=>> Building science/py-avogadrolibs build started at Mon Apr 1 08:10:16 BST 2024 port directory: /usr/ports/science/py-avogadrolibs package name: py39-avogadrolibs-1.99.0 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 886 Feb 14 06:15 /usr/ports/science/py-avogadrolibs/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: e2d8c2cf8a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 18 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/18/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py39 MAKE_ARGS= FLAVOR=py39 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39 TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39 TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.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 DESTDIR=/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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-- CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/avogadrolibs" EXAMPLESDIR="share/examples/avogadrolibs" DATADIR="share/avogadrolibs" WWWDIR="www/avogadrolibs" ETCDIR="etc/avogadrolibs" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/avogadrolibs DOCSDIR=/usr/local/share/doc/avogadrolibs EXAMPLESDIR=/usr/local/share/examples/avogadrolibs WWWDIR=/usr/local/www/avogadrolibs ETCDIR=/usr/local/etc/avogadrolibs --End SUB_LIST-- ---Begin make.conf--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 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) 89999 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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-avogadrolibs-1.99.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py39-avogadrolibs-1.99.0 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py39-avogadrolibs-1.99.0 for building => SHA256 Checksum OK for OpenChemistry-avogadrolibs-1.99.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py39-avogadrolibs-1.99.0 for building ===> Extracting for py39-avogadrolibs-1.99.0 => SHA256 Checksum OK for OpenChemistry-avogadrolibs-1.99.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py39-avogadrolibs-1.99.0 ===> Applying FreeBSD patches for py39-avogadrolibs-1.99.0 from /usr/ports/science/py-avogadrolibs/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/include/pybind11/pybind11.h - not found ===> Installing existing package /packages/All/pybind11-2.11.1.pkg [pkg-builder.dan.net.uk] Installing pybind11-2.11.1... [pkg-builder.dan.net.uk] Extracting pybind11-2.11.1: .......... done ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/include/pybind11/pybind11.h - found ===> Returning to build of py39-avogadrolibs-1.99.0 ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/bin/cmake - found ===> Returning to build of py39-avogadrolibs-1.99.0 ===> py39-avogadrolibs-1.99.0 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,2: ..... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> py39-avogadrolibs-1.99.0 depends on executable: ninja - found ===> Returning to build of py39-avogadrolibs-1.99.0 ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.4.0_3.pkg [pkg-builder.dan.net.uk] Installing eigen-3.4.0_3... [pkg-builder.dan.net.uk] `-- Installing blas-3.12.0_1... [pkg-builder.dan.net.uk] | `-- Installing gcc13-13.2.0_4... [pkg-builder.dan.net.uk] | | `-- Installing binutils-2.40_5,1... [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | | `-- Installing liblz4-1.9.4_1,1... 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[pkg-builder.dan.net.uk] `-- Extracting lapack-3.12.0_2: .......... done [pkg-builder.dan.net.uk] Extracting eigen-3.4.0_3: .......... done ===== Message from gcc13-13.2.0_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/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of py39-avogadrolibs-1.99.0 ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-avogadrolibs-1.99.0 depends on shared library: libAvogadroCore.so - not found ===> Installing existing package /packages/All/avogadrolibs-1.99.0.pkg [pkg-builder.dan.net.uk] Installing avogadrolibs-1.99.0... [pkg-builder.dan.net.uk] `-- Installing glew-2.2.0_3... [pkg-builder.dan.net.uk] | `-- Installing libGLU-9.0.2_2... [pkg-builder.dan.net.uk] | | `-- Installing libglvnd-1.7.0... [pkg-builder.dan.net.uk] | | `-- Installing libX11-1.8.7_1,1... [pkg-builder.dan.net.uk] | | | `-- Installing libxcb-1.16.1... [pkg-builder.dan.net.uk] | | | `-- Installing libXau-1.0.9_1... [pkg-builder.dan.net.uk] | | | `-- Extracting libXau-1.0.9_1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | | | `-- Installing xorgproto-2023.2... [pkg-builder.dan.net.uk] | | | | `-- Extracting xorgproto-2023.2: .......... done [pkg-builder.dan.net.uk] | | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] | | | `-- Extracting libxcb-1.16.1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libX11-1.8.7_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXext-1.3.6,1... 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[pkg-builder.dan.net.uk] | | | `-- Extracting libfontenc-1.1.8: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg-builder.dan.net.uk] | | `-- Extracting dejavu-2.37_3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing font-bh-ttf-1.0.3_5... [pkg-builder.dan.net.uk] | | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg-builder.dan.net.uk] | | `-- Installing font-misc-ethiopic-1.0.4... [pkg-builder.dan.net.uk] | | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg-builder.dan.net.uk] | | `-- Installing font-misc-meltho-1.0.3_5... [pkg-builder.dan.net.uk] | | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg-builder.dan.net.uk] `-- Extracting qt5-gui-5.15.12p148: .......... done [pkg-builder.dan.net.uk] `-- Installing qt5-svg-5.15.12p6... [pkg-builder.dan.net.uk] | `-- Installing qt5-widgets-5.15.12p148... [pkg-builder.dan.net.uk] | `-- Extracting qt5-widgets-5.15.12p148: .......... done [pkg-builder.dan.net.uk] `-- Extracting qt5-svg-5.15.12p6: .......... done [pkg-builder.dan.net.uk] `-- Installing spglib-2.3.1... [pkg-builder.dan.net.uk] `-- Extracting spglib-2.3.1: .......... done [pkg-builder.dan.net.uk] Extracting avogadrolibs-1.99.0: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.13.2: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from wayland-1.22.0: -- Wayland requires XDG_RUNTIME_DIR to be defined to a path that will contain "wayland-%d" unix(4) sockets. This is usually handled by consolekit2 (via ck-launch-session) or pam_xdg (via login). ===== Message from libxkbcommon-1.6.0_2: -- 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 dejavu-2.37_3: -- 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. ===> py39-avogadrolibs-1.99.0 depends on shared library: libAvogadroCore.so - found (/usr/local/lib/libAvogadroCore.so) ===> Returning to build of py39-avogadrolibs-1.99.0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py39-avogadrolibs-1.99.0 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.build CMake Warning (dev) in CMakeLists.txt: No project() command is present. The top-level CMakeLists.txt file must contain a literal, direct call to the project() command. Add a line of code such as project(ProjectName) near the top of the file, but after cmake_minimum_required(). CMake is pretending there is a "project(Project)" command on the first line. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in CMakeLists.txt: cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is Clang 14.0.5 -- The CXX compiler identification is Clang 14.0.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Found Python: /usr/local/bin/python3.9 (found version "3.9.18") found components: Interpreter Development Development.Module Development.Embed CMake Warning at /usr/local/share/cmake/pybind11/pybind11Common.cmake:153 (message): USE -DCMAKE_CXX_STANDARD=17 instead of PYBIND11_CPP_STANDARD Call Stack (most recent call first): /usr/local/share/cmake/pybind11/pybind11Config.cmake:250 (include) CMakeLists.txt:11 (find_package) -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- Found pybind11: /usr/local/include (found version "2.11.1") -- Configuring done (3.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_COLOR_MAKEFILE CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED INSTALL_LIBRARY_DIR Python3_EXECUTABLE Python_ADDITIONAL_VERSIONS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py39-avogadrolibs-1.99.0 [ 25% 1/4] /ccache/libexec/ccache/c++ -Davogadrocorepython_EXPORTS -isystem /usr/local/include/python3.9 -isystem /usr/local/include -isystem /usr/local/include/avogadro -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -fvisibility=hidden -flto -MD -MT CMakeFiles/avogadrocorepython.dir/core.cpp.o -MF CMakeFiles/avogadrocorepython.dir/core.cpp.o.d -o CMakeFiles/avogadrocorepython.dir/core.cpp.o -c /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/avogadrolibs-1.99.0/python/core.cpp [ 50% 2/4] : && /ccache/libexec/ccache/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -flto -shared -o lib/avogadro/core.cpython-39.so CMakeFiles/avogadrocorepython.dir/core.cpp.o -Wl,-rpath,/usr/local/lib:::::::: /usr/local/lib/libAvogadroCore.so.1.99.0 && cd /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.build && /usr/bin/llvm-strip /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.build/lib/avogadro/core.cpython-39.so [ 75% 3/4] /ccache/libexec/ccache/c++ -Davogadroiopython_EXPORTS -isystem /usr/local/include/python3.9 -isystem /usr/local/include -isystem /usr/local/include/avogadro -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=gnu++17 -fPIC -fvisibility=hidden -flto -MD -MT CMakeFiles/avogadroiopython.dir/io.cpp.o -MF CMakeFiles/avogadroiopython.dir/io.cpp.o.d -o CMakeFiles/avogadroiopython.dir/io.cpp.o -c /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/avogadrolibs-1.99.0/python/io.cpp [100% 4/4] : && /ccache/libexec/ccache/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -flto -shared -o lib/avogadro/io.cpython-39.so CMakeFiles/avogadroiopython.dir/io.cpp.o -Wl,-rpath,/usr/local/lib:::::::: /usr/local/lib/libAvogadroQuantumIO.so.1.99.0 /usr/local/lib/libAvogadroIO.so.1.99.0 /usr/local/lib/libAvogadroCore.so.1.99.0 && cd /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.build && /usr/bin/llvm-strip /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.build/lib/avogadro/io.cpython-39.so =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-avogadrolibs-1.99.0 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py39-avogadrolibs-1.99.0 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/stage/usr/local/lib/python3.9/site-packages/avogadro/core.cpython-39.so -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/stage/usr/local/lib/python3.9/site-packages/avogadro/core.cpython-39.so" to "$ORIGIN:/usr/local/lib" -- Installing: /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/stage/usr/local/lib/python3.9/site-packages/avogadro/io.cpython-39.so -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/stage/usr/local/lib/python3.9/site-packages/avogadro/io.cpython-39.so" to "$ORIGIN:/usr/local/lib" -- Installing: /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/stage/usr/local/lib/python3.9/site-packages/avogadro/__init__.py -- Installing: /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/stage/usr/local/lib/python3.9/site-packages/avogadro/cjson.py -- Installing: /wrkdirs/usr/ports/science/py-avogadrolibs/work-py39/stage/usr/local/lib/python3.9/site-packages/avogadro/connect.py ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== 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=2024-04-01T07:10:16+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=e2d8c2cf8a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py39-avogadrolibs-1.99.0 ===> Building py39-avogadrolibs-1.99.0 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py39-avogadrolibs-1.99.0 build of science/py-avogadrolibs@py39 | py39-avogadrolibs-1.99.0 ended at Mon Apr 1 08:11:39 BST 2024 build time: 00:01:25