Date: Sat, 8 Jun 2019 08:28:23 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-arm64-default][biology/bolt-lmm] Failed for bolt-lmm-2.3.2 in build Message-ID: <201906080828.x588SN8V076566@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/bolt-lmm/Makefile 502673 2019-05-26 03:36:49Z jwb $ Log URL: http://thunderx1.nyi.freebsd.org/data/head-arm64-default/p503433_s348595/logs/bolt-lmm-2.3.2.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p503433_s348595 Log: =>> Building biology/bolt-lmm build started at Sat Jun 8 08:26:47 UTC 2019 port directory: /usr/ports/biology/bolt-lmm package name: bolt-lmm-2.3.2 building for: FreeBSD head-arm64-default-job-04 13.0-CURRENT FreeBSD 13.0-CURRENT 1300030 arm64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/bolt-lmm/Makefile 502673 2019-05-26 03:36:49Z jwb $ Poudriere version: 3.2.8-4-g701d8fe1 Host OSVERSION: 1300002 Jail OSVERSION: 1300030 Job Id: 04 !!! Jail is newer than host. (Jail: 1300030, Host: 1300002) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300030 UNAME_v=FreeBSD 13.0-CURRENT 1300030 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=3.2.8-4-g701d8fe1 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 bolt-lmm-2.3.2: 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 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bolt-lmm/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/bolt-lmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work HOME=/wrkdirs/usr/ports/biology/bolt-lmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bolt-lmm/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="gcc8" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing " CPP="cpp8" CPPFLAGS="" LDFLAGS=" -L/wrkdirs/usr/ports/biology/bolt-lmm/work -fstack-protector- strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 " LIBS="" CXX="g++8" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -nostdinc++ -isystem /usr/include/c++/v1 -Wl,-rpath=/usr/local/lib/gcc8 " 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-- PORTEXAMPLES="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bolt-lmm" EXAMPLESDIR="share/examples/bolt-lmm" DATADIR="share/bolt-lmm" WWWDIR="www/bolt-lmm" ETCDIR="etc/bolt-lmm" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bolt-lmm DOCSDIR=/usr/local/share/doc/bolt-lmm EXAMPLESDIR=/usr/local/share/examples/bolt-lmm WWWDIR=/usr/local/www/bolt-lmm ETCDIR=/usr/local/etc/bolt-lmm --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=1300030 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 >============================ ===> bolt-lmm-2.3.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz [head-arm64-default-job-04] Installing pkg-1.11.1... [head-arm64-default-job-04] Extracting pkg-1.11.1: .......... done ===> bolt-lmm-2.3.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bolt-lmm-2.3.2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user => BOLT-LMM_v2.3.2.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/BOLT-LMM_v2.3.2.tar.gz BOLT-LMM_v2.3.2.tar.gz 319 MB 18 MBps 17s ===> Fetching all distfiles required by bolt-lmm-2.3.2 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bolt-lmm-2.3.2 for building => SHA256 Checksum OK for BOLT-LMM_v2.3.2.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bolt-lmm-2.3.2 for building ===> Extracting for bolt-lmm-2.3.2 => SHA256 Checksum OK for BOLT-LMM_v2.3.2.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bolt-lmm-2.3.2 ===> Applying FreeBSD patches for bolt-lmm-2.3.2 =========================================================================== =======================<phase: build-depends >============================ ===> bolt-lmm-2.3.2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [head-arm64-default-job-04] Installing gmake-4.2.1_3... [head-arm64-default-job-04] `-- Installing gettext-runtime-0.19.8.1_2... [head-arm64-default-job-04] | `-- Installing indexinfo-0.3.1... [head-arm64-default-job-04] | `-- Extracting indexinfo-0.3.1: .... done [head-arm64-default-job-04] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [head-arm64-default-job-04] Extracting gmake-4.2.1_3: .......... done ===> bolt-lmm-2.3.2 depends on executable: gmake - found ===> Returning to build of bolt-lmm-2.3.2 ===> bolt-lmm-2.3.2 depends on executable: gcc8 - not found ===> Installing existing package /packages/All/gcc8-8.3.0_2.txz [head-arm64-default-job-04] Installing gcc8-8.3.0_2... [head-arm64-default-job-04] `-- Installing binutils-2.32_1,1... [head-arm64-default-job-04] `-- Extracting binutils-2.32_1,1: .......... done [head-arm64-default-job-04] `-- Installing gmp-6.1.2_1... [head-arm64-default-job-04] `-- Extracting gmp-6.1.2_1: .......... done [head-arm64-default-job-04] `-- Installing mpc-1.1.0_2... [head-arm64-default-job-04] | `-- Installing mpfr-4.0.2... [head-arm64-default-job-04] | `-- Extracting mpfr-4.0.2: .......... done [head-arm64-default-job-04] `-- Extracting mpc-1.1.0_2: ......... done [head-arm64-default-job-04] Extracting gcc8-8.3.0_2: .......... done Message from gcc8-8.3.0_2: 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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> bolt-lmm-2.3.2 depends on executable: gcc8 - found ===> Returning to build of bolt-lmm-2.3.2 ===> bolt-lmm-2.3.2 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ ===> bolt-lmm-2.3.2 depends on shared library: libnlopt.so - not found ===> Installing existing package /packages/All/nlopt-2.6.1.txz [head-arm64-default-job-04] Installing nlopt-2.6.1... [head-arm64-default-job-04] `-- Installing guile2-2.0.14_10... [head-arm64-default-job-04] | `-- Installing boehm-gc-threaded-8.0.4... [head-arm64-default-job-04] | | `-- Installing boehm-gc-8.0.4... [head-arm64-default-job-04] | | `-- Extracting boehm-gc-8.0.4: .......... done [head-arm64-default-job-04] | `-- Extracting boehm-gc-threaded-8.0.4: .......... done [head-arm64-default-job-04] | `-- Installing libffi-3.2.1_3... [head-arm64-default-job-04] | `-- Extracting libffi-3.2.1_3: .......... done [head-arm64-default-job-04] | `-- Installing libltdl-2.4.6... [head-arm64-default-job-04] | `-- Extracting libltdl-2.4.6: .......... done [head-arm64-default-job-04] | `-- Installing libunistring-0.9.10_1... [head-arm64-default-job-04] | `-- Extracting libunistring-0.9.10_1: .......... done [head-arm64-default-job-04] | `-- Installing readline-8.0.0... [head-arm64-default-job-04] | `-- Extracting readline-8.0.0: .......... done [head-arm64-default-job-04] `-- Extracting guile2-2.0.14_10: .......... done [head-arm64-default-job-04] `-- Installing py36-numpy-1.16.1_2,1... [head-arm64-default-job-04] | `-- Installing blas-3.5.0_5... [head-arm64-default-job-04] | `-- Extracting blas-3.5.0_5: ....... done [head-arm64-default-job-04] | `-- Installing cblas-1.0_11... [head-arm64-default-job-04] | `-- Extracting cblas-1.0_11: ......... done [head-arm64-default-job-04] | `-- Installing lapack-3.5.0_7... [head-arm64-default-job-04] | `-- Extracting lapack-3.5.0_7: .......... done [head-arm64-default-job-04] | `-- Installing py36-setuptools-41.0.0... [head-arm64-default-job-04] | | `-- Installing python36-3.6.8_2... [head-arm64-default-job-04] | | `-- Extracting python36-3.6.8_2: .......... done [head-arm64-default-job-04] | `-- Extracting py36-setuptools-41.0.0: .......... done [head-arm64-default-job-04] | `-- Installing suitesparse-5.2.0_3... [head-arm64-default-job-04] | | `-- Installing metis-5.1.0_7... [head-arm64-default-job-04] | | `-- Extracting metis-5.1.0_7: .......... done [head-arm64-default-job-04] | | `-- Installing openblas-0.2.20_8,1... [head-arm64-default-job-04] | | `-- Extracting openblas-0.2.20_8,1: ......... done [head-arm64-default-job-04] | `-- Extracting suitesparse-5.2.0_3: .......... done [head-arm64-default-job-04] `-- Extracting py36-numpy-1.16.1_2,1: .......... done [head-arm64-default-job-04] Extracting nlopt-2.6.1: .......... done Message from cblas-1.0_11: ===> NOTICE: The cblas port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from python36-3.6.8_2: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Message from metis-5.1.0_7: ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> bolt-lmm-2.3.2 depends on shared library: libnlopt.so - found (/usr/local/lib/libnlopt.so) ===> Returning to build of bolt-lmm-2.3.2 ===> bolt-lmm-2.3.2 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> bolt-lmm-2.3.2 depends on shared library: libboost_program_options.so - not found ===> Installing existing package /packages/All/boost-libs-1.70.0_2.txz [head-arm64-default-job-04] Installing boost-libs-1.70.0_2... [head-arm64-default-job-04] `-- Installing icu-64.2,1... [head-arm64-default-job-04] `-- Extracting icu-64.2,1: .......... done [head-arm64-default-job-04] Extracting boost-libs-1.70.0_2: .......... done Message from boost-libs-1.70.0_2: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> bolt-lmm-2.3.2 depends on shared library: libboost_program_options.so - found (/usr/local/lib/libboost_program_options.so) ===> Returning to build of bolt-lmm-2.3.2 =========================================================================== =======================<phase: configure >============================ ===> Configuring for bolt-lmm-2.3.2 =========================================================================== =======================<phase: build >============================ ===> Building for bolt-lmm-2.3.2 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bolt-lmm/work/BOLT-LMM_v2.3.2/src' g++8 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -nostdinc++ -isystem /usr/include/c++/v1 -Wl,-rpath=/usr/local/lib/gcc8 -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -o BoltMain.o -c BoltMain.cpp In file included from BoltMain.cpp:38: MemoryUtils.hpp:34:10: fatal error: xmmintrin.h: No such file or directory #include <xmmintrin.h> ^~~~~~~~~~~~~ compilation terminated. gmake[1]: *** [Makefile:116: BoltMain.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bolt-lmm/work/BOLT-LMM_v2.3.2/src' *** Error code 1 Stop. make: stopped in /usr/ports/biology/bolt-lmm
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