[package - 132powerpc64-quarterly][biology/salmon] Failed for salmon-1.10.2_2 in build
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Date: Thu, 08 Feb 2024 13:23:31 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/foul1/data/132powerpc64-quarterly/aa3532662c1f/logs/salmon-1.10.2_2.log Build URL: https://pkg-status.freebsd.org/foul1/build.html?mastername=132powerpc64-quarterly&build=aa3532662c1f Log: =>> Building biology/salmon build started at Thu Feb 8 12:38:16 UTC 2024 port directory: /usr/ports/biology/salmon package name: salmon-1.10.2_2 building for: FreeBSD 132powerpc64-quarterly-job-06 13.2-RELEASE FreeBSD 13.2-RELEASE powerpc maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1506 Feb 3 01:03 /usr/ports/biology/salmon/Makefile Ports top last git commit: aa3532662 Ports top unclean checkout: no Port dir last git commit: aa3532662 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1 Host OSVERSION: 1500003 Jail OSVERSION: 1302001 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE UNAME_r=13.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.1 MASTERMNT=/usr/local/poudriere/data/.m/132powerpc64-quarterly/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/132powerpc64-quarterly/06/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=132powerpc64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/132powerpc64-quarterly/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --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=13.2 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-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/salmon DOCSDIR=/usr/local/share/doc/salmon EXAMPLESDIR=/usr/local/share/examples/salmon WWWDIR=/usr/local/www/salmon ETCDIR=/usr/local/etc/salmon --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9.pkg [132powerpc64-quarterly-job-06] Installing pkg-1.20.9... [132powerpc64-quarterly-job-06] Extracting pkg-1.20.9: .......... done ===> salmon-1.10.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of salmon-1.10.2_2 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by salmon-1.10.2_2 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by salmon-1.10.2_2 for building => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-5aecc6e_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by salmon-1.10.2_2 for building ===> Extracting for salmon-1.10.2_2 => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-5aecc6e_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for salmon-1.10.2_2 ===> Applying FreeBSD patches for salmon-1.10.2_2 from /usr/ports/biology/salmon/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_2 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.21.pkg [132powerpc64-quarterly-job-06] Installing bash-5.2.21... [132powerpc64-quarterly-job-06] `-- Installing gettext-runtime-0.22.3... [132powerpc64-quarterly-job-06] | `-- Installing indexinfo-0.3.1... [132powerpc64-quarterly-job-06] | `-- Extracting indexinfo-0.3.1: .... done [132powerpc64-quarterly-job-06] `-- Extracting gettext-runtime-0.22.3: .......... done [132powerpc64-quarterly-job-06] `-- Installing readline-8.2.7... [132powerpc64-quarterly-job-06] `-- Extracting readline-8.2.7: .......... done [132powerpc64-quarterly-job-06] Extracting bash-5.2.21: .......... done ===> salmon-1.10.2_2 depends on executable: bash - found ===> Returning to build of salmon-1.10.2_2 ===> salmon-1.10.2_2 depends on package: cereal>=1.3.0 - not found ===> Installing existing package /packages/All/cereal-1.3.2_1.pkg [132powerpc64-quarterly-job-06] Installing cereal-1.3.2_1... [132powerpc64-quarterly-job-06] `-- Installing boost-libs-1.83.0_1... [132powerpc64-quarterly-job-06] | `-- Installing icu-74.2,1... [132powerpc64-quarterly-job-06] | `-- Extracting icu-74.2,1: .......... done [132powerpc64-quarterly-job-06] `-- Extracting boost-libs-1.83.0_1: .......... done [132powerpc64-quarterly-job-06] Extracting cereal-1.3.2_1: .......... done <snip> mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 gmake[6]: Leaving 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' 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-build [ 29%] Performing install step for 'libstadenio' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && gmake install gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' Making install in htscodecs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in htscodecs gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake install-am gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[8]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[8]: Nothing to be done for 'install-data-am'. .././../install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libhtscodecs.la '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' libtool: install: /usr/bin/install -c .libs/libhtscodecs.lai /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.la install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c .libs/libhtscodecs.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a install: DONTSTRIP set - will not strip installed binaries libtool: install: chmod 644 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a libtool: install: ranlib /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a gmake[8]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' Making install in . gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[7]: Nothing to be done for 'install-exec-am'. ./../install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include' ./../install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/htscodecs' /usr/bin/install -c -m 644 htscodecs/arith_dynamic.h htscodecs/fqzcomp_qual.h htscodecs/rANS_static.h htscodecs/rANS_static4x16.h htscodecs/tokenise_name3.h htscodecs/pack.h htscodecs/rle.h htscodecs/varint.h htscodecs/htscodecs.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/htscodecs' install: DONTSTRIP set - will not strip installed binaries gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in tests gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[7]: Nothing to be done for 'install-exec-am'. gmake[7]: Nothing to be done for 'install-data-am'. gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in io_lib gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[6]: Nothing to be done for 'install-data-am'. .././install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.la install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c .libs/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a install: DONTSTRIP set - will not strip installed binaries libtool: install: chmod 644 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a libtool: install: ranlib /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' Making install in progs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[6]: Nothing to be done for 'install-data-am'. .././install-sh -c -d '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' libtool: install: /usr/bin/install -c convert_trace /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/convert_trace install: DONTSTRIP set - will not strip installed binaries libtool: install: /usr/bin/install -c makeSCF /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/makeSCF install: DONTSTRIP set - will not strip installed binaries 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 [ 30%] 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' [ 30%] Built target libstadenio [ 31%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.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/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp [ 32%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.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.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/common.cpp [ 32%] Linking CXX static library libtwopaco.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o /usr/bin/llvm-ranlib libtwopaco.a gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 32%] Built target twopaco 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