Date: Fri, 4 Nov 2016 09:27:49 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 in configure Message-ID: <201611040927.uA49RnhQ072920@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: pawel@FreeBSD.org Ident: $FreeBSD: branches/2016Q4/biology/seqan-apps/Makefile 422156 2016-09-14 19:38:58Z pawel $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/425058/logs/seqan-apps-2.2.0.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=425058 Log: ====>> Building biology/seqan-apps build started at Fri Nov 4 09:26:16 UTC 2016 port directory: /usr/ports/biology/seqan-apps building for: FreeBSD 110armv6-quarterly-job-12 11.0-RELEASE-p2 FreeBSD 11.0-RELEASE-p2 r307935 arm maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: branches/2016Q4/biology/seqan-apps/Makefile 422156 2016-09-14 19:38:58Z pawel $ Poudriere version: 3.1.14 Host OSVERSION: 1200010 Jail OSVERSION: 1100122 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o UNAME_v=FreeBSD 11.0-RELEASE-p2 r307935 UNAME_r=11.0-RELEASE-p2 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=armv6 SAVED_TERM=screen MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/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 OSREL=11.0 _OSRELEASE=11.0-RELEASE-p2 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=28 PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool MASTERNAME=110armv6-quarterly 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=1100122 ---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=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 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 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-12] Installing pkg-1.8.7_3... [110armv6-quarterly-job-12] Extracting pkg-1.8.7_3: .......... done ===> seqan-apps-2.2.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.2.0 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user => seqan-seqan-seqan-v2.2.0_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.2.0?dummy=/seqan-seqan-seqan-v2.2.0_GH0.tar.gz fetch: https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.2.0?dummy=/seqan-seqan-seqan-v2.2.0_GH0.tar.gz: size unknown fetch: https://codeload.github.com/seqan/seqan/tar.gz/seqan-v2.2.0?dummy=/seqan-seqan-seqan-v2.2.0_GH0.tar.gz: size of remote file is not known seqan-seqan-seqan-v2.2.0_GH0.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by seqan-apps-2.2.0 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.2.0 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 for building ===> Extracting for seqan-apps-2.2.0 => 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 =========================================================================== =======================<phase: build-depends >============================ ===> seqan-apps-2.2.0 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.55.0_13.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-12] Installing boost-libs-1.55.0_13... [110armv6-quarterly-job-12] `-- Installing icu-57.1,1... [110armv6-quarterly-job-12] `-- Extracting icu-57.1,1: .......... done [110armv6-quarterly-job-12] Extracting boost-libs-1.55.0_13: .......... done Message from boost-libs-1.55.0_13: 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 depends on package: boost-libs>0 - found ===> Returning to build of seqan-apps-2.2.0 ===> seqan-apps-2.2.0 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.6.2.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-12] Installing cmake-3.6.2... [110armv6-quarterly-job-12] `-- Installing expat-2.2.0... [110armv6-quarterly-job-12] `-- Extracting expat-2.2.0: .......... done [110armv6-quarterly-job-12] `-- Installing cmake-modules-3.6.2... [110armv6-quarterly-job-12] `-- Extracting cmake-modules-3.6.2: .......... done [110armv6-quarterly-job-12] `-- Installing curl-7.50.3... [110armv6-quarterly-job-12] | `-- Installing ca_root_nss-3.27.1... [110armv6-quarterly-job-12] | `-- Extracting ca_root_nss-3.27.1: ....... done [110armv6-quarterly-job-12] `-- Extracting curl-7.50.3: .......... done [110armv6-quarterly-job-12] `-- Installing libarchive-3.2.1,1... [110armv6-quarterly-job-12] | `-- Installing liblz4-131... [110armv6-quarterly-job-12] | `-- Extracting liblz4-131: .......... done [110armv6-quarterly-job-12] | `-- Installing lzo2-2.09... [110armv6-quarterly-job-12] | `-- Extracting lzo2-2.09: .......... done [110armv6-quarterly-job-12] `-- Extracting libarchive-3.2.1,1: .......... done [110armv6-quarterly-job-12] `-- Installing jsoncpp-1.7.3... [110armv6-quarterly-job-12] `-- Extracting jsoncpp-1.7.3: .......... done [110armv6-quarterly-job-12] Extracting cmake-3.6.2: .......... 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 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqan-apps-2.2.0 ===> seqan-apps-2.2.0 depends on executable: gcc49 - not found ===> Installing existing package /packages/All/gcc49-4.9.4.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-12] Installing gcc49-4.9.4... [110armv6-quarterly-job-12] `-- Installing indexinfo-0.2.5... [110armv6-quarterly-job-12] `-- Extracting indexinfo-0.2.5: .... done [110armv6-quarterly-job-12] `-- Installing mpc-1.0.3... [110armv6-quarterly-job-12] | `-- Installing gmp-5.1.3_3... [110armv6-quarterly-job-12] | `-- Extracting gmp-5.1.3_3: .......... done [110armv6-quarterly-job-12] | `-- Installing mpfr-3.1.5... [110armv6-quarterly-job-12] | `-- Extracting mpfr-3.1.5: .......... done [110armv6-quarterly-job-12] `-- Extracting mpc-1.0.3: ...... done [110armv6-quarterly-job-12] `-- Installing binutils-2.27_4,1... [110armv6-quarterly-job-12] | `-- Installing gettext-runtime-0.19.8.1... [110armv6-quarterly-job-12] | `-- Extracting gettext-runtime-0.19.8.1: .......... done [110armv6-quarterly-job-12] `-- Extracting binutils-2.27_4,1: .......... done [110armv6-quarterly-job-12] Extracting gcc49-4.9.4: .......... done Message from gcc49-4.9.4: 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 depends on executable: gcc49 - found ===> Returning to build of seqan-apps-2.2.0 ===> seqan-apps-2.2.0 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for seqan-apps-2.2.0 ===> 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 -- 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 CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_ef885/fast" -- Looking for C++ include execinfo.h - not found -- Configuring apps/bs_tools -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- Boost version: 1.55.0 -- 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: 1.55.0 -- 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: 1.55.0 -- 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
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