Date: Wed, 31 Aug 2016 02:24:07 GMT From: pkg-fallout@FreeBSD.org To: h2+fbsdports@fsfe.org Cc: pkg-fallout@FreeBSD.org Subject: [package - 93i386-default][biology/seqan-apps] Failed for seqan-apps-2.1.1 in stage Message-ID: <201608310224.u7V2O7jA046111@beefy1.nyi.freebsd.org>
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Maintainer: h2+fbsdports@fsfe.org Last committer: junovitch@FreeBSD.org Ident: $FreeBSD: head/biology/seqan-apps/Makefile 414897 2016-05-10 00:52:04Z junovitch $ Log URL: http://beefy1.nyi.freebsd.org/data/93i386-default/421100/logs/seqan-apps-2.1.1.log Build URL: http://beefy1.nyi.freebsd.org/build.html?mastername=93i386-default&build=421100 Log: ====>> Building biology/seqan-apps build started at Wed Aug 31 01:36:28 UTC 2016 port directory: /usr/ports/biology/seqan-apps building for: FreeBSD 93i386-default-job-08 9.3-RELEASE-p45 FreeBSD 9.3-RELEASE-p45 i386 maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: head/biology/seqan-apps/Makefile 414897 2016-05-10 00:52:04Z junovitch $ Poudriere version: 3.1.14 Host OSVERSION: 1200005 Jail OSVERSION: 903000 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 UNAME_v=FreeBSD 9.3-RELEASE-p45 UNAME_r=9.3-RELEASE-p45 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=i386 LINUX_OSRELEASE=2.6.32 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/93i386-default/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/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-2.1.1 OSREL=9.3 _OSRELEASE=9.3-RELEASE-p45 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/93i386-default/ref/.p/pool MASTERNAME=93i386-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=903000 ---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 WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes 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/loca l/lib/gcc49" 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="@comment " OSREL=9.3 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--- MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /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--- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_1.txz [93i386-default-job-08] Installing pkg-1.8.7_1... [93i386-default-job-08] Extracting pkg-1.8.7_1: .......... done ===> seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.1.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.1.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.1.1 for building => SHA256 Checksum OK for seqan-seqan-seqan-v2.1.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.1.1 for building ===> Extracting for seqan-apps-2.1.1 => SHA256 Checksum OK for seqan-seqan-seqan-v2.1.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for seqan-apps-2.1.1 # missing C99 functions in FreeBSD's math.h, use C++ instead # the other way around (use math.h instead of cmath) =========================================================================== =======================<phase: build-depends >============================ ===> seqan-apps-2.1.1 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.55.0_12.txz [93i386-default-job-08] Installing boost-libs-1.55.0_12... [93i386-default-job-08] `-- Installing libiconv-1.14_9... [93i386-default-job-08] `-- Extracting libiconv-1.14_9: .......... done [93i386-default-job-08] `-- Installing icu-55.1,1... [93i386-default-job-08] `-- Extracting icu-55.1,1: .......... done [93i386-default-job-08] Extracting boost-libs-1.55.0_12: .......... done Message from boost-libs-1.55.0_12: 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-2.1.1 depends on package: boost-libs>0 - found ===> Returning to build of seqan-apps-2.1.1 ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.6.1.txz [93i386-default-job-08] Installing cmake-3.6.1... [93i386-default-job-08] `-- Installing expat-2.2.0... [93i386-default-job-08] `-- Extracting expat-2.2.0: .......... done [93i386-default-job-08] `-- Installing cmake-modules-3.6.1... [93i386-default-job-08] `-- Extracting cmake-modules-3.6.1: .......... done [93i386-default-job-08] `-- Installing curl-7.50.1... [93i386-default-job-08] | `-- Installing ca_root_nss-3.26... [93i386-default-job-08] | `-- Extracting ca_root_nss-3.26: ....... done [93i386-default-job-08] `-- Extracting curl-7.50.1: .......... done [93i386-default-job-08] `-- Installing libarchive-3.2.1,1... [93i386-default-job-08] | `-- Installing liblz4-131... [93i386-default-job-08] | `-- Extracting liblz4-131: .......... done [93i386-default-job-08] | `-- Installing lzo2-2.09... [93i386-default-job-08] | `-- Extracting lzo2-2.09: .......... done [93i386-default-job-08] `-- Extracting libarchive-3.2.1,1: .......... done [93i386-default-job-08] `-- Installing jsoncpp-1.7.3... [93i386-default-job-08] `-- Extracting jsoncpp-1.7.3: .......... done [93i386-default-job-08] `-- Installing libexecinfo-1.1_3... [93i386-default-job-08] `-- Extracting libexecinfo-1.1_3: ..... done [93i386-default-job-08] Extracting cmake-3.6.1: .......... done Message from ca_root_nss-3.26: ********************************* 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 <snip> /usr/bin/make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build [ 80%] Built target sam2matrix /usr/bin/make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/samcat /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/samcat /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake /usr/bin/make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build [ 82%] Built target samcat /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build [ 83%] Built target s4_join /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build [ 85%] Built target s4_search /usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqan_tcoffee /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqan_tcoffee /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake /usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build [ 86%] Built target seqan_tcoffee /usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqcons2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake /usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build [ 89%] Built target seqcons2 /usr/bin/make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sgip /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sgip /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake /usr/bin/make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build [ 91%] Built target sgip /usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/snp_store /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake /usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build [ 92%] Built target snp_store /usr/bin/make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/stellar /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/stellar /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake /usr/bin/make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build [ 94%] Built target stellar /usr/bin/make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/tree_recon /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/tree_recon /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake /usr/bin/make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build [ 96%] Built target tree_recon /usr/bin/make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/yara /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/yara /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/yara/CMakeFiles/yara_indexer.dir/DependInfo.cmake /usr/bin/make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/build [ 97%] Built target yara_indexer /usr/bin/make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/yara /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/yara /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/yara/CMakeFiles/yara_mapper.dir/DependInfo.cmake /usr/bin/make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/build [100%] Built target yara_mapper /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/alf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/example/small.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bisar -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/casbar -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/four2three -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/bs_tools/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/bs_tools/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/dfi -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/example/fasta1.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/example/fasta2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/fx_bam_coverage -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fx_tools/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fx_tools/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gustaf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gustaf_mate_joining -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno_modified.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno_modified_reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/stellar.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/insegt -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/annoOutput.gff -- Installing: 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/wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_plot_thumbnails -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bed_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gff_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_plot_9.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/plot.awk -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/ps2pswLinks.gawk -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/dmel.bed -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/dmel.gtf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/example.bam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/R/ngsroi_0.1.tar.gz -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/R/ngsroi_0.1.zip -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/pair_align -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/pair_align/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/pair_align/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/param_chooser -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/param_chooser/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/param_chooser/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_prepare_sam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_build_gold_standard -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_evaluate -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_prepare_sam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_build_gold_standard -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_evaluate -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rabema/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rabema/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/razers -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/reads2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/razers3 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/reads2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rep_sep -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rep_sep/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rep_sep/README /usr/local/bin/cmake -H/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 -B/wrkdirs/usr/ports/biology/seqan-apps/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 sak_doc /usr/local/bin/cmake -H/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 -B/wrkdirs/usr/ports/biology/seqan-apps/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles 3 /usr/bin/make -f CMakeFiles/Makefile2 apps/sak/CMakeFiles/sak_doc.dir/all /usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/seqan_library.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build [ 0%] Built target seqan_library /usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake /usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build [ 33%] Built target sak /usr/bin/make -f apps/sak/CMakeFiles/sak_doc.dir/build.make apps/sak/CMakeFiles/sak_doc.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak/CMakeFiles/sak_doc.dir/DependInfo.cmake Scanning dependencies of target sak_doc /usr/bin/make -f apps/sak/CMakeFiles/sak_doc.dir/build.make apps/sak/CMakeFiles/sak_doc.dir/build [ 66%] Generating README.sak.txt cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && ../../bin/sak --export-help=txt > README.sak.txt *** [apps/sak/README.sak.txt] Signal 11 Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build. *** [apps/sak/CMakeFiles/sak_doc.dir/all] Error code 1 Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build. *** [apps/sak/CMakeFiles/sak_doc.dir/rule] Error code 1 Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build. *** [sak_doc] Error code 1 Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build. -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/sak -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/README.sak.txt CMake Error at apps/sak/cmake_install.cmake:59 (file): file INSTALL cannot find "/wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak/sak.1". Call Stack (most recent call first): apps/cmake_install.cmake:48 (include) cmake_install.cmake:32 (include) *** [install/strip] Error code 1 Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build. *** [do-install] Error code 1 Stop in /usr/ports/biology/seqan-apps.
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