[package - 140releng-armv7-default][biology/seqwish] Failed for seqwish-0.7.10 in configure
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Date: Mon, 26 Aug 2024 15:30:07 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/ampere3/data/140releng-armv7-default/60a177caf143/logs/seqwish-0.7.10.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=140releng-armv7-default&build=60a177caf143 Log: =>> Building biology/seqwish build started at Mon Aug 26 15:30:01 UTC 2024 port directory: /usr/ports/biology/seqwish package name: seqwish-0.7.10 building for: FreeBSD 140releng-armv7-default-job-01 14.0-RELEASE-p9 FreeBSD 14.0-RELEASE-p9 1400097 arm maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 840 May 21 01:01 /usr/ports/biology/seqwish/Makefile Ports top last git commit: 60a177caf14 Ports top unclean checkout: no Port dir last git commit: 04eb409d363 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1-30-g79e3edcd Host OSVERSION: 1500019 Jail OSVERSION: 1400097 Job Id: 01 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400097 UNAME_v=FreeBSD 14.0-RELEASE-p9 1400097 UNAME_r=14.0-RELEASE-p9 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=3.4.1-30-g79e3edcd MASTERMNT=/usr/local/poudriere/data/.m/140releng-armv7-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/140releng-armv7-default/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=140releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/140releng-armv7-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for seqwish-0.7.10: OPENMP=on: Parallel processing support via OpenMP ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/work/.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/biology/seqwish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/work/.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 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 -fopenmp " 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" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqwish" EXAMPLESDIR="share/examples/seqwish" DATADIR="share/seqwish" WWWDIR="www/seqwish" ETCDIR="etc/seqwish" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqwish DOCSDIR=/usr/local/share/doc/seqwish EXAMPLESDIR=/usr/local/share/examples/seqwish WWWDIR=/usr/local/www/seqwish ETCDIR=/usr/local/etc/seqwish --End SUB_LIST-- ---Begin make.conf--- # 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 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # 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 ---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 MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> seqwish-0.7.10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [140releng-armv7-default-job-01] Installing pkg-1.21.3... [140releng-armv7-default-job-01] Extracting pkg-1.21.3: .......... done ===> seqwish-0.7.10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqwish-0.7.10 =========================================================================== =======================<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 MIT accepted by the user ===> Fetching all distfiles required by seqwish-0.7.10 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by seqwish-0.7.10 for building => SHA256 Checksum OK for seqwish-v0.7.10.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 MIT accepted by the user ===> Fetching all distfiles required by seqwish-0.7.10 for building ===> Extracting for seqwish-0.7.10 => SHA256 Checksum OK for seqwish-v0.7.10.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 seqwish-0.7.10 ===> Applying FreeBSD patches for seqwish-0.7.10 from /usr/ports/biology/seqwish/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> seqwish-0.7.10 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.30.2.pkg [140releng-armv7-default-job-01] Installing cmake-core-3.30.2... [140releng-armv7-default-job-01] `-- Installing expat-2.6.2... [140releng-armv7-default-job-01] `-- Extracting expat-2.6.2: .......... done [140releng-armv7-default-job-01] `-- Installing jsoncpp-1.9.5... [140releng-armv7-default-job-01] `-- Extracting jsoncpp-1.9.5: .......... done [140releng-armv7-default-job-01] `-- Installing libuv-1.48.0... [140releng-armv7-default-job-01] `-- Extracting libuv-1.48.0: .......... done [140releng-armv7-default-job-01] `-- Installing rhash-1.4.4_1... [140releng-armv7-default-job-01] | `-- Installing gettext-runtime-0.22.5... [140releng-armv7-default-job-01] | | `-- Installing indexinfo-0.3.1... [140releng-armv7-default-job-01] | | `-- Extracting indexinfo-0.3.1: .... done [140releng-armv7-default-job-01] | `-- Extracting gettext-runtime-0.22.5: .......... done [140releng-armv7-default-job-01] `-- Extracting rhash-1.4.4_1: .......... done [140releng-armv7-default-job-01] Extracting cmake-core-3.30.2: .......... done ===> seqwish-0.7.10 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqwish-0.7.10 =========================================================================== =======================<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 seqwish-0.7.10 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/seqwish/work/.build CMake Deprecation Warning at CMakeLists.txt:3 (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. -- The C compiler identification is Clang 16.0.6 -- The CXX compiler identification is Clang 16.0.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - failed -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ - broken CMake Error at /usr/local/share/cmake/Modules/CMakeTestCXXCompiler.cmake:73 (message): The C++ compiler "/usr/bin/c++" is not able to compile a simple test program. It fails with the following output: Change Dir: '/wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-5zZ1xE' Run Build Command(s): /usr/local/bin/cmake -E env VERBOSE=1 /usr/bin/make -f Makefile cmTC_8a798/fast /usr/bin/make -f CMakeFiles/cmTC_8a798.dir/build.make CMakeFiles/cmTC_8a798.dir/build Building CXX object CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -MD -MT CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o -MF CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o.d -o CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o -c /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-5zZ1xE/testCXXCompiler.cxx Linking CXX executable cmTC_8a798 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_8a798.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o -o cmTC_8a798 ld: error: unable to find library -lomp c++: error: linker command failed with exit code 1 (use -v to see invocation) *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-5zZ1xE *** Error code 1 Stop. make: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-5zZ1xE CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:6 (project) -- Configuring incomplete, errors occurred! *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqwish