Date: Sun, 17 Dec 2017 03:18:30 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-mips64-default][biology/kallisto] Failed for kallisto-0.43.1 in build Message-ID: <201712170318.vBH3IUXT068854@beefy13.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/kallisto/Makefile 455382 2017-12-02 20:44:28Z jwb $ Log URL: http://beefy13.nyi.freebsd.org/data/head-mips64-default/p456518_s326914/logs/kallisto-0.43.1.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=head-mips64-default&build=p456518_s326914 Log: =>> Building biology/kallisto build started at Sun Dec 17 03:17:49 UTC 2017 port directory: /usr/ports/biology/kallisto package name: kallisto-0.43.1 building for: FreeBSD head-mips64-default-job-10 12.0-CURRENT FreeBSD 12.0-CURRENT 1200054 mips maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/kallisto/Makefile 455382 2017-12-02 20:44:28Z jwb $ Poudriere version: 3.2.3-16-g77e43413 Host OSVERSION: 1200052 Jail OSVERSION: 1200054 Job Id: 10 !!! Jail is newer than host. (Jail: 1200054, Host: 1200052) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=mips64 UNAME_m=mips ABI_FILE=/usr/lib/crt1.o OSVERSION=1200054 UNAME_v=FreeBSD 12.0-CURRENT 1200054 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-mips64-default/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk OLDPWD=/usr/local/poudriere/data/.m/head-mips64-default/ref/.p P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS PWD=/usr/local/poudriere/data/.m/head-mips64-default/ref/.p/pool MASTERNAME=head-mips64-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root P_PYTHON_MAJOR_VER=2 POUDRIERE_VERSION=3.2.3-16-g77e43413 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local 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 kallisto-0.43.1: 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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/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/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/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 DESTDIR=/wrkdirs/usr/ports/biology/kallisto/work/stage PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -EB -mabi=64 -msoft-float -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -EB -mabi=64" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -EB -mabi=64 -msoft-float -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-- CMAKE_BUILD_TYPE="release" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/kallisto" EXAMPLESDIR="share/examples/kallisto" DATADIR="share/kallisto" WWWDIR="www/kallisto" ETCDIR="etc/kallisto" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/kallisto DOCSDIR=/usr/local/share/doc/kallisto EXAMPLESDIR=/usr/local/share/examples/kallisto WWWDIR=/usr/local/www/kallisto ETCDIR=/usr/local/etc/kallisto --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=mips MACHINE_ARCH=mips64 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 #### ARCH=mips64 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=12.0 OSVERSION=1200054 PYTHONBASE=/usr/local UID=0 _OSRELEASE=12.0-CURRENT #### Misc Poudriere #### GID=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++ AS=/nxb-bin/usr/bin/as 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) 131072 stack size (kbytes, -s) 8192 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 BSD2CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> kallisto-0.43.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.3_1.txz [head-mips64-default-job-10] Installing pkg-1.10.3_1... [head-mips64-default-job-10] Extracting pkg-1.10.3_1: .......... done ===> kallisto-0.43.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of kallisto-0.43.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.43.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.43.1 for building => SHA256 Checksum OK for pachterlab-kallisto-v0.43.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.43.1 for building ===> Extracting for kallisto-0.43.1 => SHA256 Checksum OK for pachterlab-kallisto-v0.43.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for kallisto-0.43.1 =========================================================================== =======================<phase: build-depends >============================ ===> kallisto-0.43.1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.9.6.txz [head-mips64-default-job-10] Installing cmake-3.9.6... [head-mips64-default-job-10] `-- Installing curl-7.57.0... [head-mips64-default-job-10] | `-- Installing ca_root_nss-3.34.1... [head-mips64-default-job-10] | `-- Extracting ca_root_nss-3.34.1: ........ done [head-mips64-default-job-10] | `-- Installing libnghttp2-1.28.0... [head-mips64-default-job-10] | `-- Extracting libnghttp2-1.28.0: .......... done [head-mips64-default-job-10] `-- Extracting curl-7.57.0: .......... done [head-mips64-default-job-10] `-- Installing expat-2.2.1... [head-mips64-default-job-10] `-- Extracting expat-2.2.1: .......... done [head-mips64-default-job-10] `-- Installing jsoncpp-1.8.1_2... [head-mips64-default-job-10] `-- Extracting jsoncpp-1.8.1_2: .......... done [head-mips64-default-job-10] `-- Installing libarchive-3.3.2,1... [head-mips64-default-job-10] | `-- Installing liblz4-1.8.0,1... [head-mips64-default-job-10] | `-- Extracting liblz4-1.8.0,1: .......... done [head-mips64-default-job-10] | `-- Installing lzo2-2.10_1... [head-mips64-default-job-10] | `-- Extracting lzo2-2.10_1: .......... done [head-mips64-default-job-10] `-- Extracting libarchive-3.3.2,1: .......... done [head-mips64-default-job-10] `-- Installing libuv-1.18.0... [head-mips64-default-job-10] `-- Extracting libuv-1.18.0: .......... done [head-mips64-default-job-10] `-- Installing rhash-1.3.5... [head-mips64-default-job-10] `-- Extracting rhash-1.3.5: .......... done [head-mips64-default-job-10] Extracting cmake-3.9.6: .......... done Message from ca_root_nss-3.34.1: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> kallisto-0.43.1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of kallisto-0.43.1 ===> kallisto-0.43.1 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.8.2,2.txz [head-mips64-default-job-10] Installing ninja-1.8.2,2... [head-mips64-default-job-10] `-- Installing python27-2.7.14_1... [head-mips64-default-job-10] | `-- Installing gettext-runtime-0.19.8.1_1... [head-mips64-default-job-10] | | `-- Installing indexinfo-0.3.1... [head-mips64-default-job-10] | | `-- Extracting indexinfo-0.3.1: .... done [head-mips64-default-job-10] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-mips64-default-job-10] | `-- Installing libffi-3.2.1_1... [head-mips64-default-job-10] | `-- Extracting libffi-3.2.1_1: .......... done [head-mips64-default-job-10] | `-- Installing readline-7.0.3_1... [head-mips64-default-job-10] | `-- Extracting readline-7.0.3_1: .......... done [head-mips64-default-job-10] `-- Extracting python27-2.7.14_1: .......... done [head-mips64-default-job-10] Extracting ninja-1.8.2,2: ....... done Message from python27-2.7.14_1: =========================================================================== 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 =========================================================================== ===> kallisto-0.43.1 depends on executable: ninja - found ===> Returning to build of kallisto-0.43.1 =========================================================================== =======================<phase: lib-depends >============================ ===> kallisto-0.43.1 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.10.1_1.txz [head-mips64-default-job-10] Installing hdf5-1.10.1_1... [head-mips64-default-job-10] `-- Installing hdf-szip-2.1_2... [head-mips64-default-job-10] `-- Extracting hdf-szip-2.1_2: ........ done [head-mips64-default-job-10] Extracting hdf5-1.10.1_1: .......... done ===> kallisto-0.43.1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of kallisto-0.43.1 ===> kallisto-0.43.1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) =========================================================================== =======================<phase: configure >============================ ===> Configuring for kallisto-0.43.1 ===> Performing in-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.43.1 -- The C compiler identification is GNU 4.2.1 -- The CXX compiler identification is GNU 4.2.1 -- Check for working C compiler: /nxb-bin/usr/bin/cc -- Check for working C compiler: /nxb-bin/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libm.so (found version "1.10.1") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE -- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.43.1 =========================================================================== =======================<phase: build >============================ ===> Building for kallisto-0.43.1 [1/17] /nxb-bin/usr/bin/c++ -Isrc/../ext -Isrc -I/usr/local/include -O2 -pipe -G0 -EB -mabi=64 -msoft-float -fno-strict-aliasing -O2 -pipe -G0 -EB -mabi=64 -msoft-float -fno-strict-aliasing -std=c++11 -O3 -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c src/Bootstrap.cpp FAILED: src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o /nxb-bin/usr/bin/c++ -Isrc/../ext -Isrc -I/usr/local/include -O2 -pipe -G0 -EB -mabi=64 -msoft-float -fno-strict-aliasing -O2 -pipe -G0 -EB -mabi=64 -msoft-float -fno-strict-aliasing -std=c++11 -O3 -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c src/Bootstrap.cpp cc1plus: error: unrecognized command line option "-std=c++11" ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/kallisto
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