=>> Building biology/bcftools build started at Sat May 23 23:48:44 JST 2026 port directory: /usr/ports/biology/bcftools package name: bcftools-1.23.1 building for: FreeBSD curamd64-setuptools-job-02 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1635 May 2 10:17 /usr/ports/biology/bcftools/Makefile Ports top last git commit: a8b187544 Ports top unclean checkout: yes Port dir last git commit: a8b187544 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1600018 Jail OSVERSION: 1600018 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600018 UNAME_v=FreeBSD 16.0-CURRENT 1600018 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=3.4.4 MASTERMNT=/usr/local/poudriere/data/.m/curamd64-setuptools/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/curamd64-setuptools/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=curamd64-setuptools SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/curamd64-setuptools/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 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--- ===> The following configuration options are available for bcftools-1.23.1: GPL=on: Enable modules that rely on GPL code PERL=on: Enable external PERL scripts for advanced filtering ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-libgsl --enable-perl-filters --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/bcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bcftools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.73 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- USE_GPL=1 PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/bcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bcftools/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 DEFAULT_AUTOCONF=2.73 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=" " 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="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=freebsd16 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=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.2 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/bcftools" EXAMPLESDIR="share/examples/bcftools" DATADIR="share/bcftools" WWWDIR="www/bcftools" ETCDIR="etc/bcftools" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd16 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/bcftools DOCSDIR=/usr/local/share/doc/bcftools EXAMPLESDIR=/usr/local/share/examples/bcftools WWWDIR=/usr/local/www/bcftools ETCDIR=/usr/local/etc/bcftools --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+= magick=7-x11 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5_mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= GAMMA INPUTMETHOD LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+= magick=7-x11 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5_mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= GAMMA INPUTMETHOD LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---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) 12099 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-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License MIT GPLv3 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bcftools-1.23.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [curamd64-setuptools-job-02] Installing pkg-2.7.5... [curamd64-setuptools-job-02] Extracting pkg-2.7.5: .......... done ===> bcftools-1.23.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bcftools-1.23.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT GPLv3 accepted by the user => samtools-bcftools-1.23.1_GH0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://codeload.github.com/samtools/bcftools/tar.gz/1.23.1?dummy=/samtools-bcftools-1.23.1_GH0.tar.gz fetch: https://codeload.github.com/samtools/bcftools/tar.gz/1.23.1?dummy=/samtools-bcftools-1.23.1_GH0.tar.gz: size unknown fetch: https://codeload.github.com/samtools/bcftools/tar.gz/1.23.1?dummy=/samtools-bcftools-1.23.1_GH0.tar.gz: size of remote file is not known samtools-bcftools-1.23.1_GH0.tar.gz 3676 kB 6383 kBps 00s ===> Fetching all distfiles required by bcftools-1.23.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT GPLv3 accepted by the user ===> Fetching all distfiles required by bcftools-1.23.1 for building => SHA256 Checksum OK for samtools-bcftools-1.23.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License MIT GPLv3 accepted by the user ===> Fetching all distfiles required by bcftools-1.23.1 for building ===> Extracting for bcftools-1.23.1 => SHA256 Checksum OK for samtools-bcftools-1.23.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for bcftools-1.23.1 ===> Applying FreeBSD patches for bcftools-1.23.1 from /usr/ports/biology/bcftools/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bcftools-1.23.1 depends on package: htslib>=1.22 - not found ===> Installing existing package /packages/All/htslib-1.23.1.pkg [curamd64-setuptools-job-02] Installing htslib-1.23.1... [curamd64-setuptools-job-02] `-- Installing curl-8.19.0_2... [curamd64-setuptools-job-02] | `-- Installing brotli-1.2.0,1... [curamd64-setuptools-job-02] | `-- Extracting brotli-1.2.0,1: .......... done [curamd64-setuptools-job-02] | `-- Installing libidn2-2.3.8... [curamd64-setuptools-job-02] | | `-- Installing indexinfo-0.3.1_1... [curamd64-setuptools-job-02] | | `-- Extracting indexinfo-0.3.1_1: .... done [curamd64-setuptools-job-02] | | `-- Installing libunistring-1.4.2... [curamd64-setuptools-job-02] | | `-- Extracting libunistring-1.4.2: .......... done [curamd64-setuptools-job-02] | `-- Extracting libidn2-2.3.8: .......... done [curamd64-setuptools-job-02] | `-- Installing libnghttp2-1.69.0... [curamd64-setuptools-job-02] | `-- Extracting libnghttp2-1.69.0: .......... done [curamd64-setuptools-job-02] | `-- Installing libpsl-0.21.5_2... [curamd64-setuptools-job-02] | `-- Extracting libpsl-0.21.5_2: .......... done [curamd64-setuptools-job-02] | `-- Installing libssh2-1.11.1,3... [curamd64-setuptools-job-02] | | `-- Installing openssl-3.0.20,1... [curamd64-setuptools-job-02] | | `-- Extracting openssl-3.0.20,1: .......... done [curamd64-setuptools-job-02] | `-- Extracting libssh2-1.11.1,3: .......... done [curamd64-setuptools-job-02] | `-- Installing zstd-1.5.7_1... [curamd64-setuptools-job-02] | `-- Extracting zstd-1.5.7_1: .......... done [curamd64-setuptools-job-02] `-- Extracting curl-8.19.0_2: .......... done [curamd64-setuptools-job-02] `-- Installing libdeflate-1.25... [curamd64-setuptools-job-02] `-- Extracting libdeflate-1.25: .......... done [curamd64-setuptools-job-02] Extracting htslib-1.23.1: .......... done ===> bcftools-1.23.1 depends on package: htslib>=1.22 - found ===> Returning to build of bcftools-1.23.1 ===> bcftools-1.23.1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [curamd64-setuptools-job-02] Installing gmake-4.4.1... [curamd64-setuptools-job-02] `-- Installing gettext-runtime-1.0... [curamd64-setuptools-job-02] `-- Extracting gettext-runtime-1.0: .......... done [curamd64-setuptools-job-02] Extracting gmake-4.4.1: .......... done ===> bcftools-1.23.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of bcftools-1.23.1 ===> bcftools-1.23.1 depends on package: autoconf>=2.73 - not found ===> Installing existing package /packages/All/autoconf-2.73.pkg [curamd64-setuptools-job-02] Installing autoconf-2.73... [curamd64-setuptools-job-02] `-- Installing autoconf-switch-20220527... [curamd64-setuptools-job-02] `-- Extracting autoconf-switch-20220527: .......... done [curamd64-setuptools-job-02] `-- Installing m4-1.4.21,1... [curamd64-setuptools-job-02] `-- Extracting m4-1.4.21,1: .......... done [curamd64-setuptools-job-02] `-- Installing perl5-5.42.2... [curamd64-setuptools-job-02] `-- Extracting perl5-5.42.2: .......... done [curamd64-setuptools-job-02] Extracting autoconf-2.73: .......... done ===> bcftools-1.23.1 depends on package: autoconf>=2.73 - found ===> Returning to build of bcftools-1.23.1 ===> bcftools-1.23.1 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [curamd64-setuptools-job-02] Installing automake-1.18.1... [curamd64-setuptools-job-02] Extracting automake-1.18.1: .......... done ===> bcftools-1.23.1 depends on package: automake>=1.18.1 - found ===> Returning to build of bcftools-1.23.1 ===> bcftools-1.23.1 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bcftools-1.23.1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.23.1 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.8.pkg [curamd64-setuptools-job-02] Installing gsl-2.8... [curamd64-setuptools-job-02] Extracting gsl-2.8: .......... done ===> bcftools-1.23.1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of bcftools-1.23.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for bcftools-1.23.1 configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1100: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure: loading site script /usr/ports/Templates/config.site checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C23 features... unsupported checking for cc option to enable C11 features... none needed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for cc option to support large files... none needed checking location of HTSlib source tree... none found checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... (cached) yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lgslcblas checking for gsl_multifit_gradient in -lgsl... yes checking for library containing Perl_call_pv... -lperl checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h configure: License has been changed to GPL. Linking against the GNU scientific library requires that the resulting binary is licensed using the GNU General Public License. In particular, this means you will have to follow the terms of this license in order to distribute binary copies. For more information see the INSTALL file. Text of the GNU General Public License can be found in the LICENSE file, or at http://www.gnu.org/copyleft/gpl.html Information on the GNU Scientific Library, including the rationale for its choice of license can be found at https://www.gnu.org/software/gsl/ =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for bcftools-1.23.1 echo '#define BCFTOOLS_VERSION "1.23.1"' > version.h cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -DUSE_GPL -c -o main.o main.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfindex.o vcfindex.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tabix.o tabix.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfstats.o vcfstats.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfisec.o vcfisec.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfmerge.o vcfmerge.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfquery.o vcfquery.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcffilter.o vcffilter.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -DNO_POSIX_2008_LOCALE -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -I/usr/local/lib/perl5/5.42/mach/CORE -c -o filter.o filter.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsom.o vcfsom.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfnorm.o vcfnorm.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfgtcheck.o vcfgtcheck.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfview.o vcfview.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfannotate.o vcfannotate.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfroh.o vcfroh.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconcat.o vcfconcat.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfcall.o vcfcall.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mcall.o mcall.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcmp.o vcmp.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o gvcf.o gvcf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o reheader.o reheader.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o convert.o convert.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconvert.o vcfconvert.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tsv2vcf.o tsv2vcf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfcnv.o vcfcnv.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfhead.o vcfhead.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o HMM.o HMM.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o consensus.o consensus.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ploidy.o ploidy.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bin.o bin.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hclust.o hclust.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o version.o version.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o regidx.o regidx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o smpl_ilist.o smpl_ilist.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o csq.o csq.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfbuf.o vcfbuf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mpileup.o mpileup.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf.o bam2bcf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf_indel.o bam2bcf_indel.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf_iaux.o bam2bcf_iaux.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf_edlib.o bam2bcf_edlib.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o read_consensus.o read_consensus.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam_sample.o bam_sample.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsort.o vcfsort.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cols.o cols.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o extsort.o extsort.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o dist.o dist.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o abuf.o abuf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ccall.o ccall.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o em.o em.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o prob1.o prob1.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kmin.o kmin.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o str_finder.o str_finder.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o gff.o gff.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o edlib.o edlib.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mpileup2/mpileup.o mpileup2/mpileup.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o polysomy.o polysomy.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o peakfit.o peakfit.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -DPLUGINPATH='"/usr/local/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c cc -rdynamic -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o mpileup2/mpileup.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz -L/usr/local/lib -lgsl -lgslcblas -Wl,-R/usr/local/lib/perl5/5.42/mach/CORE -pthread -Wl,-E -fstack-protector-strong -L/usr/local/lib -L/usr/local/lib/perl5/5.42/mach/CORE -lperl -ldl -lm -lcrypt -lutil -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-rbuf.o test/test-rbuf.c cc -o test/test-rbuf test/test-rbuf.o -lz -L/usr/local/lib cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-regidx.o test/test-regidx.c cc -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/GTisec.so version.c plugins/GTisec.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/GTsubset.so version.c plugins/GTsubset.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/allele-length.so version.c plugins/allele-length.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/contrast.so version.c plugins/contrast.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/counts.so version.c plugins/counts.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/dosage.so version.c plugins/dosage.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -DNO_POSIX_2008_LOCALE -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -I/usr/local/lib/perl5/5.42/mach/CORE -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fill-tags.so version.c plugins/fill-tags.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fixref.so version.c plugins/fixref.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/frameshifts.so version.c plugins/frameshifts.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/gvcfz.so version.c plugins/gvcfz.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/impute-info.so version.c plugins/impute-info.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/indel-stats.so version.c plugins/indel-stats.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/mendelian2.so version.c plugins/mendelian2.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/missing2ref.so version.c plugins/missing2ref.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/parental-origin.so version.c plugins/parental-origin.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/prune.so version.c plugins/prune.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/scatter.so version.c plugins/scatter.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/setGT.so version.c plugins/setGT.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/split-vep.so version.c plugins/split-vep.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/split.so version.c plugins/split.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/tag2tag.so version.c plugins/tag2tag.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/trio-stats.so version.c plugins/trio-stats.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/variant-distance.so version.c plugins/variant-distance.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/vcf2table.so version.c plugins/vcf2table.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/vrfs.so version.c plugins/vrfs.c -L/usr/local/lib =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bcftools-1.23.1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.9.pkg [curamd64-setuptools-job-02] Installing bash-5.3.9... [curamd64-setuptools-job-02] Extracting bash-5.3.9: .......... done ===> bcftools-1.23.1 depends on executable: bash - found ===> Returning to build of bcftools-1.23.1 ===> bcftools-1.23.1 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for bcftools-1.23.1 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/share/man/man1 /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/libexec/bcftools install -s -m 555 bcftools /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin install -m 555 misc/color-chrs.pl misc/gff2gff misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/roh-viz misc/run-roh.pl misc/vcfutils.pl misc/vrfs-variances /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin install -m 444 doc/bcftools.1 /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/share/man/man1 install -s -m 555 plugins/*.so /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/libexec/bcftools /bin/mv /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/color-chrs.pl /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/color-chrs /bin/mv /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/guess-ploidy.py /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/guess-ploidy /bin/mv //wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/plot-roh.py /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/plot-roh /bin/mv /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/run-roh.pl /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/run-roh /bin/mv /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/vcfutils.pl /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/vcfutils /bin/mv /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/plot-vcfstats /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/ ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-05-23T14:48:44+0000' 'PKG_NOTE_ports_top_git_hash=a8b187544' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=a8b187544' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.4' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for bcftools-1.23.1 ===> Building bcftools-1.23.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bcftools-1.23.1 build of biology/bcftools | bcftools-1.23.1 ended at Sat May 23 23:52:30 JST 2026 build time: 00:04:45