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Maintainer: y...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere3/data/141releng-armv7-default/332c73b035e3/logs/fastani-1.34.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=141releng-armv7-default&build=332c73b035e3 Log: =>> Building biology/fastani build started at Thu Nov 7 18:18:01 UTC 2024 port directory: /usr/ports/biology/fastani package name: fastani-1.34 building for: FreeBSD 141releng-armv7-default-job-09 14.1-RELEASE-p5 FreeBSD 14.1-RELEASE-p5 1401000 arm maintained by: y...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 597 Oct 1 01:02 /usr/ports/biology/fastani/Makefile Ports top last git commit: 332c73b035e Ports top unclean checkout: no Port dir last git commit: 89f62deb8a9 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1401000 Job Id: 09 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1401000 UNAME_v=FreeBSD 14.1-RELEASE-p5 1401000 UNAME_r=14.1-RELEASE-p5 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/141releng-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/141releng-armv7-default/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=141releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/141releng-armv7-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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--- ---End OPTIONS List--- --MAINTAINER-- y...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastani/work/.cache HOME=/wrkdirs/usr/ports/biology/fastani/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastani/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastani/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-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastani/work/.cache HOME=/wrkdirs/usr/ports/biology/fastani/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastani/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastani/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 DESTDIR=/wrkdirs/usr/ports/biology/fastani/work/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 " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0 644" 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=14.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/fastani" EXAMPLESDIR="share/examples/fastani" DATADIR="share/fastani" WWWDIR="www/fastani" ETCDIR="etc/fastani" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fastani DOCSDIR=/usr/local/share/doc/fastani EXAMPLESDIR=/usr/local/share/examples/fastani WWWDIR=/usr/local/www/fastani ETCDIR=/usr/local/etc/fastani --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 APACHE20 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastani-1.34 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [141releng-armv7-default-job-09] Installing pkg-1.21.3... [141releng-armv7-default-job-09] Extracting pkg-1.21.3: .......... done ===> fastani-1.34 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fastani-1.34 =========================================================================== =======================<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 APACHE20 accepted by the user ===> Fetching all distfiles required by fastani-1.34 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by fastani-1.34 for building => SHA256 Checksum OK for ParBLiSS-FastANI-v1.34_GH0.tar.gz. => SHA256 Checksum OK for catchorg-Catch2-359542d_GH0.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 APACHE20 accepted by the user ===> Fetching all distfiles required by fastani-1.34 for building ===> Extracting for fastani-1.34 => SHA256 Checksum OK for ParBLiSS-FastANI-v1.34_GH0.tar.gz. => SHA256 Checksum OK for catchorg-Catch2-359542d_GH0.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 fastani-1.34 ===> Applying FreeBSD patches for fastani-1.34 from /usr/ports/biology/fastani/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastani-1.34 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.30.5.pkg [141releng-armv7-default-job-09] Installing cmake-core-3.30.5... [141releng-armv7-default-job-09] `-- Installing expat-2.6.3... [141releng-armv7-default-job-09] `-- Extracting expat-2.6.3: .......... done [141releng-armv7-default-job-09] `-- Installing jsoncpp-1.9.6_1... [141releng-armv7-default-job-09] `-- Extracting jsoncpp-1.9.6_1: .......... done [141releng-armv7-default-job-09] `-- Installing libuv-1.49.1... [141releng-armv7-default-job-09] `-- Extracting libuv-1.49.1: .......... done [141releng-armv7-default-job-09] `-- Installing rhash-1.4.4_1... [141releng-armv7-default-job-09] | `-- Installing gettext-runtime-0.22.5... [141releng-armv7-default-job-09] | | `-- Installing indexinfo-0.3.1... [141releng-armv7-default-job-09] | | `-- Extracting indexinfo-0.3.1: .... done [141releng-armv7-default-job-09] | `-- Extracting gettext-runtime-0.22.5: .......... done [141releng-armv7-default-job-09] `-- Extracting rhash-1.4.4_1: .......... done [141releng-armv7-default-job-09] Extracting cmake-core-3.30.5: .......... done ===> fastani-1.34 depends on file: /usr/local/bin/cmake - found ===> Returning to build of fastani-1.34 ===> fastani-1.34 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,4.pkg [141releng-armv7-default-job-09] Installing ninja-1.11.1,4... [141releng-armv7-default-job-09] `-- Installing python311-3.11.10... [141releng-armv7-default-job-09] | `-- Installing libffi-3.4.6... [141releng-armv7-default-job-09] | `-- Extracting libffi-3.4.6: .......... done [141releng-armv7-default-job-09] | `-- Installing mpdecimal-4.0.0... [141releng-armv7-default-job-09] | `-- Extracting mpdecimal-4.0.0: .......... done [141releng-armv7-default-job-09] | `-- Installing readline-8.2.13_2... [141releng-armv7-default-job-09] | `-- Extracting readline-8.2.13_2: .......... done [141releng-armv7-default-job-09] `-- Extracting python311-3.11.10: .......... done [141releng-armv7-default-job-09] Extracting ninja-1.11.1,4: ........ done ===== Message from python311-3.11.10: -- 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 ===> fastani-1.34 depends on executable: ninja - found ===> Returning to build of fastani-1.34 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastani-1.34 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [141releng-armv7-default-job-09] Installing gsl-2.7.1_1... [141releng-armv7-default-job-09] Extracting gsl-2.7.1_1: .......... done ===> fastani-1.34 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of fastani-1.34 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for fastani-1.34 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/fastani/work/.build -- The CXX compiler identification is Clang 18.1.5 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/lib/libz.so (found suitable version "1.3.1", minimum required is "1.1") Using zlib library v1.3.1 -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND) NOTE: OpenMP not found; Compiling as a single threaded app... -- Found GSL: /usr/local/include (found suitable version "2.7.1", minimum required is "1.6") GSL v2.7.1 Found: -- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/fastani/work/.build =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for fastani-1.34 [ 33% 2/3] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/main.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/main.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/main.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/main.cpp [ 66% 2/3] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp FAILED: CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp:11:10: fatal error: 'omp.h' file not found 11 | #include <omp.h> | ^~~~~~~ 1 error generated. ninja: build stopped: subcommand failed. ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/fastani