Date: Fri, 29 Jan 2021 21:52:24 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 13stable-armv6-quarterly][biology/pooler] Failed for pooler-1.75 in build Message-ID: <202101292152.10TLqOv6070922@beefy8.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: ssb22@cam.ac.uk Last committer: jwb@FreeBSD.org Ident: $FreeBSD: branches/2021Q1/biology/pooler/Makefile 555418 2020-11-15 18:50:17Z jwb $ Log URL: http://beefy8.nyi.freebsd.org/data/13stable-armv6-quarterly/562611/logs/pooler-1.75.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=13stable-armv6-quarterly&build=562611 Log: =>> Building biology/pooler build started at Fri Jan 29 21:51:52 UTC 2021 port directory: /usr/ports/biology/pooler package name: pooler-1.75 building for: FreeBSD 13stable-armv6-quarterly-job-13 13.0-ALPHA2 FreeBSD 13.0-ALPHA2 1300136 arm maintained by: ssb22@cam.ac.uk Makefile ident: $FreeBSD: branches/2021Q1/biology/pooler/Makefile 555418 2020-11-15 18:50:17Z jwb $ Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1300121 Jail OSVERSION: 1300136 Job Id: 13 !!! Jail is newer than host. (Jail: 1300136, Host: 1300121) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300136 UNAME_v=FreeBSD 13.0-ALPHA2 1300136 UNAME_r=13.0-ALPHA2 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=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/13stable-armv6-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/13stable-armv6-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=13stable-armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/13stable-armv6-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--- ---End OPTIONS List--- --MAINTAINER-- ssb22@cam.ac.uk --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pooler/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pooler/work HOME=/wrkdirs/usr/ports/biology/pooler/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pooler/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/pooler/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pooler/work HOME=/wrkdirs/usr/ports/biology/pooler/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pooler/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="gcc9" CFLAGS="-O2 -pipe -fopenmp -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing " CPP="cpp9" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -L/u sr/local/lib/gcc9 " LIBS="" CXX="g++9" CXXFLAGS="-O2 -pipe -fopenmp -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 " 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=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pooler" EXAMPLESDIR="share/examples/pooler" DATADIR="share/pooler" WWWDIR="www/pooler" ETCDIR="etc/pooler" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pooler DOCSDIR=/usr/local/share/doc/pooler EXAMPLESDIR=/usr/local/share/examples/pooler WWWDIR=/usr/local/www/pooler ETCDIR=/usr/local/etc/pooler --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=armv6 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 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv6-unknown-freebsd13.0-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 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=13.0-ALPHA2 OSREL=13.0 OSVERSION=1300136 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 APACHE20 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> pooler-1.75 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.1.txz [13stable-armv6-quarterly-job-13] Installing pkg-1.16.1... [13stable-armv6-quarterly-job-13] Extracting pkg-1.16.1: .......... done ===> pooler-1.75 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pooler-1.75 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License APACHE20 accepted by the user => ssb22-PrimerPooler-v1.75_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/ssb22/PrimerPooler/tar.gz/v1.75?dummy=/ssb22-PrimerPooler-v1.75_GH0.tar.gz fetch: https://codeload.github.com/ssb22/PrimerPooler/tar.gz/v1.75?dummy=/ssb22-PrimerPooler-v1.75_GH0.tar.gz: size unknown fetch: https://codeload.github.com/ssb22/PrimerPooler/tar.gz/v1.75?dummy=/ssb22-PrimerPooler-v1.75_GH0.tar.gz: size of remote file is not known ssb22-PrimerPooler-v1.75_GH0.tar.gz 123 kB 6336 kBps 00s ===> Fetching all distfiles required by pooler-1.75 for building =========================================================================== =======================<phase: checksum >============================ ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by pooler-1.75 for building => SHA256 Checksum OK for ssb22-PrimerPooler-v1.75_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by pooler-1.75 for building ===> Extracting for pooler-1.75 => SHA256 Checksum OK for ssb22-PrimerPooler-v1.75_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for pooler-1.75 =========================================================================== =======================<phase: build-depends >============================ ===> pooler-1.75 depends on executable: gcc9 - not found ===> Installing existing package /packages/All/gcc9-9.3.0_1.txz [13stable-armv6-quarterly-job-13] Installing gcc9-9.3.0_1... [13stable-armv6-quarterly-job-13] `-- Installing binutils-2.33.1_4,1... [13stable-armv6-quarterly-job-13] | `-- Installing gettext-runtime-0.21... [13stable-armv6-quarterly-job-13] | | `-- Installing indexinfo-0.3.1... [13stable-armv6-quarterly-job-13] | | `-- Extracting indexinfo-0.3.1: .... done [13stable-armv6-quarterly-job-13] | `-- Extracting gettext-runtime-0.21: .......... done [13stable-armv6-quarterly-job-13] `-- Extracting binutils-2.33.1_4,1: .......... done [13stable-armv6-quarterly-job-13] `-- Installing gmp-6.2.1... [13stable-armv6-quarterly-job-13] `-- Extracting gmp-6.2.1: .......... done [13stable-armv6-quarterly-job-13] `-- Installing mpc-1.1.0_2... [13stable-armv6-quarterly-job-13] | `-- Installing mpfr-4.1.0... [13stable-armv6-quarterly-job-13] | `-- Extracting mpfr-4.1.0: .......... done [13stable-armv6-quarterly-job-13] `-- Extracting mpc-1.1.0_2: ......... done [13stable-armv6-quarterly-job-13] Extracting gcc9-9.3.0_1: .......... done ===== Message from gcc9-9.3.0_1: -- 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/gcc9 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> pooler-1.75 depends on executable: gcc9 - found ===> Returning to build of pooler-1.75 ===> pooler-1.75 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for pooler-1.75 =========================================================================== =======================<phase: build >============================ ===> Building for pooler-1.75 chmod +w 128.h 32.h 32-64.h 2>/dev/null || true sed -e s/64/128/g < 64.h > 128.h sed -e s/64/32/g < 64.h > 32.h sed -e s/64/32/g -e s/128/64/g < 64-128.h > 32-64.h chmod -w 128.h 32.h 32-64.h /nxb-bin/usr/bin/cc -O2 -pipe -fopenmp -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing *.c -o pooler -lm In file included from bit-common.c:63: In file included from ./bit-choice.h:23: In file included from ./triangle.h:44: ./openmp.h:19:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from genome.c:28: ./openmp.h:19:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. In file included from pool-split.c:25: ./openmp.h:19:10: fatal error: 'omp.h' file not found #include <omp.h> ^~~~~~~ 1 error generated. *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/pooler/work/PrimerPooler-1.75/pooler *** Error code 1 Stop. make: stopped in /usr/ports/biology/pooler
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