[package - main-amd64-default][biology/biostar-tools] Failed for biostar-tools-2.1 in run-depends
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Mon, 19 Oct 2026 17:51:10 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: ports@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy24/data/main-amd64-default/pbdf56c40600a_s02971f2000/logs/biostar-tools-2.1.log Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pbdf56c40600a_s02971f2000 Log: =>> Building biology/biostar-tools build started at Mon Oct 19 17:51:00 UTC 2026 port directory: /usr/ports/biology/biostar-tools package name: biostar-tools-2.1 building for: FreeBSD main-amd64-default-job-07 16.0-CURRENT FreeBSD 16.0-CURRENT 1600028 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2827 Oct 18 01:01 /usr/ports/biology/biostar-tools/Makefile Ports top last git commit: bdf56c40600a34c93ce4badad821d77ad8025535 Ports top unclean checkout: no Port dir last git commit: 10768ab4fb59ecbdb1be619e896d75ba9f66af26 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8-3-gd92fb7c0 Host OSVERSION: 1600022 Jail OSVERSION: 1600028 Job Id: 07 !!! Jail is newer than host. (Jail: 1600028, Host: 1600022) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600028 UNAME_v=FreeBSD 16.0-CURRENT 1600028 UNAME_r=16.0-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=3.4.8-3-gd92fb7c0 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-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-amd64-default/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8-3-gd92fb7c0 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-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.12" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/biostar-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/biostar-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biostar-tools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biostar-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/biostar-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/biostar-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biostar-tools/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- PYTHON_INCLUDEDIR=include/python3.12 PYTHON_LIBDIR=lib/python3.12 PYTHON_PLATFORM=freebsd16 PYTHON_SITELIBDIR=lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" OSREL=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/biostar-tools" EXAMPLESDIR="share/examples/biostar-tools" DATADIR="share/biostar-tools" WWWDIR="www/biostar-tools" ETCDIR="etc/biostar-tools" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.12 PYTHON_LIBDIR=/usr/local/lib/python3.12 PYTHON_PLATFORM=freebsd16 PYTHON_SITELIBDIR=/usr/local/lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biostar-tools DOCSDIR=/usr/local/share/doc/biostar-tools EXAMPLESDIR=/usr/local/share/examples/biostar-tools WWWDIR=/usr/local/www/biostar-tools ETCDIR=/usr/local/etc/biostar-tools --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 (kbytes, -y) unlimited virtual machines (-V) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The biostar-tools port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License NA accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> biostar-tools-2.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.8.4.pkg [main-amd64-default-job-07] Installing pkg-2.8.4... [main-amd64-default-job-07] Extracting pkg-2.8.4: .......... done ===> biostar-tools-2.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of biostar-tools-2.1 =========================================================================== =======================<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 ===> NOTICE: The biostar-tools port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License NA accepted by the user ===> Fetching all distfiles required by biostar-tools-2.1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The biostar-tools port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License NA accepted by the user ===> Fetching all distfiles required by biostar-tools-2.1 for building <snip> The trimmomatic port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.1 depends on package: trimmomatic>0 - found ===> Returning to build of biostar-tools-2.1 ===> biostar-tools-2.1 depends on package: fastqc>0 - not found ===> Installing existing package /packages/All/fastqc-0.12.1_2.pkg [main-amd64-default-job-07] Installing fastqc-0.12.1_2... [main-amd64-default-job-07] Extracting fastqc-0.12.1_2: .......... done ===== Message from fastqc-0.12.1_2: -- ===> NOTICE: The fastqc port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.1 depends on package: fastqc>0 - found ===> Returning to build of biostar-tools-2.1 ===> biostar-tools-2.1 depends on package: picard-tools>0 - found ===> biostar-tools-2.1 depends on package: ncbi-blast+>0 - not found ===> Installing existing package /packages/All/ncbi-blast+-2.17.0_1.pkg [main-amd64-default-job-07] Installing ncbi-blast+-2.17.0_1... [main-amd64-default-job-07] `-- Installing elfutils-0.187_3... [main-amd64-default-job-07] | `-- Installing argp-standalone-1.5.0_1... [main-amd64-default-job-07] | `-- Extracting argp-standalone-1.5.0_1: ......... done [main-amd64-default-job-07] `-- Extracting elfutils-0.187_3: .......... done [main-amd64-default-job-07] `-- Installing libuv-1.52.1... [main-amd64-default-job-07] `-- Extracting libuv-1.52.1: .......... done [main-amd64-default-job-07] `-- Installing lmdb0-0.9.36... [main-amd64-default-job-07] `-- Extracting lmdb0-0.9.36: .......... done [main-amd64-default-job-07] `-- Installing lzo2-2.10_2... [main-amd64-default-job-07] `-- Extracting lzo2-2.10_2: .......... done [main-amd64-default-job-07] `-- Installing p5-JSON-4.10... [main-amd64-default-job-07] `-- Extracting p5-JSON-4.10: .......... done [main-amd64-default-job-07] `-- Installing p5-List-MoreUtils-0.430... [main-amd64-default-job-07] | `-- Installing p5-Exporter-Tiny-1.006003... [main-amd64-default-job-07] | `-- Extracting p5-Exporter-Tiny-1.006003: .......... done [main-amd64-default-job-07] | `-- Installing p5-List-MoreUtils-XS-0.430... [main-amd64-default-job-07] | `-- Extracting p5-List-MoreUtils-XS-0.430: ....... done [main-amd64-default-job-07] `-- Extracting p5-List-MoreUtils-0.430: .......... done [main-amd64-default-job-07] Extracting ncbi-blast+-2.17.0_1: .......... done ===== Message from ncbi-blast+-2.17.0_1: -- ===> NOTICE: The ncbi-blast+ port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.1 depends on package: ncbi-blast+>0 - found ===> Returning to build of biostar-tools-2.1 ===> biostar-tools-2.1 depends on package: cd-hit>0 - not found ===> Installing existing package /packages/All/cd-hit-4.8.1_3.pkg [main-amd64-default-job-07] Installing cd-hit-4.8.1_3... [main-amd64-default-job-07] Extracting cd-hit-4.8.1_3: .......... done ===== Message from cd-hit-4.8.1_3: -- ===> NOTICE: The cd-hit port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.1 depends on package: cd-hit>0 - found ===> Returning to build of biostar-tools-2.1 ===> biostar-tools-2.1 depends on package: py312-biopython>0 - not found ===> Installing existing package /packages/All/py312-biopython-1.85_4.pkg [main-amd64-default-job-07] Installing py312-biopython-1.85_4... [main-amd64-default-job-07] `-- Installing py312-numpy-2.4.6_1,1... [main-amd64-default-job-07] | `-- Installing gcc14-14.2.0_7... [main-amd64-default-job-07] | | `-- Installing binutils-2.44,1... [main-amd64-default-job-07] | | `-- Extracting binutils-2.44,1: .......... done [main-amd64-default-job-07] | | `-- Installing gmp-6.3.0... [main-amd64-default-job-07] | | `-- Extracting gmp-6.3.0: .......... done [main-amd64-default-job-07] | | `-- Installing mpc-1.4.1... [main-amd64-default-job-07] | | `-- Installing mpfr-4.2.2,1... [main-amd64-default-job-07] | | `-- Extracting mpfr-4.2.2,1: .......... done [main-amd64-default-job-07] | | `-- Extracting mpc-1.4.1: .......... done [main-amd64-default-job-07] | `-- Extracting gcc14-14.2.0_7: .......... done [main-amd64-default-job-07] | `-- Installing openblas-0.3.34_1,2... [main-amd64-default-job-07] | `-- Extracting openblas-0.3.34_1,2: .......... done [main-amd64-default-job-07] `-- Extracting py312-numpy-2.4.6_1,1: .......... done [main-amd64-default-job-07] `-- Installing py312-reportlab-4.4.10... [main-amd64-default-job-07] | `-- Installing adobe-cmaps-20051217_4... [main-amd64-default-job-07] | `-- Extracting adobe-cmaps-20051217_4: .......... done [main-amd64-default-job-07] | `-- Installing py312-pillow-12.3.0... [main-amd64-default-job-07] | | `-- Installing libavif-1.4.2... [main-amd64-default-job-07] | | `-- Installing aom-3.15.1... [main-amd64-default-job-07] | | | `-- Installing vmaf-3.2.1... [main-amd64-default-job-07] | | | `-- Extracting vmaf-3.2.1: .......... done [main-amd64-default-job-07] | | `-- Extracting aom-3.15.1: .......... done [main-amd64-default-job-07] | | `-- Installing dav1d-1.5.4... [main-amd64-default-job-07] | | `-- Extracting dav1d-1.5.4: .......... done [main-amd64-default-job-07] | | `-- Installing gdk-pixbuf2-2.44.1... [main-amd64-default-job-07] | | | `-- Installing libxml2-2.15.4... [main-amd64-default-job-07] | | | `-- Extracting libxml2-2.15.4: .......... done [main-amd64-default-job-07] | | | `-- Installing shared-mime-info-2.4_2... [main-amd64-default-job-07] | | | `-- Extracting shared-mime-info-2.4_2: ......... done [main-amd64-default-job-07] | | `-- Extracting gdk-pixbuf2-2.44.1: .......... done [main-amd64-default-job-07] | | `-- Installing libyuv-0.0.1973... [main-amd64-default-job-07] | | `-- Extracting libyuv-0.0.1973: .......... done [main-amd64-default-job-07] | | `-- Extracting libavif-1.4.2: .......... done [main-amd64-default-job-07] | | `-- Installing libimagequant-4.4.1_8... [main-amd64-default-job-07] | | `-- Extracting libimagequant-4.4.1_8: ......... done [main-amd64-default-job-07] | | `-- Installing libraqm-0.11.0... [main-amd64-default-job-07] | | `-- Installing fribidi-1.0.17... [main-amd64-default-job-07] | | `-- Extracting fribidi-1.0.17: .......... done [main-amd64-default-job-07] | | `-- Extracting libraqm-0.11.0: .......... done [main-amd64-default-job-07] | | `-- Installing openjpeg-2.5.4_2... [main-amd64-default-job-07] | | `-- Extracting openjpeg-2.5.4_2: .......... done [main-amd64-default-job-07] | | `-- Installing py312-tkinter-3.12.15_11... [main-amd64-default-job-07] | | `-- Installing tcl86-8.6.18_1... [main-amd64-default-job-07] | | `-- Extracting tcl86-8.6.18_1: .......... done [main-amd64-default-job-07] | | `-- Installing tk86-8.6.18... [main-amd64-default-job-07] | | | `-- Installing libXScrnSaver-1.2.5... [main-amd64-default-job-07] | | | `-- Extracting libXScrnSaver-1.2.5: .......... done [main-amd64-default-job-07] | | `-- Extracting tk86-8.6.18: .......... done [main-amd64-default-job-07] | | `-- Extracting py312-tkinter-3.12.15_11: ......... done [main-amd64-default-job-07] | `-- Extracting py312-pillow-12.3.0: .......... done [main-amd64-default-job-07] `-- Extracting py312-reportlab-4.4.10: .......... done [main-amd64-default-job-07] Extracting py312-biopython-1.85_4: .......... done ==> Running trigger: gdk-pixbuf-query-loaders.ucl Generating gdk-pixbuf modules cache ==> Running trigger: shared-mime-info.ucl Building the Shared MIME-Info database cache ===== Message from gcc14-14.2.0_7: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from libraqm-0.11.0: -- ===> NOTICE: The libraqm port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> biostar-tools-2.1 depends on package: py312-biopython>0 - found ===> Returning to build of biostar-tools-2.1 ===> biostar-tools-2.1 depends on package: py312-pysam>0 - not found ===> Installing existing package /packages/All/py312-pysam-0.24.1.pkg [main-amd64-default-job-07] Installing py312-pysam-0.24.1... [main-amd64-default-job-07] `-- Installing py312-cython-3.2.9... [main-amd64-default-job-07] `-- Extracting py312-cython-3.2.9: .......... done [main-amd64-default-job-07] Extracting py312-pysam-0.24.1: .......... done ===> biostar-tools-2.1 depends on package: py312-pysam>0 - found ===> Returning to build of biostar-tools-2.1 ===> biostar-tools-2.1 depends on package: freebayes>0 - not found ===> Installing existing package /packages/All/freebayes-1.3.10.pkg [main-amd64-default-job-07] Installing freebayes-1.3.10... pkg-static: Missing shlib libvcflib.so required by freebayes Failed to install the following 1 package(s): /packages/All/freebayes-1.3.10.pkg *** Error code 1 Stop. make: stopped making "run-depends" in /usr/ports/biology/biostar-tools