[package - 135arm64-default][biology/rna-seq] Failed for rna-seq-0.1.4 in run-depends
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Date: Mon, 14 Jul 2025 06:57:47 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/ampere3/data/135arm64-default/b3423aefe7f1/logs/rna-seq-0.1.4.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=135arm64-default&build=b3423aefe7f1 Log: =>> Building biology/rna-seq build started at Mon Jul 14 06:50:22 UTC 2025 port directory: /usr/ports/biology/rna-seq package name: rna-seq-0.1.4 building for: FreeBSD 135arm64-default-job-10 13.5-RELEASE-p2 FreeBSD 13.5-RELEASE-p2 arm64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 704 Aug 5 2023 /usr/ports/biology/rna-seq/Makefile Ports top last git commit: b3423aefe7f Ports top unclean checkout: no Port dir last git commit: 3a654ece10c Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2-12-g74a54a88 Host OSVERSION: 1500035 Jail OSVERSION: 1305000 Job Id: 10 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p2 UNAME_r=13.5-RELEASE-p2 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=3.4.2-12-g74a54a88 MASTERMNT=/usr/local/poudriere/data/.m/135arm64-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/135arm64-default/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=135arm64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/135arm64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2-12-g74a54a88 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-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/rna-seq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/rna-seq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/rna-seq/work/.cache HOME=/wrkdirs/usr/ports/biology/rna-seq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/rna-seq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/rna-seq/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/rna-seq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/rna-seq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/rna-seq/work/.cache HOME=/wrkdirs/usr/ports/biology/rna-seq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/rna-seq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/rna-seq/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/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/rna-seq" EXAMPLESDIR="share/examples/rna-seq" DATADIR="share/rna-seq" WWWDIR="www/rna-seq" ETCDIR="etc/rna-seq" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/rna-seq DOCSDIR=/usr/local/share/doc/rna-seq EXAMPLESDIR=/usr/local/share/examples/rna-seq WWWDIR=/usr/local/www/rna-seq ETCDIR=/usr/local/etc/rna-seq --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) 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 NA accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rna-seq-0.1.4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.2.1.pkg [135arm64-default-job-10] Installing pkg-2.2.1... [135arm64-default-job-10] Extracting pkg-2.2.1: .......... done ===> rna-seq-0.1.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rna-seq-0.1.4 =========================================================================== =======================<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 NA accepted by the user ===> Fetching all distfiles required by rna-seq-0.1.4 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License NA accepted by the user ===> Fetching all distfiles required by rna-seq-0.1.4 for building =========================================================================== =======================<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 NA accepted by the user ===> Fetching all distfiles required by rna-seq-0.1.4 for building ===> Extracting for rna-seq-0.1.4 =========================================================================== =======================<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 rna-seq-0.1.4 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rna-seq-0.1.4 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.13.pkg [135arm64-default-job-10] Installing python311-3.11.13... [135arm64-default-job-10] `-- Installing gettext-runtime-0.23.1... [135arm64-default-job-10] | `-- Installing indexinfo-0.3.1_1... [135arm64-default-job-10] | `-- Extracting indexinfo-0.3.1_1: .... done [135arm64-default-job-10] `-- Extracting gettext-runtime-0.23.1: .......... done [135arm64-default-job-10] `-- Installing libffi-3.5.1... [135arm64-default-job-10] `-- Extracting libffi-3.5.1: .......... done [135arm64-default-job-10] `-- Installing mpdecimal-4.0.1... [135arm64-default-job-10] `-- Extracting mpdecimal-4.0.1: .......... done [135arm64-default-job-10] `-- Installing readline-8.2.13_2... [135arm64-default-job-10] `-- Extracting readline-8.2.13_2: .......... done [135arm64-default-job-10] Extracting python311-3.11.13: .......... done ===== Message from python311-3.11.13: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> rna-seq-0.1.4 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of rna-seq-0.1.4 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 <snip> [135arm64-default-job-10] | | | `-- Extracting py311-fs2-2.4.16_1: .......... done [135arm64-default-job-10] | | | `-- Installing py311-unicodedata2-16.0.0... [135arm64-default-job-10] | | | `-- Extracting py311-unicodedata2-16.0.0: ......... done [135arm64-default-job-10] | | | `-- Installing py311-zopfli-0.2.3... [135arm64-default-job-10] | | | `-- Extracting py311-zopfli-0.2.3: .......... done [135arm64-default-job-10] | | | `-- Extracting py311-fonttools-4.58.4: .......... done [135arm64-default-job-10] | | | `-- Installing py311-importlib-resources-6.5.2... [135arm64-default-job-10] | | | `-- Extracting py311-importlib-resources-6.5.2: .......... done [135arm64-default-job-10] | | | `-- Installing py311-kiwisolver-1.4.8,1... [135arm64-default-job-10] | | | `-- Extracting py311-kiwisolver-1.4.8,1: .......... done [135arm64-default-job-10] | | | `-- Installing py311-pluggy-1.6.0... [135arm64-default-job-10] | | | `-- Extracting py311-pluggy-1.6.0: .......... done [135arm64-default-job-10] | | | `-- Installing py311-pyparsing-3.2.3... [135arm64-default-job-10] | | | `-- Extracting py311-pyparsing-3.2.3: .......... done [135arm64-default-job-10] | | | `-- Installing py311-tornado-6.5... [135arm64-default-job-10] | | | `-- Extracting py311-tornado-6.5: .......... done [135arm64-default-job-10] | | `-- Extracting py311-matplotlib-3.8.0_1: .......... done [135arm64-default-job-10] | | `-- Installing py311-pydot-4.0.1... [135arm64-default-job-10] | | | `-- Installing graphviz-12.2.1_2... [135arm64-default-job-10] | | | `-- Installing cairo-1.18.2,3... [135arm64-default-job-10] | | | | `-- Installing pixman-0.46.2... [135arm64-default-job-10] | | | | `-- Extracting pixman-0.46.2: ......... done [135arm64-default-job-10] | | | `-- Extracting cairo-1.18.2,3: .......... done [135arm64-default-job-10] | | | `-- Installing libXaw-1.0.16,2... [135arm64-default-job-10] | | | | `-- Installing libXmu-1.1.4,1... [135arm64-default-job-10] | | | | `-- Extracting libXmu-1.1.4,1: .......... done [135arm64-default-job-10] | | | | `-- Installing libXpm-3.5.17_1... [135arm64-default-job-10] | | | | `-- Extracting libXpm-3.5.17_1: .......... done [135arm64-default-job-10] | | | `-- Extracting libXaw-1.0.16,2: .......... done [135arm64-default-job-10] | | | `-- Installing libgd-2.3.3_13,1... [135arm64-default-job-10] | | | `-- Extracting libgd-2.3.3_13,1: .......... done [135arm64-default-job-10] | | | `-- Installing libltdl-2.5.4... [135arm64-default-job-10] | | | `-- Extracting libltdl-2.5.4: .......... done [135arm64-default-job-10] | | | `-- Installing pango-1.56.1... [135arm64-default-job-10] | | | | `-- Installing libthai-0.1.29_1... [135arm64-default-job-10] | | | | `-- Installing libdatrie-0.2.13_2... [135arm64-default-job-10] | | | | `-- Extracting libdatrie-0.2.13_2: .......... done [135arm64-default-job-10] | | | | `-- Extracting libthai-0.1.29_1: .......... done [135arm64-default-job-10] | | | `-- Extracting pango-1.56.1: .......... done [135arm64-default-job-10] | | | `-- Extracting graphviz-12.2.1_2: .......... done [135arm64-default-job-10] | | `-- Extracting py311-pydot-4.0.1: .......... done [135arm64-default-job-10] | | `-- Installing py311-pygraphviz-1.6_1... [135arm64-default-job-10] | | `-- Extracting py311-pygraphviz-1.6_1: .......... done [135arm64-default-job-10] | | `-- Installing py311-scikit-sparse-0.4.16... [135arm64-default-job-10] | | | `-- Installing py311-scipy-1.11.1_4,1... [135arm64-default-job-10] | | | `-- Installing blas-3.12.1... [135arm64-default-job-10] | | | `-- Extracting blas-3.12.1: ........ done [135arm64-default-job-10] | | | `-- Extracting py311-scipy-1.11.1_4,1: .......... done [135arm64-default-job-10] | | `-- Extracting py311-scikit-sparse-0.4.16: .......... done [135arm64-default-job-10] | | `-- Extracting py311-networkx-3.5,2: .......... done [135arm64-default-job-10] | `-- Extracting py311-colormath-3.0.0_3: .......... done [135arm64-default-job-10] `-- Extracting py311-spectra-0.0.11_2: .......... done [135arm64-default-job-10] `-- Installing py311-tqdm-4.67.1... [135arm64-default-job-10] `-- Extracting py311-tqdm-4.67.1: .......... done [135arm64-default-job-10] `-- Installing py311-typeguard-4.4.4... [135arm64-default-job-10] `-- Extracting py311-typeguard-4.4.4: .......... done [135arm64-default-job-10] Extracting py311-multiqc-1.25.2_2: .......... 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 py311-pandas-2.2.3_1,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===== Message from libimagequant-4.3.4_4: -- ===> NOTICE: The libimagequant 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 ===== Message from libraqm-0.10.2: -- ===> 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 ===== Message from py311-urllib3-1.26.20,1: -- Since version 1.25 HTTPS connections are now verified by default which is done via "cert_reqs = 'CERT_REQUIRED'". While certificate verification can be disabled via "cert_reqs = 'CERT_NONE'", it's highly recommended to leave it on. Various consumers of net/py-urllib3 already have implemented routines that either explicitly enable or disable HTTPS certificate verification (e.g. via configuration settings, CLI arguments, etc.). Yet it may happen that there are still some consumers which don't explicitly enable/disable certificate verification for HTTPS connections which could then lead to errors (as is often the case with self-signed certificates). In case of an error one should try first to temporarily disable certificate verification of the problematic urllib3 consumer to see if that approach will remedy the issue. ===== Message from boost-libs-1.88.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===== Message from postgresql17-client-17.5: -- The PostgreSQL port has a collection of "side orders": postgresql-docs For all of the html documentation p5-Pg A perl5 API for client access to PostgreSQL databases. postgresql-tcltk If you want tcl/tk client support. postgresql-jdbc For Java JDBC support. postgresql-odbc For client access from unix applications using ODBC as access method. Not needed to access unix PostgreSQL servers from Win32 using ODBC. See below. ruby-postgres, py-psycopg For client access to PostgreSQL databases using the ruby & python languages. postgresql-plperl, postgresql-pltcl & postgresql-plruby For using perl5, tcl & ruby as procedural languages. postgresql-contrib Lots of contributed utilities, postgresql functions and datatypes. There you find pg_standby, pgcrypto and many other cool things. etc... ===> rna-seq-0.1.4 depends on package: py311-multiqc>0 - found ===> Returning to build of rna-seq-0.1.4 ===> rna-seq-0.1.4 depends on package: biolibc-tools>0 - not found ===> Installing existing package /packages/All/biolibc-tools-0.1.5.pkg [135arm64-default-job-10] Installing biolibc-tools-0.1.5... [135arm64-default-job-10] `-- Installing xxhash-0.8.3... [135arm64-default-job-10] `-- Extracting xxhash-0.8.3: .......... done [135arm64-default-job-10] Extracting biolibc-tools-0.1.5: .......... done ===> rna-seq-0.1.4 depends on package: biolibc-tools>0 - found ===> Returning to build of rna-seq-0.1.4 ===> rna-seq-0.1.4 depends on package: gffread>0 - not found ===> Installing existing package /packages/All/gffread-0.12.7.pkg [135arm64-default-job-10] Installing gffread-0.12.7... [135arm64-default-job-10] Extracting gffread-0.12.7: .... done ===> rna-seq-0.1.4 depends on package: gffread>0 - found ===> Returning to build of rna-seq-0.1.4 ===> rna-seq-0.1.4 depends on package: kallisto>0 - not found ===> Installing existing package /packages/All/kallisto-0.51.1_1,1.pkg [135arm64-default-job-10] Installing kallisto-0.51.1_1,1... [135arm64-default-job-10] `-- Installing htslib-1.22... [135arm64-default-job-10] `-- Extracting htslib-1.22: .......... done [135arm64-default-job-10] Extracting kallisto-0.51.1_1,1: .......... done ===> rna-seq-0.1.4 depends on package: kallisto>0 - found ===> Returning to build of rna-seq-0.1.4 ===> rna-seq-0.1.4 depends on package: hisat2>0 - not found ===> Installing existing package /packages/All/hisat2-2.2.1_2.pkg [135arm64-default-job-10] Installing hisat2-2.2.1_2... [135arm64-default-job-10] Extracting hisat2-2.2.1_2: .......... done ===> rna-seq-0.1.4 depends on package: hisat2>0 - found ===> Returning to build of rna-seq-0.1.4 ===> rna-seq-0.1.4 depends on package: rna-STAR>0 - not found ===> Installing existing package /packages/All/rna-STAR-2.7.11.a_1.pkg [135arm64-default-job-10] Installing rna-STAR-2.7.11.a_1... pkg-static: Missing shlib dependency: libstdc++.so.6 Failed to install the following 1 package(s): /packages/All/rna-STAR-2.7.11.a_1.pkg *** Error code 1 Stop. make: stopped in /usr/ports/biology/rna-seq