From nobody Thu Oct 05 09:49:37 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4S1Rc20wJNz4w6Kw for ; Thu, 5 Oct 2023 09:49:38 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4S1Rc164ydz3KNf for ; Thu, 5 Oct 2023 09:49:37 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1696499377; a=rsa-sha256; cv=none; b=lt3D6nnMV3DiUU6X39hYTQ19S3oLXyBolHslWv/Vvi84t1uOVM48RVBLoK9gSnq7x0QIs/ GBP1PhgOgx5TVl5j0DFCdF+1tkm2UFpuCSjSANq7apx1ollleDWrTdPNyr4e8ZMWdan/lv VCk0dPjq0fs/9j+rne3g8SLi0KyGWTanNB3nkiWc9qkQxrXuJDkhuaRcFsMVVhLZGhox7d d6Qg0HvGX70WdpIKkjZ4mM4LgIh96bNo5SndThY749GNCCyncBNQoK/p3tDFTbn0Yk6b7p ks1a+iwbyxwZgRO6PR/Ocv+b2G7qFQYjWt0eqoG99xsTyLUGq2wytapmZd+Rzg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1696499377; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=2caiaQbp7JeFZD3vWJ1VQCjnBU/LqcXgh2wlmz9oNlc=; b=DlZIMT+/E/8x8WukB++2XT0X7Vw2HZkylr7Y2tAjtHYrqKhhTRCuxW+0jn/dBLBuKjCFKa 63iiX7bu+gRy7jYjVwigbPgwIW9ckNIHbycyyvneeFlwQUYGGbF0ywRslulLDmEzV8tkUZ BLzMR1lYqLEqJRA+hpAyRWFf2/9uNNn5yDnTYtFJdDjo2Lp2HgTAm73HGqWtaj3urD7EFi B1evsBEdKv2WE4WvUJdhksBYAeu3NeGVQA2tgQD0y6boI3k44Q9+OIGI4wzHV7Jsa7A4d8 osWTRiR1v1vxrCvIh0KMXHRxz01SewNVGQ/YguCINtoAX0Btusmtg8IZ3mfDXQ== Received: from beefy8.nyi.freebsd.org (beefy8.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:17]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4S1Rc158Xxz1FlD for ; Thu, 5 Oct 2023 09:49:37 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 635f by beefy8.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy8.nyi.freebsd.org); Thu, 05 Oct 2023 09:49:37 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - 132releng-armv6-quarterly][biology/smithwaterman] Failed for smithwaterman-g20160702 in build Date: Thu, 05 Oct 2023 09:49:37 +0000 Message-Id: <651e86b1.635f.65698a06@beefy8.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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/132releng-armv6-quarterly/46c5200e9027/logs/smithwaterman-g20160702.log Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=132releng-armv6-quarterly&build=46c5200e9027 Log: =>> Building biology/smithwaterman build started at Thu Oct 5 09:49:17 UTC 2023 port directory: /usr/ports/biology/smithwaterman package name: smithwaterman-g20160702 building for: FreeBSD 132releng-armv6-quarterly-job-07 13.2-RELEASE-p4 FreeBSD 13.2-RELEASE-p4 1302001 arm maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1500000 Jail OSVERSION: 1302001 Job Id: 07 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p4 1302001 UNAME_r=13.2-RELEASE-p4 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/132releng-armv6-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/132releng-armv6-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=132releng-armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/132releng-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-- 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=13.2 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=3 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd13.2-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd13.2-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 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd13.2-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=13.2-RELEASE-p4 OSREL=13.2 OSVERSION=1302001 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-- =================================================== ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> smithwaterman-g20160702 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.7.pkg [132releng-armv6-quarterly-job-07] Installing pkg-1.20.7... [132releng-armv6-quarterly-job-07] Extracting pkg-1.20.7: .......... done ===> smithwaterman-g20160702 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of smithwaterman-g20160702 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by smithwaterman-g20160702 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for smithwaterman-g20160702 =========================================================================== =================================================== ===> smithwaterman-g20160702 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [132releng-armv6-quarterly-job-07] Installing gmake-4.3_2... [132releng-armv6-quarterly-job-07] `-- Installing gettext-runtime-0.22_1... [132releng-armv6-quarterly-job-07] | `-- Installing indexinfo-0.3.1... [132releng-armv6-quarterly-job-07] | `-- Extracting indexinfo-0.3.1: .... done [132releng-armv6-quarterly-job-07] `-- Extracting gettext-runtime-0.22_1: .......... done [132releng-armv6-quarterly-job-07] Extracting gmake-4.3_2: .......... done ===> smithwaterman-g20160702 depends on package: gmake>=4.3 - found ===> Returning to build of smithwaterman-g20160702 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for smithwaterman-g20160702 =========================================================================== =================================================== ===> 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. qemu: uncaught target signal 6 (Abort trap) - core dumped gmake[1]: *** [/usr/ports/biology/smithwaterman/files/Makefile:54: sw.o] Abort trap gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/smithwaterman/work/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7' *** Error code 1 Stop. make: stopped in /usr/ports/biology/smithwaterman