From nobody Thu May 04 05:12:15 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 4QBhl36PvHz49gGQ for ; Thu, 4 May 2023 05:12:15 +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 4QBhl341nTz3kBH for ; Thu, 4 May 2023 05:12:15 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1683177135; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=sMipJRGn3Xw/XpJqGeZOld8Wvk5cxS1zMs0wLTAWqP8=; b=x8AJbfokCRiqvOv9ory5do1k75Lgo9btG9dJum9WBeFGFSdY+UkMU4C4fiUsu+Lk7TBYuI aFga1k2obGYZaqvWMD7KQwpw888+zmrOD2VxV/+HKEGNUYhGJ2mFQf6hp1Xnr7RuMVCrZs MUS0ZMJy82J9kgXSuHoiej6Lhyk+wbXXYcxIeQozAMVmjjVfG7zIxxv08gwY1MI4ZXBI9i X1hV7/LUL/kaHMey0VcbIbLsvTYmtaNxNH1eEyYl0Fan8efBWjW+5GLPpIwWpSX/vu0z6W hJamFiwMZGN1TEMSkmcsBHhNtN50uv3tdSnJi1j9zhNNUuYepPz7zY39XJLmOg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1683177135; a=rsa-sha256; cv=none; b=UPk1fa7f1n1iwzwLvwztSJduSRwLxV378F8UFHzRIvm/P9oKeGRCg6xv9tiHGla3SwTd8c SnNvnaEMGae+gU3mIk3Lg/dPSuh40sjlKBaiTfhYb49/3Odf1gZ71P8+ELK9Down4Vuamd 8ivgtlRHROoykFvVB/vnTFEkhMuJRc6DP44ohbecQzBGnvAb5m4wEU9TSKwz4TE/qZoyiK KRyNTABhp7Pna2CqHrZ5oPZKJIH6TV/L7b8sXVfM/E9a3mYCiu2GCGBiTO6r+0iRk1p3mW rxvDi9k0qb11wGD/ZXaPKUL19Xa8pTE6ms3lQwegt8xyPkGFVmELiwh1vIbJHQ== 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 4QBhl33689zybl for ; Thu, 4 May 2023 05:12:15 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 13d43 by beefy8.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy8.nyi.freebsd.org); Thu, 04 May 2023 05:12:15 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - main-armv6-default][biology/bamutil] Failed for bamutil-1.0.15 in build Date: Thu, 04 May 2023 05:12:15 +0000 Message-Id: <64533eaf.13d43.10d83c6@beefy8.nyi.freebsd.org> From: X-ThisMailContainsUnwantedMimeParts: N 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/main-armv6-default/p54373d87b552_s4194bbb34c/logs/bamutil-1.0.15.log Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=p54373d87b552_s4194bbb34c Log: =>> Building biology/bamutil build started at Thu May 4 05:12:01 UTC 2023 port directory: /usr/ports/biology/bamutil package name: bamutil-1.0.15 building for: FreeBSD main-armv6-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400088 arm maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400078 Jail OSVERSION: 1400088 Job Id: 05 !!! Jail is newer than host. (Jail: 1400088, Host: 1400078) !!! !!! 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=1400088 UNAME_v=FreeBSD 14.0-CURRENT 1400088 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/bamutil/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bamutil/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bamutil/work/.cache HOME=/wrkdirs/usr/ports/biology/bamutil/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bamutil/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bamutil/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-- LIB_PATH_GENERAL=/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen INSTALLDIR=/wrkdirs/usr/ports/biology/bamutil/work/stage/usr/local/bin XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bamutil/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bamutil/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bamutil/work/.cache HOME=/wrkdirs/usr/ports/biology/bamutil/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bamutil/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bamutil/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/bamutil" EXAMPLESDIR="share/examples/bamutil" DATADIR="share/bamutil" WWWDIR="www/bamutil" ETCDIR="etc/bamutil" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bamutil DOCSDIR=/usr/local/share/doc/bamutil EXAMPLESDIR=/usr/local/share/examples/bamutil WWWDIR=/usr/local/www/bamutil ETCDIR=/usr/local/etc/bamutil --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 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) 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 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) 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=1400088 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 GPLv3 accepted by the user =========================================================================== =================================================== ===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-armv6-default-job-05] Installing pkg-1.19.1_1... [main-armv6-default-job-05] Extracting pkg-1.19.1_1: .......... done ===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bamutil-1.0.15 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bamutil-1.0.15 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bamutil-1.0.15 for building => SHA256 Checksum OK for statgen-bamUtil-v1.0.15_GH0.tar.gz. => SHA256 Checksum OK for statgen-libStatGen-v1.0.15_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bamutil-1.0.15 for building ===> Extracting for bamutil-1.0.15 => SHA256 Checksum OK for statgen-bamUtil-v1.0.15_GH0.tar.gz. => SHA256 Checksum OK for statgen-libStatGen-v1.0.15_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bamutil-1.0.15 ===> Applying FreeBSD patches for bamutil-1.0.15 from /usr/ports/biology/bamutil/files =========================================================================== =================================================== ===> bamutil-1.0.15 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-armv6-default-job-05] Installing gmake-4.3_2... [main-armv6-default-job-05] `-- Installing gettext-runtime-0.21.1... [main-armv6-default-job-05] | `-- Installing indexinfo-0.3.1... [main-armv6-default-job-05] | `-- Extracting indexinfo-0.3.1: .... done [main-armv6-default-job-05] `-- Extracting gettext-runtime-0.21.1: .......... done [main-armv6-default-job-05] Extracting gmake-4.3_2: .......... done ===> bamutil-1.0.15 depends on package: gmake>=4.3 - found ===> Returning to build of bamutil-1.0.15 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for bamutil-1.0.15 =========================================================================== =================================================== ===> Building for bamutil-1.0.15 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src' gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory opt ln -s ../samtools/bgzf.h ../include/bgzf.h ln -s ../samtools/knetfile.h ../include/knetfile.h ln -s ../samtools/khash.h ../include/khash.h ln -s ../samtools/bam.h ../include/bam.h mkdir -p obj cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. Stack dump: 0. Program arguments: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -strict-aliasing -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o bgzf.c 1. parser at end of file 2. Code generation #0 0x04745d04 0x4745d04 0x4743ba0 #1 0x04745d04 0x46ed2dc 0x46ed49c #2 0x04745d04 (+0x4745d04) Stack dump without symbol names (ensure you have llvm-symbolizer in your PATH or set the environment var `LLVM_SYMBOLIZER_PATH` to point to it): 0 cc 0x04745d04 std::__1::enable_if<__is_cpp17_forward_iterator::value, std::__1::basic_string, std::__1::allocator>&>::type std::__1::basic_string, std::__1::allocator>::append[abi:v15007](char const*, char const*) + 2574684 1 cc 0x04743ba0 std::__1::enable_if<__is_cpp17_forward_iterator::value, std::__1::basic_string, std::__1::allocator>&>::type std::__1::basic_string, std::__1::allocator>::append[abi:v15007](char const*, char const*) + 2566136 2 cc 0x046ed2dc std::__1::enable_if<__is_cpp17_forward_iterator::value, std::__1::basic_string, std::__1::allocator>&>::type std::__1::basic_string, std::__1::allocator>::append[abi:v15007](char const*, char const*) + 2211636 3 cc 0x046ed49c std::__1::enable_if<__is_cpp17_forward_iterator::value, std::__1::basic_string, std::__1::allocator>&>::type std::__1::basic_string, std::__1::allocator>::append[abi:v15007](char const*, char const*) + 2212084 4 libthr.so.3 0xf4e6f4ec pthread_sigmask + 1448 cc: error: clang frontend command failed with exit code 139 (use -v to see invocation) qemu: uncaught target signal 4 (Illegal instruction) - core dumped gmake[4]: *** [../Makefiles/Makefile.common:74: obj/bgzf.o] Illegal instruction gmake[3]: *** [Makefiles/Makefile.base:15: samtools] Error 2 gmake[2]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.ext:50: /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen.a] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src' gmake[1]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.base:15: src] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15' *** Error code 1 Stop. make: stopped in /usr/ports/biology/bamutil