[package - main-arm64-default][biology/salmon] Failed for salmon-1.10.2_5 in build
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Date: Sun, 17 Nov 2024 08:49:33 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/ampere2/data/main-arm64-default/pdfee61567d9e_s36887e04947/logs/salmon-1.10.2_5.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=pdfee61567d9e_s36887e04947 Log: =>> Building biology/salmon build started at Sun Nov 17 08:46:42 UTC 2024 port directory: /usr/ports/biology/salmon package name: salmon-1.10.2_5 building for: FreeBSD main-arm64-default-job-04 15.0-CURRENT FreeBSD 15.0-CURRENT 1500026 arm64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1490 Oct 6 01:01 /usr/ports/biology/salmon/Makefile Ports top last git commit: dfee61567d9 Ports top unclean checkout: no Port dir last git commit: 55cfbcf56c3 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1500026 Job Id: 04 !!! Jail is newer than host. (Jail: 1500026, Host: 1500023) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500026 UNAME_v=FreeBSD 15.0-CURRENT 1500026 UNAME_r=15.0-CURRENT 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/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/main-arm64-default/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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 MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -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="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="inst all -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=15.0 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-- 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--- # 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 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-- ulimit: can't get limit: Invalid argument cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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_5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [main-arm64-default-job-04] Installing pkg-1.21.3... [main-arm64-default-job-04] Extracting pkg-1.21.3: .......... done ===> salmon-1.10.2_5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of salmon-1.10.2_5 =========================================================================== =======================<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_5 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_5 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_5 for building ===> Extracting for salmon-1.10.2_5 => 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_5 ===> Applying FreeBSD patches for salmon-1.10.2_5 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_5 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.37.pkg <snip> /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o get_comment get_comment.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o scf_update scf_update.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o get_comment get_comment.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o hash_list hash_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o hash_tar hash_tar.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 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o hash_extract hash_extract.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o hash_list hash_list.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 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o trace_dump trace_dump.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o append_sff append_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o hash_sff hash_sff.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o ztr_dump ztr_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf_dump_all srf_dump_all.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o append_sff append_sff.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 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o ztr_dump ztr_dump.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf_index_hash srf_index_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf_extract_linear srf_extract_linear.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf_dump_all srf_dump_all.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf_extract_hash srf_extract_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf_index_hash srf_index_hash.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 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf_extract_linear srf_extract_linear.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf2fastq srf2fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf_extract_hash srf_extract_hash.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf2fastq srf2fastq.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf2fasta srf2fasta.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf_filter srf_filter.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf_info srf_info.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o srf_list srf_list.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o hash_exp hash_exp.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o cram_dump cram_dump.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o cram_index cram_index.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o scramble scramble.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o scram_merge scram_merge.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o scram_pileup scram_pileup.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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o scram_flagstat scram_flagstat.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 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o scram_test scram_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 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -lpthread -fstack-protector-strong -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o cram_size cram_size.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 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -fstack-protector-strong -o cram_filter cram_filter.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[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' Making all in tests gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -MT cram_io_test.o -MD -MP -MF .deps/cram_io_test.Tpo -c -o cram_io_test.o cram_io_test.c mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -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 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fsigned-char -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[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[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' gmake[3]: 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 [ 15%] Performing install step for 'libstadenio' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && gmake install gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' Making install in htscodecs gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in htscodecs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake install-am gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[7]: Nothing to be done for 'install-data-am'. mkdir -p '/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 libtool: install: /usr/bin/install -c .libs/libhtscodecs.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a 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[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' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' Making install in . gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[6]: Nothing to be done for 'install-exec-am'. mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include' mkdir -p '/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' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in tests gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/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/htscodecs/tests' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in io_lib gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[5]: Nothing to be done for 'install-data-am'. mkdir -p '/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 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 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[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' Making install in progs gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[5]: Nothing to be done for 'install-data-am'. mkdir -p '/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 libtool: install: /usr/bin/install -c makeSCF /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/makeSCF libtool: install: /usr/bin/install -c extract_seq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_seq libtool: install: /usr/bin/install -c extract_qual /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_qual libtool: install: /usr/bin/install -c extract_fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/index_tar libtool: install: /usr/bin/install -c scf_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_dump libtool: install: /usr/bin/install -c scf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_info libtool: install: /usr/bin/install -c scf_update /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_update libtool: install: /usr/bin/install -c get_comment /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/get_comment libtool: install: /usr/bin/install -c hash_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_tar libtool: install: /usr/bin/install -c hash_extract /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_extract libtool: install: /usr/bin/install -c hash_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_list libtool: install: /usr/bin/install -c trace_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/trace_dump libtool: install: /usr/bin/install -c hash_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_sff libtool: install: /usr/bin/install -c append_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/append_sff libtool: install: /usr/bin/install -c ztr_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/ztr_dump 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 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 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 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 libtool: install: /usr/bin/install -c srf2fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fastq libtool: install: /usr/bin/install -c srf2fasta /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fasta libtool: install: /usr/bin/install -c srf_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_filter libtool: install: /usr/bin/install -c srf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_info libtool: install: /usr/bin/install -c srf_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_list libtool: install: /usr/bin/install -c hash_exp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_exp libtool: install: /usr/bin/install -c cram_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_dump libtool: install: /usr/bin/install -c cram_index /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_index libtool: install: /usr/bin/install -c scramble /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scramble libtool: install: /usr/bin/install -c scram_merge /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_merge libtool: install: /usr/bin/install -c scram_pileup /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_pileup libtool: install: /usr/bin/install -c scram_flagstat /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_flagstat libtool: install: /usr/bin/install -c scram_test /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_test libtool: install: /usr/bin/install -c cram_size /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_size libtool: install: /usr/bin/install -c cram_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_filter gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' Making install in tests gmake[4]: Entering 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/tests' gmake[5]: Nothing to be done for 'install-exec-am'. gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man1' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man3' /usr/bin/install -c io_lib-config '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man4' /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' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib' /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' /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' /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' /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' 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' gmake[3]: 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[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 16%] Built target libstadenio gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake: *** [Makefile:169: all] Error 2 ===> 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 making "build" in /usr/ports/biology/salmon