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Maintainer: j...@freebsd.org Log URL: http://ampere1.nyi.freebsd.org/data/122arm64-quarterly/493e57809108/logs/bolt-lmm-2.3.4_4.log Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=122arm64-quarterly&build=493e57809108 Log: =>> Building biology/bolt-lmm build started at Thu Dec 9 02:21:22 UTC 2021 port directory: /usr/ports/biology/bolt-lmm package name: bolt-lmm-2.3.4_4 building for: FreeBSD 122arm64-quarterly-job-06 12.2-RELEASE FreeBSD 12.2-RELEASE arm64 maintained by: j...@freebsd.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400008 Jail OSVERSION: 1202000 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1202000 UNAME_v=FreeBSD 12.2-RELEASE UNAME_r=12.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/122arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/122arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=122arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/122arm64-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for bolt-lmm-2.3.4_4: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- j...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bolt-lmm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bolt-lmm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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" OBJCOPY="/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" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc10" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -fno-strict-aliasing " CPP="cpp10" CPPFLAGS="" LDFLAGS=" -L/wrkdirs/usr/ports/biology/bolt-lmm/work -fstack-protect or-strong -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 " LIBS="" CXX="g++10" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -nostdinc++ -isystem /usr/include/c++/v1 -Wl,-rpath=/usr/local/lib/gcc10 " 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-- PORTEXAMPLES="" OSREL=12.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bolt-lmm" EXAMPLESDIR="share/examples/bolt-lmm" DATADIR="share/bolt-lmm" WWWDIR="www/bolt-lmm" ETCDIR="etc/bolt-lmm" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bolt-lmm DOCSDIR=/usr/local/share/doc/bolt-lmm EXAMPLESDIR=/usr/local/share/examples/bolt-lmm WWWDIR=/usr/local/www/bolt-lmm ETCDIR=/usr/local/etc/bolt-lmm --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 #### /usr/local/etc/poudriere.d/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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 10.0.1 (g...@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: aarch64-unknown-freebsd12.2 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.1 (g...@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: aarch64-unknown-freebsd12.2 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.1 (g...@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: aarch64-unknown-freebsd12.2 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.2-RELEASE OSREL=12.2 OSVERSION=1202000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1048576 stack size (kbytes, -s) 1048576 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) 1024 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 >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [122arm64-quarterly-job-06] Installing pkg-1.17.5... [122arm64-quarterly-job-06] Extracting pkg-1.17.5: .......... done ===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bolt-lmm-2.3.4_4 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bolt-lmm-2.3.4_4 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bolt-lmm-2.3.4_4 for building => SHA256 Checksum OK for BOLT-LMM_v2.3.4.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bolt-lmm-2.3.4_4 for building ===> Extracting for bolt-lmm-2.3.4_4 => SHA256 Checksum OK for BOLT-LMM_v2.3.4.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bolt-lmm-2.3.4_4 ===> Applying FreeBSD patches for bolt-lmm-2.3.4_4 from /usr/ports/biology/bolt-lmm/files =========================================================================== =======================<phase: build-depends >============================ ===> bolt-lmm-2.3.4_4 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [122arm64-quarterly-job-06] Installing gmake-4.3_2... [122arm64-quarterly-job-06] `-- Installing gettext-runtime-0.21... [122arm64-quarterly-job-06] | `-- Installing indexinfo-0.3.1... [122arm64-quarterly-job-06] | `-- Extracting indexinfo-0.3.1: .... done [122arm64-quarterly-job-06] `-- Extracting gettext-runtime-0.21: .......... done [122arm64-quarterly-job-06] Extracting gmake-4.3_2: .......... done ===> bolt-lmm-2.3.4_4 depends on package: gmake>=4.3 - found ===> Returning to build of bolt-lmm-2.3.4_4 ===> bolt-lmm-2.3.4_4 depends on executable: gcc10 - not found ===> Installing existing package /packages/All/gcc10-10.3.0.pkg [122arm64-quarterly-job-06] Installing gcc10-10.3.0... [122arm64-quarterly-job-06] `-- Installing binutils-2.37_2,1... [122arm64-quarterly-job-06] `-- Extracting binutils-2.37_2,1: .......... done [122arm64-quarterly-job-06] `-- Installing gmp-6.2.1... [122arm64-quarterly-job-06] `-- Extracting gmp-6.2.1: .......... done [122arm64-quarterly-job-06] `-- Installing mpc-1.2.1... [122arm64-quarterly-job-06] | `-- Installing mpfr-4.1.0_1... [122arm64-quarterly-job-06] | `-- Extracting mpfr-4.1.0_1: .......... done [122arm64-quarterly-job-06] `-- Extracting mpc-1.2.1: ......... done [122arm64-quarterly-job-06] Extracting gcc10-10.3.0: .......... done ===== Message from gcc10-10.3.0: -- 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/gcc10 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> bolt-lmm-2.3.4_4 depends on executable: gcc10 - found ===> Returning to build of bolt-lmm-2.3.4_4 ===> bolt-lmm-2.3.4_4 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ ===> bolt-lmm-2.3.4_4 depends on shared library: libnlopt.so - not found ===> Installing existing package /packages/All/nlopt-2.7.0.pkg [122arm64-quarterly-job-06] Installing nlopt-2.7.0... [122arm64-quarterly-job-06] `-- Installing guile2-2.2.7_1... [122arm64-quarterly-job-06] | `-- Installing boehm-gc-threaded-8.0.6... [122arm64-quarterly-job-06] | | `-- Installing boehm-gc-8.0.6... [122arm64-quarterly-job-06] | | `-- Extracting boehm-gc-8.0.6: .......... done [122arm64-quarterly-job-06] | `-- Extracting boehm-gc-threaded-8.0.6: .......... done [122arm64-quarterly-job-06] | `-- Installing libffi-3.3_1... [122arm64-quarterly-job-06] | `-- Extracting libffi-3.3_1: .......... done [122arm64-quarterly-job-06] | `-- Installing libltdl-2.4.6... [122arm64-quarterly-job-06] | `-- Extracting libltdl-2.4.6: .......... done [122arm64-quarterly-job-06] | `-- Installing libunistring-0.9.10_1... [122arm64-quarterly-job-06] | `-- Extracting libunistring-0.9.10_1: .......... done [122arm64-quarterly-job-06] | `-- Installing readline-8.1.1... [122arm64-quarterly-job-06] | `-- Extracting readline-8.1.1: .......... done [122arm64-quarterly-job-06] `-- Extracting guile2-2.2.7_1: .......... done [122arm64-quarterly-job-06] `-- Installing py38-numpy-1.16.6_2,1... [122arm64-quarterly-job-06] | `-- Installing openblas-0.3.16,1... [122arm64-quarterly-job-06] | `-- Extracting openblas-0.3.16,1: .......... done [122arm64-quarterly-job-06] | `-- Installing py38-setuptools-57.0.0... [122arm64-quarterly-job-06] | | `-- Installing python38-3.8.12... [122arm64-quarterly-job-06] | | `-- Installing mpdecimal-2.5.1... [122arm64-quarterly-job-06] | | `-- Extracting mpdecimal-2.5.1: .......... done [122arm64-quarterly-job-06] | | `-- Extracting python38-3.8.12: .......... done [122arm64-quarterly-job-06] | `-- Extracting py38-setuptools-57.0.0: .......... done [122arm64-quarterly-job-06] | `-- Installing suitesparse-umfpack-5.7.9... [122arm64-quarterly-job-06] | | `-- Installing metis-5.1.0_8... [122arm64-quarterly-job-06] | | `-- Extracting metis-5.1.0_8: .......... done [122arm64-quarterly-job-06] | | `-- Installing suitesparse-amd-2.4.6... [122arm64-quarterly-job-06] | | `-- Installing suitesparse-config-5.10.1... [122arm64-quarterly-job-06] | | `-- Extracting suitesparse-config-5.10.1: ......... done [122arm64-quarterly-job-06] | | `-- Extracting suitesparse-amd-2.4.6: .......... done [122arm64-quarterly-job-06] | | `-- Installing suitesparse-camd-2.4.6... [122arm64-quarterly-job-06] | | `-- Extracting suitesparse-camd-2.4.6: ......... done [122arm64-quarterly-job-06] | | `-- Installing suitesparse-ccolamd-2.9.6... [122arm64-quarterly-job-06] | | `-- Extracting suitesparse-ccolamd-2.9.6: ........ done [122arm64-quarterly-job-06] | | `-- Installing suitesparse-cholmod-3.0.14... [122arm64-quarterly-job-06] | | `-- Installing suitesparse-colamd-2.9.6... [122arm64-quarterly-job-06] | | `-- Extracting suitesparse-colamd-2.9.6: ........ done [122arm64-quarterly-job-06] | | `-- Extracting suitesparse-cholmod-3.0.14: .......... done [122arm64-quarterly-job-06] | `-- Extracting suitesparse-umfpack-5.7.9: .......... done [122arm64-quarterly-job-06] `-- Extracting py38-numpy-1.16.6_2,1: .......... done [122arm64-quarterly-job-06] Extracting nlopt-2.7.0: .......... done ===== Message from python38-3.8.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py38-gdbm databases/py-gdbm@py38 py38-sqlite3 databases/py-sqlite3@py38 py38-tkinter x11-toolkits/py-tkinter@py38 ===== Message from metis-5.1.0_8: -- ===> NOTICE: The metis 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 ===> bolt-lmm-2.3.4_4 depends on shared library: libnlopt.so - found (/usr/local/lib/libnlopt.so) ===> Returning to build of bolt-lmm-2.3.4_4 ===> bolt-lmm-2.3.4_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> bolt-lmm-2.3.4_4 depends on shared library: libboost_program_options.so - not found ===> Installing existing package /packages/All/boost-libs-1.72.0_5.pkg [122arm64-quarterly-job-06] Installing boost-libs-1.72.0_5... [122arm64-quarterly-job-06] `-- Installing icu-69.1,1... [122arm64-quarterly-job-06] `-- Extracting icu-69.1,1: .......... done [122arm64-quarterly-job-06] Extracting boost-libs-1.72.0_5: .......... done ===== Message from boost-libs-1.72.0_5: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> bolt-lmm-2.3.4_4 depends on shared library: libboost_program_options.so - found (/usr/local/lib/libboost_program_options.so) ===> Returning to build of bolt-lmm-2.3.4_4 =========================================================================== =======================<phase: configure >============================ ===> Configuring for bolt-lmm-2.3.4_4 =========================================================================== =======================<phase: build >============================ ===> Building for bolt-lmm-2.3.4_4 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bolt-lmm/work/BOLT-LMM_v2.3.4/src' g++10 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -nostdinc++ -isystem /usr/include/c++/v1 -Wl,-rpath=/usr/local/lib/gcc10 -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o BoltMain.o -c BoltMain.cpp g++10 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -nostdinc++ -isystem /usr/include/c++/v1 -Wl,-rpath=/usr/local/lib/gcc10 -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o Bolt.o -c Bolt.cpp In file included from Bolt.cpp:49: MemoryUtils.hpp:34:10: fatal error: xmmintrin.h: No such file or directory 34 | #include <xmmintrin.h> | ^~~~~~~~~~~~~ compilation terminated. In file included from BoltMain.cpp:38: MemoryUtils.hpp:34:10: fatal error: xmmintrin.h: No such file or directory 34 | #include <xmmintrin.h> | ^~~~~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:134: BoltMain.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... gmake[1]: *** [Makefile:134: Bolt.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bolt-lmm/work/BOLT-LMM_v2.3.4/src' ===> 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/bolt-lmm
