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Date:      Sun, 21 Jul 2019 07:34:10 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_6 in package
Message-ID:  <201907210734.x6L7YApq026076@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: jbeich@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q3/biology/seqan-apps/Makefile 498698 2019-04-12 06:36:31Z jbeich $
Log URL:        http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/506961/logs/seqan-apps-2.4.0_6.log
Build URL:      http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=506961
Log:

=>> Building biology/seqan-apps
build started at Sun Jul 21 03:34:25 UTC 2019
port directory: /usr/ports/biology/seqan-apps
package name: seqan-apps-2.4.0_6
building for: FreeBSD 120armv7-quarterly-job-17 12.0-RELEASE-p7 FreeBSD 12.0-RELEASE-p7 1200086 arm
maintained by: h2+fbsdports@fsfe.org
Makefile ident:      $FreeBSD: branches/2019Q3/biology/seqan-apps/Makefile 498698 2019-04-12 06:36:31Z jbeich $
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---Begin OPTIONS List---
===> The following configuration options are available for seqan-apps-2.4.0_6:
====> 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---

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h2+fbsdports@fsfe.org
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--PLIST_SUB--
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--End PLIST_SUB--

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=======================<phase: check-sanity   >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   seqan-apps-2.4.0_6 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.11.1.txz
[120armv7-quarterly-job-17] Installing pkg-1.11.1...
[120armv7-quarterly-job-17] Extracting pkg-1.11.1: .......... done
===>   seqan-apps-2.4.0_6 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of seqan-apps-2.4.0_6
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.4.0_6 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
<snip>
/usr/local/lib/gcc8/include/c++/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc8/include/c++/bits/vector.tcc: In member function 'void MasonSimulatorApp::_initContigPicker()':
/usr/local/lib/gcc8/include/c++/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
[123/133] : && /usr/local/bin/g++8  -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o  -o bin/mason_simulator  -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && :
[124/133] /usr/local/bin/g++8  -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -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  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8    -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -MF apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o.d -o apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp
[125/133] : && /usr/local/bin/g++8  -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o  -o bin/mason_frag_sequencing  -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && :
[126/133] /usr/local/bin/g++8  -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -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  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8    -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -MF apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o.d -o apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp
[127/133] : && /usr/local/bin/g++8  -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o  -o bin/mason_methylation  -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && :
[128/133] /usr/local/bin/g++8  -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -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  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8    -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -MF apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o.d -o apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp
[129/133] : && /usr/local/bin/g++8  -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o  -o bin/mason_variator  -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && :
[130/133] /usr/local/bin/g++8  -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -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  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8    -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -MF apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o.d -o apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp
[131/133] : && /usr/local/bin/g++8  -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o  -o bin/mason_genome  -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && :
[132/133] /usr/local/bin/g++8  -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -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  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8    -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -MF apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o.d -o apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp
[133/133] : && /usr/local/bin/g++8  -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -W -Wall -pedantic -fopenmp -O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8  -Wl,-rpath=/usr/local/lib/gcc8  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o  -o bin/mason_materializer  -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && :
===========================================================================
=======================<phase: run-depends    >============================
===>   seqan-apps-2.4.0_6 depends on executable: gcc8 - found
===========================================================================
=======================<phase: stage          >============================
===>  Staging for seqan-apps-2.4.0_6
===>   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_6
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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