[package - 124i386-default][biology/py-PySCeS] Failed for py39-PySCeS-1.1.1 in build
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Date: Fri, 15 Dec 2023 22:09:09 UTC
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy5/data/124i386-default/8e6cecbea178/logs/py39-PySCeS-1.1.1.log Build URL: https://pkg-status.freebsd.org/beefy5/build.html?mastername=124i386-default&build=8e6cecbea178 Log: =>> Building biology/py-PySCeS build started at Fri Dec 15 22:08:35 UTC 2023 port directory: /usr/ports/biology/py-PySCeS package name: py39-PySCeS-1.1.1 building for: FreeBSD 124i386-default-job-10 12.4-RELEASE-p9 FreeBSD 12.4-RELEASE-p9 i386 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1385 Jul 27 01:01 /usr/ports/biology/py-PySCeS/Makefile Ports top last git commit: 8e6cecbea17 Ports top unclean checkout: no Port dir last git commit: 3cea739c6a8 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.0 Host OSVERSION: 1500006 Jail OSVERSION: 1204000 Job Id: 10 ---Begin Environment--- SHELL=/bin/csh BLOCKSIZE=K MAIL=/var/mail/root OSVERSION=1204000 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 UNAME_m=i386 UNAME_p=i386 UNAME_r=12.4-RELEASE-p9 LOCALBASE=/usr/local UNAME_v=FreeBSD 12.4-RELEASE-p9 USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.0 MASTERMNT=/usr/local/poudriere/data/.m/124i386-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/124i386-default/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=124i386-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/124i386-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.0 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-- F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-PySCeS/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCO PY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" 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=" -lpython3.9 -shared -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd12 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=12.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/PySCeS" EXAMPLESDIR="share/examples/PySCeS" DATADIR="share/PySCeS" WWWDIR="www/PySCeS" ETCDIR="etc/PySCeS" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd12 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/PySCeS DOCSDIR=/usr/local/share/doc/PySCeS EXAMPLESDIR=/usr/local/share/examples/PySCeS WWWDIR=/usr/local/www/PySCeS ETCDIR=/usr/local/etc/PySCeS --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### 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) 524288 stack size (kbytes, -s) 65536 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-PySCeS-1.1.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9.pkg [124i386-default-job-10] Installing pkg-1.20.9... [124i386-default-job-10] Extracting pkg-1.20.9: .......... done ===> py39-PySCeS-1.1.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-PySCeS-1.1.1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py39-PySCeS-1.1.1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py39-PySCeS-1.1.1 for building => SHA256 Checksum OK for pysces-1.1.1.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py39-PySCeS-1.1.1 for building ===> Extracting for py39-PySCeS-1.1.1 => SHA256 Checksum OK for pysces-1.1.1.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py39-PySCeS-1.1.1 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py39-PySCeS-1.1.1 depends on package: py39-scikit-build>0 - not found ===> Installing existing package /packages/All/py39-scikit-build-0.16.7_1.pkg [124i386-default-job-10] Installing py39-scikit-build-0.16.7_1... [124i386-default-job-10] `-- Installing py39-distro-1.8.0_2... [124i386-default-job-10] | `-- Installing python39-3.9.18... [124i386-default-job-10] | | `-- Installing gettext-runtime-0.22.3... [124i386-default-job-10] | | `-- Installing indexinfo-0.3.1... [124i386-default-job-10] | | `-- Extracting indexinfo-0.3.1: .... done [124i386-default-job-10] | | `-- Extracting gettext-runtime-0.22.3: .......... done [124i386-default-job-10] | | `-- Installing libffi-3.4.4... [124i386-default-job-10] | | `-- Extracting libffi-3.4.4: .......... done [124i386-default-job-10] | | `-- Installing mpdecimal-2.5.1... [124i386-default-job-10] | | `-- Extracting mpdecimal-2.5.1: .......... done [124i386-default-job-10] | | `-- Installing readline-8.2.1... [124i386-default-job-10] | | `-- Extracting readline-8.2.1: .......... done [124i386-default-job-10] | `-- Extracting python39-3.9.18: .......... done [124i386-default-job-10] `-- Extracting py39-distro-1.8.0_2: .......... done [124i386-default-job-10] `-- Installing py39-packaging-23.2... [124i386-default-job-10] `-- Extracting py39-packaging-23.2: .......... done [124i386-default-job-10] `-- Installing py39-wheel-0.42.0... [124i386-default-job-10] `-- Extracting py39-wheel-0.42.0: .......... done [124i386-default-job-10] Extracting py39-scikit-build-0.16.7_1: .......... done ===== <snip> 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). ===> py39-PySCeS-1.1.1 depends on package: py39-matplotlib>0 - found ===> Returning to build of py39-PySCeS-1.1.1 ===> py39-PySCeS-1.1.1 depends on package: py39-scipy>0 - not found ===> Installing existing package /packages/All/py39-scipy-1.11.1.pkg [124i386-default-job-10] Installing py39-scipy-1.11.1... [124i386-default-job-10] `-- Installing blas-3.11.0_1... [124i386-default-job-10] `-- Extracting blas-3.11.0_1: ........ done [124i386-default-job-10] Extracting py39-scipy-1.11.1: .......... done ===> py39-PySCeS-1.1.1 depends on package: py39-scipy>0 - found ===> Returning to build of py39-PySCeS-1.1.1 ===> py39-PySCeS-1.1.1 depends on executable: gfortran12 - found ===> py39-PySCeS-1.1.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-PySCeS-1.1.1 depends on file: /usr/local/bin/python3.9 - found ===> py39-PySCeS-1.1.1 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py39-PySCeS-1.1.1 setuptools is available. bdist_conda not available. 'install_dir' :: /usr/local/lib/python3.9/site-packages/pysces 'model_dir' :: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/Pysces/psc 'output_dir' :: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/Pysces 'gnuplot_dir' :: None 'silentstart' :: False 'change_dir_on_start' :: False 'custom_datatype' :: None Default configuration file installed Building pitcon Building nleq2 running config =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py39-PySCeS-1.1.1 setuptools is available. bdist_conda not available. 'install_dir' :: /usr/local/lib/python3.9/site-packages/pysces 'model_dir' :: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/Pysces/psc 'output_dir' :: /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/Pysces 'gnuplot_dir' :: None 'silentstart' :: False 'change_dir_on_start' :: False 'custom_datatype' :: None Default configuration file installed Building pitcon Building nleq2 -------------------------------------------------------------------------------- -- Trying 'Ninja' generator -------------------------------- --------------------------- ---------------------- ----------------- ------------ ------- -- 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 <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions. Not searching for unused variables given on the command line. CMake Error: CMake was unable to find a build program corresponding to "Ninja". CMAKE_MAKE_PROGRAM is not set. You probably need to select a different build tool. -- Configuring incomplete, errors occurred! -- ------- ------------ ----------------- ---------------------- --------------------------- -------------------------------- -- Trying 'Ninja' generator - failure -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Trying 'Unix Makefiles' generator -------------------------------- --------------------------- ---------------------- ----------------- ------------ ------- -- 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 <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions. Not searching for unused variables given on the command line. -- The C compiler identification is Clang 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - failed -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc - broken CMake Error at /usr/local/share/cmake/Modules/CMakeTestCCompiler.cmake:67 (message): The C compiler "/usr/bin/cc" is not able to compile a simple test program. It fails with the following output: Change Dir: '/wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-xXY5W2' Run Build Command(s): /usr/local/bin/cmake -E env VERBOSE=1 /usr/bin/make -f Makefile cmTC_58c44/fast /usr/bin/make -f CMakeFiles/cmTC_58c44.dir/build.make CMakeFiles/cmTC_58c44.dir/build Building C object CMakeFiles/cmTC_58c44.dir/testCCompiler.c.o /usr/bin/cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT CMakeFiles/cmTC_58c44.dir/testCCompiler.c.o -MF CMakeFiles/cmTC_58c44.dir/testCCompiler.c.o.d -o CMakeFiles/cmTC_58c44.dir/testCCompiler.c.o -c /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-xXY5W2/testCCompiler.c Linking C executable cmTC_58c44 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_58c44.dir/link.txt --verbose=1 /usr/bin/cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpython3.9 -shared -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -fstack-protector-strong CMakeFiles/cmTC_58c44.dir/testCCompiler.c.o -o cmTC_58c44 ld: error: unable to find library -lpython3.9 cc: error: linker command failed with exit code 1 (use -v to see invocation) *** Error code 1 Stop. make[2]: stopped in /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-xXY5W2 *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/py-PySCeS/work-py39/pysces-1.1.1/_cmake_test_compile/build/CMakeFiles/CMakeScratch/TryCompile-xXY5W2 CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:3 (ENABLE_LANGUAGE) -- Configuring incomplete, errors occurred! -- ------- ------------ ----------------- ---------------------- --------------------------- -------------------------------- -- Trying 'Unix Makefiles' generator - failure -------------------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 1, in <module> File "setup.py", line 185, in <module> setup( File "/usr/local/lib/python3.9/site-packages/skbuild/setuptools_wrap.py", line 634, in setup env = cmkr.configure( File "/usr/local/lib/python3.9/site-packages/skbuild/cmaker.py", line 236, in configure generator = self.platform.get_best_generator( File "/usr/local/lib/python3.9/site-packages/skbuild/platform_specifics/abstract.py", line 182, in get_best_generator .format(line="*" * 80, installation_help=self.generator_installation_help) File "/usr/local/lib/python3.9/site-packages/skbuild/platform_specifics/abstract.py", line 42, in generator_installation_help raise NotImplementedError # pragma: no cover NotImplementedError *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-PySCeS