[package - main-i386-default][biology/salmon] Failed for salmon-1.10.2 in build
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Date: Sat, 22 Jul 2023 20:49:40 UTC
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: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p150bed43bfd4_sbc310a95c5/logs/salmon-1.10.2.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p150bed43bfd4_sbc310a95c5
Log:
=>> Building biology/salmon
build started at Sat Jul 22 20:48:33 UTC 2023
port directory: /usr/ports/biology/salmon
package name: salmon-1.10.2
building for: FreeBSD main-i386-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400093
Job Id: 10
!!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
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--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/salmon/work/.cache HOME=/wrkdirs/usr/ports/biology/salmon/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/salmon/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/salmon/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/salmon/work/.cache HOME=/wrkdirs/usr/ports/biology/salmon/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/salmon/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/salmon/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig DONTSTRIP=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lpthread -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/
usr/local" BSD_INSTALL_PROGRAM="install -m 555" BSD_INSTALL_LIB="install -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="debug" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/salmon" EXAMPLESDIR="share/examples/salmon" DATADIR="share/salmon" WWWDIR="www/salmon" ETCDIR="etc/salmon"
--End PLIST_SUB--
--SUB_LIST--
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MACHINE=i386
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ARCH=${MACHINE_ARCH}
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--End resource limits--
=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> salmon-1.10.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[main-i386-default-job-10] Installing pkg-1.20.4...
[main-i386-default-job-10] Extracting pkg-1.20.4: .......... done
===> salmon-1.10.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of salmon-1.10.2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
=> COMBINE-lab-salmon-v1.10.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz
fetch: https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz: size of remote file is not known
COMBINE-lab-salmon-v1.10.2_GH0.tar.gz 7024 kB 10 MBps 00s
=> COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz
fetch: https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz: size of remote file is not known
COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz 3289 kB 5536 kBps 00s
=> jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz
fetch: https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz: size of remote file is not known
jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz 3302 kB 4721 kBps 01s
=> samtools-htscodecs-5aecc6e_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz
fetch: https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz: size of remote file is not known
samtools-htscodecs-5aecc6e_GH0.tar.gz 3116 kB 15 MBps 00s
===> Fetching all distfiles required by salmon-1.10.2 for building
===========================================================================
<snip>
libtool: install: /usr/bin/install -c extract_seq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_seq
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c extract_qual /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_qual
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c extract_fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_fastq
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c index_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/index_tar
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c scf_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_dump
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c scf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_info
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c scf_update /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_update
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c get_comment /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/get_comment
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c hash_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_tar
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c hash_extract /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_extract
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c hash_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_list
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c trace_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/trace_dump
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c hash_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_sff
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c append_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/append_sff
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c ztr_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/ztr_dump
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf_dump_all /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_dump_all
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf_index_hash /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_index_hash
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf_extract_linear /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_extract_linear
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf_extract_hash /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_extract_hash
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf2fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fastq
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf2fasta /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fasta
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_filter
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_info
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c srf_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_list
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c hash_exp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_exp
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c cram_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_dump
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c cram_index /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_index
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c scramble /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scramble
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c scram_merge /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_merge
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c scram_pileup /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_pileup
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c scram_flagstat /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_flagstat
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c scram_test /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_test
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c cram_size /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_size
install: DONTSTRIP set - will not strip installed binaries
libtool: install: /usr/bin/install -c cram_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_filter
install: DONTSTRIP set - will not strip installed binaries
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs'
Making install in tests
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests'
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests'
gmake[6]: Nothing to be done for 'install-exec-am'.
gmake[6]: Nothing to be done for 'install-data-am'.
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib'
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib'
./install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin'
/usr/bin/install -c io_lib-config '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin'
install: DONTSTRIP set - will not strip installed binaries
./install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man1'
/usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man1'
install: DONTSTRIP set - will not strip installed binaries
./install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man3'
/usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man3'
install: DONTSTRIP set - will not strip installed binaries
./install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man4'
/usr/bin/install -c -m 644 man/man4/Read.4 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man4'
install: DONTSTRIP set - will not strip installed binaries
./install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib'
/usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib'
install: DONTSTRIP set - will not strip installed binaries
/usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib'
install: DONTSTRIP set - will not strip installed binaries
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib'
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib'
cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-install
[ 16%] Completed 'libstadenio'
/usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles/libstadenio-complete
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-done
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
[ 16%] Built target libstadenio
[ 17%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp
gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
[ 18%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
[ 19%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
LLVM ERROR: out of memory
Allocation failed
PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
Stack dump:
0. Program arguments: /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o -MF CMakeFiles/twopaco.dir/constructor.cpp.o.d -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp
1. LLVM ERROR: out of memory
Allocation failed
LLVM ERROR: out of memory
Allocation failed
[ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
[ 20%] Built target ksw2pp_sse2
gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
[ 21%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
[ 21%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
[ 22%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
[ 22%] Built target ksw2pp_sse4
[ 22%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp
[ 23%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
gmake[3]: *** [external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make:93: external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o] Abort trap (core dumped)
gmake[3]: *** Waiting for unfinished jobs....
gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
[ 23%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/kalloc.c
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/kalloc.c:49:74: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
fprintf(stderr, "[morecore] %lu bytes requested but not available.\n", rnu * sizeof(size_t));
~~~ ^~~~~~~~~~~~~~~~~~~~
%u
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/kalloc.c:213:4: warning: format specifies type 'unsigned long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
km->total_allocated, n_units * sizeof(size_t), n_blocks, max_block * sizeof(size_t), frag);
^~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/kalloc.c:213:25: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
km->total_allocated, n_units * sizeof(size_t), n_blocks, max_block * sizeof(size_t), frag);
^~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/kalloc.c:213:61: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
km->total_allocated, n_units * sizeof(size_t), n_blocks, max_block * sizeof(size_t), frag);
^~~~~~~~~~~~~~~~~~~~~~~~~~
4 warnings generated.
[ 24%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extd.c
[ 25%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extz.c
[ 26%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_gg.c
[ 27%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_gg2.c
[ 27%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c
[ 28%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++14 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
gmake[2]: *** [CMakeFiles/Makefile2:326: external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/all] Error 2
gmake[2]: *** Waiting for unfinished jobs....
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
[ 28%] Built target ksw2pp_basic
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
gmake[1]: *** [Makefile:169: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/salmon