the Pulseaudio might be needed to rescan it again, e.g. `pacmd exit`. Pulseaudio has separate input and output configure lines. You can change them with using following commands: To change the default sink (output): # pacmd set-default-sink 3 To change the default source (input): # pacmd set-default-source 3 This can also be set in /usr/local/etc/pulse/default.pa Replace the number '3' with the new default you want to set. The audio/freedesktop-sound-theme is needed if the default sound files are uncommented in the /usr/local/etc/pulse/default.pa file. ===> py311-pymol-3.0.0_3 depends on package: py311-qt5-pyqt>=5.15.11 - found ===> Returning to build of py311-pymol-3.0.0_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for py311-pymol-3.0.0_3 ===> Generating temporary packing list /usr/local/lib/python3.11/site-packages/setuptools/command/sdist.py:123: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. !! ******************************************************************************** Custom 'build_py' does not implement 'get_data_files_without_manifest'. Please extend command classes from setuptools instead of distutils. See https://peps.python.org/pep-0632/ for details. ******************************************************************************** !! self._add_data_files(self._safe_data_files(build_py)) copying data -> /wrkdirs/usr/ports/science/py-pymol/work-py311/stage/usr/local/lib/python3.11/site-packages/pymol/pymol_path/data copying test -> /wrkdirs/usr/ports/science/py-pymol/work-py311/stage/usr/local/lib/python3.11/site-packages/pymol/pymol_path/test copying examples -> /wrkdirs/usr/ports/science/py-pymol/work-py311/stage/usr/local/lib/python3.11/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-3.11 Link: @bin/pymol --> bin/pymol-3.11 ====> Compressing man pages (compress-man) if [ -d "/wrkdirs/usr/ports/science/py-pymol/work-py311/stage/usr/local/lib/python3.11/site-packages/pymol-3.0.0-py3.11.egg-info" ]; then /bin/ls /wrkdirs/usr/ports/science/py-pymol/work-py311/stage/usr/local/lib/python3.11/site-packages/pymol-3.0.0-py3.11.egg-info | while read f; do echo lib/python3.11/site-packages/pymol-3.0.0-py3.11.egg-info/${f} >> /wrkdirs/usr/ports/science/py-pymol/work-py311/.PLIST.mktmp; done; fi; =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-06-06T06:02:23+0000' 'PKG_NOTE_ports_top_git_hash=a8b187544' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=a8b187544' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.4' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for py311-pymol-3.0.0_3 ===> Building py311-pymol-3.0.0_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-pymol-3.0.0_3 build of science/py-pymol@py311 | py311-pymol-3.0.0_3 ended at Sat Jun 6 15:29:30 JST 2026 build time: 00:30:27