[package - 120armv6-quarterly][biology/seqan-apps] Failed for seqan-apps-2.4.0_5 in package
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu May 16 09:48:06 UTC 2019
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 at fsfe.org
Last committer: tcberner at FreeBSD.org
Ident: $FreeBSD: branches/2019Q2/biology/seqan-apps/Makefile 488341 2018-12-25 20:25:39Z tcberner $
Log URL: http://beefy15.nyi.freebsd.org/data/120armv6-quarterly/501102/logs/seqan-apps-2.4.0_5.log
Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=120armv6-quarterly&build=501102
Log:
=>> Building biology/seqan-apps
build started at Thu May 16 04:50:05 UTC 2019
port directory: /usr/ports/biology/seqan-apps
package name: seqan-apps-2.4.0_5
building for: FreeBSD 120armv6-quarterly-job-22 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 arm
maintained by: h2+fbsdports at fsfe.org
Makefile ident: $FreeBSD: branches/2019Q2/biology/seqan-apps/Makefile 488341 2018-12-25 20:25:39Z tcberner $
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===> 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
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=======================<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
[120armv6-quarterly-job-22] Installing pkg-1.10.5_5...
[120armv6-quarterly-job-22] 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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