[package - 150amd64-default][biology/salmon] Failed for salmon-1.10.3_1 in build-depends
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Date: Tue, 10 Mar 2026 13:58:19 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/beefy23/data/150amd64-default/7db22f508e75/logs/salmon-1.10.3_1.log Build URL: https://pkg-status.freebsd.org/beefy23/build.html?mastername=150amd64-default&build=7db22f508e75 Log: =>> Building biology/salmon build started at Tue Mar 10 13:58:16 UTC 2026 port directory: /usr/ports/biology/salmon package name: salmon-1.10.3_1 building for: FreeBSD 150amd64-default-job-07 15.0-RELEASE-p4 FreeBSD 15.0-RELEASE-p4 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1937 Dec 20 01:01 /usr/ports/biology/salmon/Makefile Ports top last git commit: 7db22f508e754c67b1cf1932bc77a708dce453d4 Ports top unclean checkout: no Port dir last git commit: 0729671e31677625693578f8a890e7a5ad555b7f Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.6 Host OSVERSION: 1600007 Jail OSVERSION: 1500068 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p4 UNAME_r=15.0-RELEASE-p4 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=3.4.6 MASTERMNT=/usr/local/poudriere/data/.m/150amd64-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/150amd64-default/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=150amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/150amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.6 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=/usr/local/bin/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 " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -isystem /usr/local/include " BSD_INSTALL_PROGRAM=" install -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--- 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 pipebuf (-y) 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-1.10.3_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [150amd64-default-job-07] Installing pkg-2.6.2... [150amd64-default-job-07] Extracting pkg-2.6.2: .......... done ===> salmon-1.10.3_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of salmon-1.10.3_1 =========================================================================== =======================<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-1.10.3_1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: FETCH_REGET=0 NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by salmon-1.10.3_1 for building => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.3_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.3_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-15-1_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-de42211_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-1.10.3_1 for building ===> Extracting for salmon-1.10.3_1 => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.3_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.3_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-15-1_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-de42211_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-1.10.3_1 ===> Applying FreeBSD patches for salmon-1.10.3_1 from /usr/ports/biology/salmon/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.3_1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.9.pkg [150amd64-default-job-07] Installing bash-5.3.9... [150amd64-default-job-07] `-- Installing gettext-runtime-0.26... [150amd64-default-job-07] | `-- Installing indexinfo-0.3.1_1... [150amd64-default-job-07] | `-- Extracting indexinfo-0.3.1_1: .... done [150amd64-default-job-07] `-- Extracting gettext-runtime-0.26: .......... done [150amd64-default-job-07] Extracting bash-5.3.9: .......... done ===> salmon-1.10.3_1 depends on executable: bash - found ===> Returning to build of salmon-1.10.3_1 ===> salmon-1.10.3_1 depends on package: cereal>=1.3.0 - not found ===> Installing existing package /packages/All/cereal-1.3.2_1.pkg [150amd64-default-job-07] Installing cereal-1.3.2_1... [150amd64-default-job-07] `-- Installing boost-libs-1.89.0_2... [150amd64-default-job-07] | `-- Installing icu-76.1,1... [150amd64-default-job-07] | `-- Extracting icu-76.1,1: .......... done [150amd64-default-job-07] | `-- Installing zstd-1.5.7_1... [150amd64-default-job-07] | `-- Extracting zstd-1.5.7_1: .......... done [150amd64-default-job-07] `-- Extracting boost-libs-1.89.0_2: .......... done [150amd64-default-job-07] Extracting cereal-1.3.2_1: .......... done ===== Message from boost-libs-1.89.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> salmon-1.10.3_1 depends on package: cereal>=1.3.0 - found ===> Returning to build of salmon-1.10.3_1 ===> salmon-1.10.3_1 depends on package: libgff==2.0.0 - not found ===> Installing existing package /packages/All/libgff-2.0.1.pkg [150amd64-default-job-07] Installing libgff-2.0.1... [150amd64-default-job-07] Extracting libgff-2.0.1: .......... done ===> salmon-1.10.3_1 depends on package: libgff==2.0.0 - not found *** Error code 1 Stop. make: stopped making "build-depends" in /usr/ports/biology/salmon