=>> Building biology/bio-mocha build started at Fri Jan 23 15:30:12 EST 2026 port directory: /usr/ports/biology/bio-mocha package name: bio-mocha-1.20_1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1507 Jun 29 2025 /usr/ports/biology/bio-mocha/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 49752ef6cd89 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 07 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --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/bio-mocha/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work/.cache HOME=/wrkdirs/usr/ports/biology/bio-mocha/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bio-mocha/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bio-mocha/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work/.cache HOME=/wrkdirs/usr/ports/biology/bio-mocha/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bio-mocha/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bio-mocha/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=2.72 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=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 PERL_VERSION=5.42.0 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/bio-mocha" EXAMPLESDIR="share/examples/bio-mocha" DATADIR="share/bio-mocha" WWWDIR="www/bio-mocha" ETCDIR="etc/bio-mocha" --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/bio-mocha DOCSDIR=/usr/local/share/doc/bio-mocha EXAMPLESDIR=/usr/local/share/examples/bio-mocha WWWDIR=/usr/local/www/bio-mocha ETCDIR=/usr/local/etc/bio-mocha --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### 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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bio-mocha-1.20_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> bio-mocha-1.20_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bio-mocha-1.20_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bio-mocha-1.20_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bio-mocha-1.20_1 for building => SHA256 Checksum OK for bio-mocha_1.20-20240505.tar.gz. => SHA256 Checksum OK for samtools-bcftools-1.20-1.22_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bio-mocha-1.20_1 for building ===> Extracting for bio-mocha-1.20_1 => SHA256 Checksum OK for bio-mocha_1.20-20240505.tar.gz. => SHA256 Checksum OK for samtools-bcftools-1.20-1.22_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for bio-mocha-1.20_1 ===> Applying FreeBSD patches for bio-mocha-1.20_1 from /usr/ports/biology/bio-mocha/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bio-mocha-1.20_1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.9.pkg [pkg.DaveG.ca] Installing bash-5.3.9... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting bash-5.3.9: .......... done ===> bio-mocha-1.20_1 depends on executable: bash - found ===> Returning to build of bio-mocha-1.20_1 ===> bio-mocha-1.20_1 depends on package: htslib>=1.22 - not found ===> Installing existing package /packages/All/htslib-1.22.pkg [pkg.DaveG.ca] Installing htslib-1.22... [pkg.DaveG.ca] `-- Installing curl-8.17.0... [pkg.DaveG.ca] | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] `-- Installing libdeflate-1.25... [pkg.DaveG.ca] `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] Extracting htslib-1.22: .......... done ===> bio-mocha-1.20_1 depends on package: htslib>=1.22 - found ===> Returning to build of bio-mocha-1.20_1 ===> bio-mocha-1.20_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> bio-mocha-1.20_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of bio-mocha-1.20_1 ===> bio-mocha-1.20_1 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [pkg.DaveG.ca] Installing autoconf-2.72_1... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72_1: .......... done ===> bio-mocha-1.20_1 depends on package: autoconf>=2.72_1 - found ===> Returning to build of bio-mocha-1.20_1 ===> bio-mocha-1.20_1 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [pkg.DaveG.ca] Installing automake-1.18.1... [pkg.DaveG.ca] Extracting automake-1.18.1: .......... done ===> bio-mocha-1.20_1 depends on package: automake>=1.18.1 - found ===> Returning to build of bio-mocha-1.20_1 ===> bio-mocha-1.20_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> bio-mocha-1.20_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of bio-mocha-1.20_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bio-mocha-1.20_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bio-mocha-1.20_1 configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: 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 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 enable large file support... 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 library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for bio-mocha-1.20_1 echo '#define BCFTOOLS_VERSION "1.22"' > version.h 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 -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 -DPLUGINPATH='"/usr/local/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c 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 -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 -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/extendFMT.so version.c plugins/extendFMT.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 -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/mocha.so version.c plugins/mocha.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/mochatools.so version.c plugins/mochatools.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 plugins/mochatools.c:109:9: warning: variable 'i' set but not used [-Wunused-but-set-variable] 109 | int i = 0; | ^ cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o main.o main.c cc -o test/test-rbuf test/test-rbuf.o -lz -L/usr/local/lib cc -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -L/usr/local/lib 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 vcfplugin.o -lhts -lm -lz -L/usr/local/lib -lpthread 1 warning generated. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bio-mocha-1.20_1 depends on package: bcftools>=1.20 - not found ===> Installing existing package /packages/All/bcftools-1.22.pkg [pkg.DaveG.ca] Installing bcftools-1.22... [pkg.DaveG.ca] `-- Installing gsl-2.7.1_1... [pkg.DaveG.ca] `-- Extracting gsl-2.7.1_1: .......... done [pkg.DaveG.ca] Extracting bcftools-1.22: .......... done ===> bio-mocha-1.20_1 depends on package: bcftools>=1.20 - found ===> Returning to build of bio-mocha-1.20_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for bio-mocha-1.20_1 ===> Generating temporary packing list /bin/mkdir -p /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.22/plugins/extendFMT.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.22/plugins/mocha.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.22/plugins/mochatools.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools (cd /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.22/MoCha && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/share/bio-mocha) ====> 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=2026-01-23T20:30:12+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=49752ef6cd89' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for bio-mocha-1.20_1 ===> Building bio-mocha-1.20_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bio-mocha-1.20_1 build of biology/bio-mocha | bio-mocha-1.20_1 ended at Fri Jan 23 15:31:05 EST 2026 build time: 00:00:57