[package - main-armv6-default][biology/smithwaterman] Failed for smithwaterman-g20160702 in build
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Date: Tue, 25 Jul 2023 06:07:54 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: jwb@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy8/data/main-armv6-default/p629834653cee_s789df254cc/logs/smithwaterman-g20160702.log Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=p629834653cee_s789df254cc Log: =>> Building biology/smithwaterman build started at Tue Jul 25 06:07:26 UTC 2023 port directory: /usr/ports/biology/smithwaterman package name: smithwaterman-g20160702 building for: FreeBSD main-armv6-default-job-03 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400088 Jail OSVERSION: 1400093 Job Id: 03 !!! Jail is newer than host. (Jail: 1400093, Host: 1400088) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1400093 UNAME_v=FreeBSD 14.0-CURRENT 1400093 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=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-armv6-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-armv6-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/smithwaterman/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work/.cache HOME=/wrkdirs/usr/ports/biology/smithwaterman/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/smithwaterman/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/smithwaterman/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/smithwaterman/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work/.cache HOME=/wrkdirs/usr/ports/biology/smithwaterman/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/smithwaterman/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/smithwaterman/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="/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/smithwaterman" EXAMPLESDIR="share/examples/smithwaterman" DATADIR="share/smithwaterman" WWWDIR="www/smithwaterman" ETCDIR="etc/smithwaterman" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/smithwaterman DOCSDIR=/usr/local/share/doc/smithwaterman EXAMPLESDIR=/usr/local/share/examples/smithwaterman WWWDIR=/usr/local/www/smithwaterman ETCDIR=/usr/local/etc/smithwaterman --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 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-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_53255a77=yes CC_OUTPUT_9d218390_911cfe02=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes CC_OUTPUT_9d218390_af59ad06=yes CC_OUTPUT_9d218390_a15f3fcf=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400093 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 GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> smithwaterman-g20160702 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [main-armv6-default-job-03] Installing pkg-1.20.4... [main-armv6-default-job-03] Extracting pkg-1.20.4: .......... done ===> smithwaterman-g20160702 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of smithwaterman-g20160702 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by smithwaterman-g20160702 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by smithwaterman-g20160702 for building => SHA256 Checksum OK for ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by smithwaterman-g20160702 for building ===> Extracting for smithwaterman-g20160702 => SHA256 Checksum OK for ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for smithwaterman-g20160702 =========================================================================== =======================<phase: build-depends >============================ ===> smithwaterman-g20160702 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-armv6-default-job-03] Installing gmake-4.3_2... [main-armv6-default-job-03] `-- Installing gettext-runtime-0.22_1... [main-armv6-default-job-03] | `-- Installing indexinfo-0.3.1... [main-armv6-default-job-03] | `-- Extracting indexinfo-0.3.1: .... done [main-armv6-default-job-03] `-- Extracting gettext-runtime-0.22_1: .......... done [main-armv6-default-job-03] Extracting gmake-4.3_2: .......... done ===> smithwaterman-g20160702 depends on package: gmake>=4.3 - found ===> Returning to build of smithwaterman-g20160702 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for smithwaterman-g20160702 =========================================================================== =======================<phase: build >============================ ===> Building for smithwaterman-g20160702 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/smithwaterman/work/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7' /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o disorder.o disorder.cpp -I. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o smithwaterman.o smithwaterman.cpp -I. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o Repeats.o Repeats.cpp -I. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o LeftAlign.o LeftAlign.cpp -I. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o IndelAllele.o IndelAllele.cpp -I. /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o disorder.o -I. -o smithwaterman ar rs libsw.a disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o ar: warning: creating libsw.a /nxb-bin/usr/bin/c++ -shared -Wl,-soname,libsw.so.1 -o libsw.so.1 disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o ld -r disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -o sw.o -L. gmake[1]: *** [/usr/ports/biology/smithwaterman/files/Makefile:54: sw.o] Abort trap (core dumped) gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/smithwaterman/work/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7' *** Error code 1 Stop. make: stopped in /usr/ports/biology/smithwaterman