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Maintainer: h2+fbsdpo...@fsfe.org Last committer: ger...@freebsd.org Ident: $FreeBSD: head/biology/seqan-apps/Makefile 427129 2016-11-25 21:27:37Z gerald $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p428262_s309780/logs/seqan-apps-2.2.0_1.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p428262_s309780 Log: ====>> Building biology/seqan-apps build started at Tue Dec 13 12:46:02 UTC 2016 port directory: /usr/ports/biology/seqan-apps building for: FreeBSD head-armv6-default-job-16 12.0-CURRENT FreeBSD 12.0-CURRENT r309780 arm maintained by: h2+fbsdpo...@fsfe.org Makefile ident: $FreeBSD: head/biology/seqan-apps/Makefile 427129 2016-11-25 21:27:37Z gerald $ Poudriere version: 3.1.14 Host OSVERSION: 1200010 Jail OSVERSION: 1200018 Job Id: 16 !!! Jail is newer than host. (Jail: 1200018, Host: 1200010) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o UNAME_v=FreeBSD 12.0-CURRENT r309780 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=armv6 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref QEMU_EMULATING=1 UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=seqan-apps-2.2.0_1 OSREL=12.0 _OSRELEASE=12.0-CURRENT PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1200018 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" 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 LIBDIR="/usr/lib" CC="gcc49" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing" CPP="cpp49" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49" LIBS="" CXX="g++49" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc4 9" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" 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" RM_I386="" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/seqan-apps" EXAMPLESDIR="share/examples/seqan-apps" DATADIR="share/seqan-apps" WWWDIR="www/seqan-apps" ETCDIR="etc/seqan-apps" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan-apps DOCSDIR=/usr/local/share/doc/seqan-apps EXAMPLESDIR=/usr/local/share/examples/seqan-apps WWWDIR=/usr/local/www/seqan-apps ETCDIR=/usr/local/etc/seqan-apps --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 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 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 READELF=/nxb-bin/usr/bin/readelf 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--- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> seqan-apps-2.2.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4.txz [head-armv6-default-job-16] Installing pkg-1.9.4... [head-armv6-default-job-16] Extracting pkg-1.9.4: .......... done ===> seqan-apps-2.2.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.2.0_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.2.0_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.2.0_1 for building => SHA256 Checksum OK for seqan-seqan-seqan-v2.2.0_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.2.0_1 for building ===> Extracting for seqan-apps-2.2.0_1 => SHA256 Checksum OK for seqan-seqan-seqan-v2.2.0_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for seqan-apps-2.2.0_1 =========================================================================== =======================<phase: build-depends >============================ ===> seqan-apps-2.2.0_1 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.62.0_1.txz [head-armv6-default-job-16] Installing boost-libs-1.62.0_1... [head-armv6-default-job-16] `-- Installing icu-58.2,1... [head-armv6-default-job-16] `-- Extracting icu-58.2,1: .......... done [head-armv6-default-job-16] Extracting boost-libs-1.62.0_1: .......... done Message from boost-libs-1.62.0_1: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> seqan-apps-2.2.0_1 depends on package: boost-libs>0 - found ===> Returning to build of seqan-apps-2.2.0_1 ===> seqan-apps-2.2.0_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.7.1.txz [head-armv6-default-job-16] Installing cmake-3.7.1... [head-armv6-default-job-16] `-- Installing expat-2.2.0_1... [head-armv6-default-job-16] `-- Extracting expat-2.2.0_1: .......... done [head-armv6-default-job-16] `-- Installing cmake-modules-3.7.1... [head-armv6-default-job-16] `-- Extracting cmake-modules-3.7.1: .......... done [head-armv6-default-job-16] `-- Installing curl-7.51.0_2... [head-armv6-default-job-16] | `-- Installing ca_root_nss-3.27.1... [head-armv6-default-job-16] | `-- Extracting ca_root_nss-3.27.1: ........ done [head-armv6-default-job-16] `-- Extracting curl-7.51.0_2: .......... done [head-armv6-default-job-16] `-- Installing libarchive-3.2.2,1... [head-armv6-default-job-16] | `-- Installing liblz4-131... [head-armv6-default-job-16] | `-- Extracting liblz4-131: .......... done [head-armv6-default-job-16] | `-- Installing lzo2-2.09... [head-armv6-default-job-16] | `-- Extracting lzo2-2.09: .......... done [head-armv6-default-job-16] `-- Extracting libarchive-3.2.2,1: .......... done [head-armv6-default-job-16] `-- Installing jsoncpp-1.7.7... [head-armv6-default-job-16] `-- Extracting jsoncpp-1.7.7: .......... done [head-armv6-default-job-16] `-- Installing libuv-1.10.1... [head-armv6-default-job-16] `-- Extracting libuv-1.10.1: .......... done [head-armv6-default-job-16] Extracting cmake-3.7.1: .......... done Message from ca_root_nss-3.27.1: ********************************* 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 *************************************************************************** ===> seqan-apps-2.2.0_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqan-apps-2.2.0_1 ===> seqan-apps-2.2.0_1 depends on executable: gcc49 - not found ===> Installing existing package /packages/All/gcc-4.9.4.txz [head-armv6-default-job-16] Installing gcc-4.9.4... [head-armv6-default-job-16] `-- Installing indexinfo-0.2.6... [head-armv6-default-job-16] `-- Extracting indexinfo-0.2.6: .... done [head-armv6-default-job-16] `-- Installing mpc-1.0.3... [head-armv6-default-job-16] | `-- Installing gmp-5.1.3_3... [head-armv6-default-job-16] | `-- Extracting gmp-5.1.3_3: .......... done [head-armv6-default-job-16] | `-- Installing mpfr-3.1.5... [head-armv6-default-job-16] | `-- Extracting mpfr-3.1.5: .......... done [head-armv6-default-job-16] `-- Extracting mpc-1.0.3: ...... done [head-armv6-default-job-16] `-- Installing binutils-2.27_5,1... [head-armv6-default-job-16] | `-- Installing gettext-runtime-0.19.8.1_1... [head-armv6-default-job-16] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-armv6-default-job-16] `-- Extracting binutils-2.27_5,1: .......... done [head-armv6-default-job-16] Extracting gcc-4.9.4: .......... done Message from gcc-4.9.4: 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/gcc49 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> seqan-apps-2.2.0_1 depends on executable: gcc49 - found ===> Returning to build of seqan-apps-2.2.0_1 ===> seqan-apps-2.2.0_1 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for seqan-apps-2.2.0_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build -- The CXX compiler identification is GNU 4.9.4 -- Check for working CXX compiler: /usr/local/bin/g++49 -- Check for working CXX compiler: /usr/local/bin/g++49 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_f6be0/fast" -- Detecting CXX compile features - failed -- Initializing SeqAn Build System... -- Selected repository dir: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0 -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring apps -- Configuring apps/alf -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Failed -- Performing Test CXX14_FLAG -- Performing Test CXX14_FLAG - Success -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Configuring apps/bs_tools -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- Boost version: 1.62.0 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/dfi -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/fiona -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Boost version: 1.62.0 -- Not building fiona on 32bit architectures. -- Configuring apps/fx_tools -- Configuring apps/gustaf -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/insegt -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/mason2 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/micro_razers -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/ngs_roi -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/pair_align -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/param_chooser -- Configuring apps/rabema -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/razers -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/razers3 -- Found BZip2: /usr/lib/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/rep_sep -- Configuring apps/sak -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/sam2matrix -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/samcat -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/searchjoin -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/seqan_tcoffee -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/seqcons2 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/sgip -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/snp_store -- Boost version: 1.62.0 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/splazers -- Not building splazers on 32bit architectures. -- Configuring apps/stellar -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/tree_recon -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/yara -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Unsupported platform FreeBSD, disabling CTD support. -- Configuring incomplete, errors occurred! See also "/wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/CMakeOutput.log". See also "/wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/CMakeError.log". *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqan-apps _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
