Date: Fri, 28 Jun 2019 11:13:23 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120armv7-quarterly][biology/seqan-apps] Failed for seqan-apps-2.4.0_5 in package Message-ID: <201906281113.x5SBDNA3063451@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: h2+fbsdports@fsfe.org Last committer: tcberner@FreeBSD.org Ident: $FreeBSD: branches/2019Q2/biology/seqan-apps/Makefile 488341 2018-12-25 20:25:39Z tcberner $ Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/505060/logs/seqan-apps-2.4.0_5.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=505060 Log: =>> Building biology/seqan-apps build started at Fri Jun 28 06:53:54 UTC 2019 port directory: /usr/ports/biology/seqan-apps package name: seqan-apps-2.4.0_5 building for: FreeBSD 120armv7-quarterly-job-12 12.0-RELEASE-p6 FreeBSD 12.0-RELEASE-p6 1200086 arm maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: branches/2019Q2/biology/seqan-apps/Makefile 488341 2018-12-25 20:25:39Z tcberner $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300031 Jail OSVERSION: 1200086 Job Id: 12 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p6 1200086 UNAME_r=12.0-RELEASE-p6 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/120armv7-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh 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 seqan-apps-2.4.0_5: ====> Options available for the radio ARCH: you can only select none or one of them SSE4=off: Use SSE4 and POPCNT instructions AVX2=off: Use SSE4, AVX2 and POPCNT instructions NATIVE=off: Use all available instruction sets (-march=native) ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- h2+fbsdports@fsfe.org --End MAINTAINER-- --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" PATH=/wrkdirs/usr/ports/biology/seqan-apps/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/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/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 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 CC="gcc8" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing " CPP="cpp8" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local /lib/gcc8 -L/usr/local/lib/gcc8 " LIBS="" CXX="g++8" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 " 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=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local 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 PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p6 OSREL=12.0 OSVERSION=1200086 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=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) 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-2.4.0_5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120armv7-quarterly-job-12] Installing pkg-1.10.5_5... [120armv7-quarterly-job-12] Extracting pkg-1.10.5_5: .......... done ===> seqan-apps-2.4.0_5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.4.0_5 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_5 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user <snip> [130/133] : && /usr/local/bin/g++8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/razers/CMakeFiles/razers.dir/razers.cpp.o apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o -o bin/razers -lexecinfo -lelf && : [131/133] /usr/local/bin/g++8 -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=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-v2.4.0/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o -MF apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o.d -o apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers3/razers.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:60: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h: In instantiation of 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = int; T2 = unsigned int]': /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = int; T2 = unsigned int]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1983:9: required from 'void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore<TSpec, TConfig>&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig<MyFragStoreConfig>; TScore = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TShrinkMatches = seqan::True]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1221:40: required from 'int seqan::dumpMatches(seqan::FragmentStore<TSpec, TConfig>&, TCounts&, seqan::CharString, seqan::RazerSOptions<TSpec>&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig<MyFragStoreConfig>; TCounts = seqan::String<seqan::String<short unsigned int> >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode<seqan::RazerSLocal, seqan::RazerSGapped, seqan::RazerSErrors, seqan::NMatchesNone_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore<TSpec, TConfig>&, TCounts&, seqan::CharString, seqan::RazerSOptions<TSpec>&, seqan::RazerSMode<TAlignMode, TGapMode, seqan::Tag<seqan::Nothing_>, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig<MyFragStoreConfig>; TCounts = seqan::String<seqan::String<short unsigned int> >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String<char, seqan::Alloc<> >]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore<TSpec, TConfig>&, TCounts&, seqan::CharString, seqan::RazerSOptions<TSpec>&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig<MyFragStoreConfig>; TCounts = seqan::String<seqan::String<short unsigned int> >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet<seqan::String<char, seqan::Alloc<> > >&, seqan::StringSet<seqan::String<char, seqan::Alloc<> > >&, seqan::RazerSOptions<TSpec>&) [with TSpec = seqan::RazerSSpec<>]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:66: required from here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:939:18: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare] if (!(value1 == value2)) ~~~~~~~~^~~~~~~~~~ [132/133] /usr/local/bin/g++8 -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=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-v2.4.0/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o -MF apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o.d -o apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/razers3/param_tabs.cpp [133/133] : && /usr/local/bin/g++8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o -o bin/razers3 -lexecinfo -lelf -lz -lbz2 && : =========================================================================== =======================<phase: run-depends >============================ ===> seqan-apps-2.4.0_5 depends on executable: gcc8 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for seqan-apps-2.4.0_5 ===> Generating temporary packing list [0/1] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /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: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/annotations.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/readOutput.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/tupleOutput.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_frag_sequencing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_genome -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_materializer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_methylation -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_simulator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_splicing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_variator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_frag_sequencing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_genome -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_materializer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_methylation -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_simulator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_splicing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_variator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/example/adeno_virus.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/micro_razers -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/reads.fa.result -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bam2roi -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_feature_projection -- Installing: /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 [1/2] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && /wrkdirs/usr/ports/biology/seqan-apps/work/.build/bin/sak --export-help=txt > README.sak.txt [2/2] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && /wrkdirs/usr/ports/biology/seqan-apps/work/.build/bin/sak --export-help=man > sak.1 -- 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 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/man/man1/sak.1 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/sam2matrix -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sam2matrix/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sam2matrix/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/samcat -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/samcat/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/samcat/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/s4_search -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/s4_join -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/searchjoin/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/searchjoin/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/seqan_tcoffee -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqan_tcoffee/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqan_tcoffee/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqan_tcoffee/example/seq.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/seqcons2 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqcons2/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqcons2/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/sgip -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_m2D_m196.A01 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_r01_m200.A00 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_r01_m200.A01 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_r01_m200.B00 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_r01_m200.B01 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/latin-4 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/lattice-4 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/sts-7 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/snp_store -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/snp_store/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/snp_store/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/snp_store/example/exampleGenome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/snp_store/example/exampleReads.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/stellar -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/example/NC_001474.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/example/NC_001477.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/example/reads.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/tree_recon -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/example/example.dist -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/yara_indexer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/yara_mapper -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/yara/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/yara/README.rst ====> Compressing man pages (compress-man) =========================================================================== =======================<phase: package >============================ ===> Building package for seqan-apps-2.4.0_5 pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/compute_gain:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/fiona:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/splazers:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/LICENSE:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/README:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/example/reads.fa:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/LICENSE:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/README:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/example/genome.fa:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/example/reads.fa:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/example/reads.fa.result:No such file or directory *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqan-apps
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