Date: Fri, 29 Mar 2019 05:40:07 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-arm64-default][biology/bowtie2] Failed for bowtie2-2.3.5 in build Message-ID: <201903290540.x2T5e7ah093093@thunderx1.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 Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/bowtie2/Makefile 496155 2019-03-18 17:30:25Z jwb $ Log URL: http://thunderx1.nyi.freebsd.org/data/head-arm64-default/p496405_s345355/logs/bowtie2-2.3.5.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p496405_s345355 Log: =>> Building biology/bowtie2 build started at Fri Mar 29 05:39:32 UTC 2019 port directory: /usr/ports/biology/bowtie2 package name: bowtie2-2.3.5 building for: FreeBSD head-arm64-default-job-17 13.0-CURRENT FreeBSD 13.0-CURRENT 1300017 arm64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/bowtie2/Makefile 496155 2019-03-18 17:30:25Z jwb $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300002 Jail OSVERSION: 1300017 Job Id: 17 !!! Jail is newer than host. (Jail: 1300017, Host: 1300002) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300017 UNAME_v=FreeBSD 13.0-CURRENT 1300017 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-3-g02cc9753 MASTERMNT=/usr/local/poudriere/data/.m/head-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-arm64-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--- ===> The following configuration options are available for bowtie2-2.3.5: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie2/work HOME=/wrkdirs/usr/ports/biology/bowtie2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bowtie2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie2/work HOME=/wrkdirs/usr/ports/biology/bowtie2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bowtie2/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="cc" CFLAGS="-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd13 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.1 PERL_VER=5.28 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.28 DOCSDIR="share/doc/bowtie2" EXAMPLESDIR="share/examples/bowtie2" DATADIR="share/bowtie2" WWWDIR="www/bowtie2" ETCDIR="etc/bowtie2" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bowtie2 DOCSDIR=/usr/local/share/doc/bowtie2 EXAMPLESDIR=/usr/local/share/examples/bowtie2 WWWDIR=/usr/local/www/bowtie2 ETCDIR=/usr/local/etc/bowtie2 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300017 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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 >============================ ===> bowtie2-2.3.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-arm64-default-job-17] Installing pkg-1.10.5_5... [head-arm64-default-job-17] Extracting pkg-1.10.5_5: .......... done ===> bowtie2-2.3.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bowtie2-2.3.5 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3+ accepted by the user => BenLangmead-bowtie2-v2.3.5_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/BenLangmead/bowtie2/tar.gz/v2.3.5?dummy=/BenLangmead-bowtie2-v2.3.5_GH0.tar.gz fetch: https://codeload.github.com/BenLangmead/bowtie2/tar.gz/v2.3.5?dummy=/BenLangmead-bowtie2-v2.3.5_GH0.tar.gz: size unknown fetch: https://codeload.github.com/BenLangmead/bowtie2/tar.gz/v2.3.5?dummy=/BenLangmead-bowtie2-v2.3.5_GH0.tar.gz: size of remote file is not known BenLangmead-bowtie2-v2.3.5_GH0.tar.gz 10 MB 8048 kBps 02s ===> Fetching all distfiles required by bowtie2-2.3.5 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by bowtie2-2.3.5 for building => SHA256 Checksum OK for BenLangmead-bowtie2-v2.3.5_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by bowtie2-2.3.5 for building ===> Extracting for bowtie2-2.3.5 => SHA256 Checksum OK for BenLangmead-bowtie2-v2.3.5_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bowtie2-2.3.5 ===> Applying FreeBSD patches for bowtie2-2.3.5 =========================================================================== =======================<phase: build-depends >============================ ===> bowtie2-2.3.5 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [head-arm64-default-job-17] Installing gmake-4.2.1_3... [head-arm64-default-job-17] `-- Installing gettext-runtime-0.19.8.1_2... [head-arm64-default-job-17] | `-- Installing indexinfo-0.3.1... [head-arm64-default-job-17] | `-- Extracting indexinfo-0.3.1: .... done [head-arm64-default-job-17] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [head-arm64-default-job-17] Extracting gmake-4.2.1_3: .......... done ===> bowtie2-2.3.5 depends on executable: gmake - found ===> Returning to build of bowtie2-2.3.5 ===> bowtie2-2.3.5 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.16.txz [head-arm64-default-job-17] Installing python27-2.7.16... [head-arm64-default-job-17] `-- Installing libffi-3.2.1_3... [head-arm64-default-job-17] `-- Extracting libffi-3.2.1_3: .......... done [head-arm64-default-job-17] `-- Installing readline-7.0.5... [head-arm64-default-job-17] `-- Extracting readline-7.0.5: .......... done [head-arm64-default-job-17] Extracting python27-2.7.16: .......... done Message from python27-2.7.16: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> bowtie2-2.3.5 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of bowtie2-2.3.5 =========================================================================== =======================<phase: lib-depends >============================ ===> bowtie2-2.3.5 depends on shared library: libtbb.so - not found ===> Installing existing package /packages/All/tbb-2019.1_1.txz [head-arm64-default-job-17] Installing tbb-2019.1_1... [head-arm64-default-job-17] Extracting tbb-2019.1_1: .......... done ===> bowtie2-2.3.5 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) ===> Returning to build of bowtie2-2.3.5 =========================================================================== =======================<phase: configure >============================ ===> Configuring for bowtie2-2.3.5 =========================================================================== =======================<phase: build >============================ ===> Building for bowtie2-2.3.5 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.3.5' usage: dirname string [...] Makefile:219: *** bowtie2 compilation requires a 64-bit platform . Stop. gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bowtie2/work/bowtie2-2.3.5' *** Error code 1 Stop. make: stopped in /usr/ports/biology/bowtie2
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