Date: Fri, 10 Sep 2021 02:19:32 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - main-armv7-default][biology/star] Failed for rna-STAR-2.7.3.a_1 in build Message-ID: <202109100219.18A2JWQb072759@beefy12.nyi.freebsd.org>
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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: jwb@FreeBSD.org Log URL: http://beefy12.nyi.freebsd.org/data/main-armv7-default/pfda1da2d7917_s9939af1a16/logs/rna-STAR-2.7.3.a_1.log Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=pfda1da2d7917_s9939af1a16 Log: =>> Building biology/star build started at Fri Sep 10 02:18:48 UTC 2021 port directory: /usr/ports/biology/star package name: rna-STAR-2.7.3.a_1 building for: FreeBSD main-armv7-default-job-08 14.0-CURRENT FreeBSD 14.0-CURRENT 1400032 arm maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400003 Jail OSVERSION: 1400032 Job Id: 08 !!! Jail is newer than host. (Jail: 1400032, Host: 1400003) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1400032 UNAME_v=FreeBSD 14.0-CURRENT 1400032 UNAME_r=14.0-CURRENT 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 LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/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--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/star/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/star/work HOME=/wrkdirs/usr/ports/biology/star/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/star/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/star/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/star/work HOME=/wrkdirs/usr/ports/biology/star/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/star/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/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-- OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/STAR" EXAMPLESDIR="share/examples/STAR" DATADIR="share/STAR" WWWDIR="www/STAR" ETCDIR="etc/STAR" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/STAR DOCSDIR=/usr/local/share/doc/STAR EXAMPLESDIR=/usr/local/share/examples/STAR WWWDIR=/usr/local/www/STAR ETCDIR=/usr/local/etc/STAR --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 ARCH=${MACHINE_ARCH} #### /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_9d218390=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: armv7-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: armv7-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: armv7-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400032 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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) 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 >============================ ===> rna-STAR-2.7.3.a_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.1.pkg [main-armv7-default-job-08] Installing pkg-1.17.1... [main-armv7-default-job-08] Extracting pkg-1.17.1: .......... done ===> rna-STAR-2.7.3.a_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rna-STAR-2.7.3.a_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by rna-STAR-2.7.3.a_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by rna-STAR-2.7.3.a_1 for building <snip> In file included from ./Transcriptome.h:6: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from Transcriptome_geneCountsAddAlign.cpp:1: In file included from ./Transcriptome.h:6: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from Transcriptome_geneFullAlignOverlap.cpp:1: In file included from ./Transcriptome.h:6: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from Transcriptome_quantAlign.cpp:1: In file included from ./Transcriptome.h:6: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from Variation.cpp:1: In file included from ./Variation.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from alignSmithWaterman.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from bamRemoveDuplicates.cpp:2: In file included from ./bamRemoveDuplicates.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from bamSortByCoordinate.cpp:1: In file included from ./bamSortByCoordinate.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from binarySearch2.cpp:1: In file included from ./binarySearch2.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from blocksOverlap.cpp:1: In file included from ./blocksOverlap.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from extendAlign.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from genomeParametersWrite.cpp:1: In file included from ./genomeParametersWrite.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from genomeSAindex.cpp:1: In file included from ./genomeSAindex.h:3: In file included from ./PackedArray.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from genomeScanFastaFiles.cpp:1: In file included from ./genomeScanFastaFiles.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from insertSeqSA.cpp:5: In file included from ./insertSeqSA.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from loadGTF.cpp:1: In file included from ./loadGTF.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from mapThreadsSpawn.cpp:1: In file included from ./mapThreadsSpawn.h:3: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from outputSJ.cpp:1: In file included from ./ReadAlignChunk.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from readLoad.cpp:1: In file included from ./readLoad.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from serviceFuns.cpp:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from signalFromBAM.cpp:1: In file included from ./signalFromBAM.h:6: In file included from ./Stats.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from sjAlignSplit.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from sjdbBuildIndex.cpp:1: In file included from ./sjdbBuildIndex.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from sjdbInsertJunctions.cpp:1: In file included from ./sjdbInsertJunctions.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from sjdbLoadFromFiles.cpp:1: In file included from ./sjdbLoadFromFiles.h:5: In file included from ./SjdbClass.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from sjdbLoadFromStream.cpp:1: In file included from ./sjdbLoadFromStream.h:5: In file included from ./SjdbClass.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from sjdbPrepare.cpp:1: In file included from ./sjdbPrepare.h:4: In file included from ./SjdbClass.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from stitchAlignToTranscript.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from stitchGapIndel.cpp:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from stitchWindowAligns.cpp:1: In file included from ./stitchWindowAligns.h:1: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from streamFuns.cpp:1: In file included from ./streamFuns.h:4: In file included from ./Parameters.h:4: ./IncludeDefine.h:24:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. Makefile:104: Depend.list: No such file or directory gmake[1]: *** [Makefile:103: Depend.list] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source' *** Error code 1 Stop. make: stopped in /usr/ports/biology/star
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