Date: Tue, 11 Jul 2017 02:15:09 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110armv6-quarterly][biology/seqan-apps] Failed for seqan-apps-2.2.0_4 in build Message-ID: <201707110215.v6B2F9BN049075@beefy15.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: h2+fbsdports@fsfe.org Last committer: linimon@FreeBSD.org Ident: $FreeBSD: branches/2017Q3/biology/seqan-apps/Makefile 441431 2017-05-21 23:37:34Z linimon $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/445463/logs/seqan-apps-2.2.0_4.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=445463 Log: ====>> Building biology/seqan-apps build started at Tue Jul 11 02:11:23 UTC 2017 port directory: /usr/ports/biology/seqan-apps building for: FreeBSD 110armv6-quarterly-job-03 11.0-RELEASE-p10 FreeBSD 11.0-RELEASE-p10 r317487 arm maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: branches/2017Q3/biology/seqan-apps/Makefile 441431 2017-05-21 23:37:34Z linimon $ Poudriere version: 3.1.19-48-g1bf78d5a Host OSVERSION: 1200033 Jail OSVERSION: 1100122 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p10 r317487 UNAME_r=11.0-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=seqan-apps-2.2.0_4 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool MASTERNAME=110armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.19-48-g1bf78d5a 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= ---End Poudriere Port Flags/Env--- ---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" DESTDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/stage PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc5" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc5 -fno-strict-aliasing" CPP="cpp5" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5" LIBS="" CXX="g++5" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc5 -f no-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc5" 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" RM_I386="" OSREL=11.0 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 PACKAGE_BUILDING=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 #### ARCH=armv6 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native\|linux _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ _OSRELEASE=11.0-RELEASE-p10 #### 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 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--- --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-- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> seqan-apps-2.2.0_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-03] Installing pkg-1.10.1... [110armv6-quarterly-job-03] Extracting pkg-1.10.1: .......... done ===> seqan-apps-2.2.0_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.2.0_4 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.2.0_4 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.2.0_4 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_4 for building ===> Extracting for seqan-apps-2.2.0_4 => 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_4 =========================================================================== =======================<phase: build-depends >============================ ===> seqan-apps-2.2.0_4 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.64.0.txz <snip> [110armv6-quarterly-job-03] `-- Installing jsoncpp-1.8.1... [110armv6-quarterly-job-03] `-- Extracting jsoncpp-1.8.1: .......... done [110armv6-quarterly-job-03] `-- Installing libarchive-3.3.1,1... [110armv6-quarterly-job-03] | `-- Installing liblz4-1.7.5,1... [110armv6-quarterly-job-03] | `-- Extracting liblz4-1.7.5,1: .......... done [110armv6-quarterly-job-03] | `-- Installing lzo2-2.10_1... [110armv6-quarterly-job-03] | `-- Extracting lzo2-2.10_1: .......... done [110armv6-quarterly-job-03] `-- Extracting libarchive-3.3.1,1: .......... done [110armv6-quarterly-job-03] `-- Installing libuv-1.12.0... [110armv6-quarterly-job-03] `-- Extracting libuv-1.12.0: .......... done [110armv6-quarterly-job-03] `-- Installing rhash-1.3.4... [110armv6-quarterly-job-03] `-- Extracting rhash-1.3.4: .......... done [110armv6-quarterly-job-03] Extracting cmake-3.8.2: .......... done Message from ca_root_nss-3.31: ********************************* 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_4 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqan-apps-2.2.0_4 ===> seqan-apps-2.2.0_4 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.7.2,2.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-03] Installing ninja-1.7.2,2... [110armv6-quarterly-job-03] `-- Installing python27-2.7.13_6... [110armv6-quarterly-job-03] | `-- Installing gettext-runtime-0.19.8.1_1... [110armv6-quarterly-job-03] | | `-- Installing indexinfo-0.2.6... [110armv6-quarterly-job-03] | | `-- Extracting indexinfo-0.2.6: .... done [110armv6-quarterly-job-03] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110armv6-quarterly-job-03] | `-- Installing libffi-3.2.1... [110armv6-quarterly-job-03] | `-- Extracting libffi-3.2.1: .......... done [110armv6-quarterly-job-03] | `-- Installing readline-7.0.3... [110armv6-quarterly-job-03] | `-- Extracting readline-7.0.3: .......... done [110armv6-quarterly-job-03] `-- Extracting python27-2.7.13_6: .......... done [110armv6-quarterly-job-03] Extracting ninja-1.7.2,2: ....... done Message from python27-2.7.13_6: =========================================================================== 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 =========================================================================== ===> seqan-apps-2.2.0_4 depends on executable: ninja - found ===> Returning to build of seqan-apps-2.2.0_4 ===> seqan-apps-2.2.0_4 depends on executable: gcc5 - not found ===> Installing existing package /packages/All/gcc5-5.4.0_2.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-03] Installing gcc5-5.4.0_2... [110armv6-quarterly-job-03] `-- Installing binutils-2.28,1... [110armv6-quarterly-job-03] `-- Extracting binutils-2.28,1: .......... done [110armv6-quarterly-job-03] `-- Installing gmp-6.1.2... [110armv6-quarterly-job-03] `-- Extracting gmp-6.1.2: .......... done [110armv6-quarterly-job-03] `-- Installing mpc-1.0.3... [110armv6-quarterly-job-03] | `-- Installing mpfr-3.1.5_1... [110armv6-quarterly-job-03] | `-- Extracting mpfr-3.1.5_1: .......... done [110armv6-quarterly-job-03] `-- Extracting mpc-1.0.3: ...... done [110armv6-quarterly-job-03] Extracting gcc5-5.4.0_2: .......... done Message from gcc5-5.4.0_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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> seqan-apps-2.2.0_4 depends on executable: gcc5 - found ===> Returning to build of seqan-apps-2.2.0_4 ===> seqan-apps-2.2.0_4 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for seqan-apps-2.2.0_4 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build -- The CXX compiler identification is GNU 5.4.0 -- Check for working CXX compiler: /usr/local/bin/g++5 -- Check for working CXX compiler: /usr/local/bin/g++5 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- 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: 1.64.0 -- Found PythonInterp: /usr/local/bin/python2.7 (found version "2.7.13") -- Configuring apps/dfi -- Configuring apps/fiona -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Boost version: 1.64.0 -- Not building fiona on 32bit architectures. -- Configuring apps/fx_tools -- Configuring apps/gustaf -- Configuring apps/insegt -- Configuring apps/mason2 -- Configuring apps/micro_razers -- Configuring apps/ngs_roi -- Configuring apps/pair_align -- Configuring apps/param_chooser -- Configuring apps/rabema -- Configuring apps/razers -- Configuring apps/razers3 -- Found BZip2: /usr/lib/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Configuring apps/rep_sep -- Configuring apps/sak -- Configuring apps/sam2matrix -- Configuring apps/samcat -- Configuring apps/searchjoin -- Configuring apps/seqan_tcoffee -- Configuring apps/seqcons2 -- Configuring apps/sgip -- Configuring apps/snp_store -- Boost version: 1.64.0 -- Configuring apps/splazers -- Not building splazers on 32bit architectures. -- Configuring apps/stellar -- Configuring apps/tree_recon -- Configuring apps/yara -- Unsupported platform FreeBSD, disabling CTD support. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/seqan-apps/work/.build =========================================================================== =======================<phase: build >============================ ===> Building for seqan-apps-2.2.0_4 [1/133] /usr/local/bin/g++5 -DSEQAN_APP_VERSION=\"1.1.6\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc5 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc5 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc5 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc5 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/alf/CMakeFiles/alf.dir/alf.cpp.o -MF apps/alf/CMakeFiles/alf.dir/alf.cpp.o.d -o apps/alf/CMakeFiles/alf.dir/alf.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/alf/alf.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_allocator.h:47:0, from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic.h:74, from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/alf/alf.cpp:44: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning is a GCC extension #warning "No supported platform for SIMD vectorization!" ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning "No supported platform for SIMD vectorization!" [-Wcpp] [2/133] : && /usr/local/bin/g++5 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc5 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc5 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc5 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc5 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 apps/alf/CMakeFiles/alf.dir/alf.cpp.o -o bin/alf -lpthread -lexecinfo -lelf && : FAILED: bin/alf : && /usr/local/bin/g++5 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc5 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc5 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc5 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc5 -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 apps/alf/CMakeFiles/alf.dir/alf.cpp.o -o bin/alf -lpthread -lexecinfo -lelf && : //usr/lib/libexecinfo.so: undefined reference to `_Unwind_Backtrace@GCC_3.3' collect2: error: ld returned 1 exit status ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqan-apps
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