=>> Building biology/bcf-score build started at Sat May 3 21:09:06 BST 2025 port directory: /usr/ports/biology/bcf-score package name: bcf-score-1.20_1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1923 Jan 27 13:48 /usr/ports/biology/bcf-score/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 8ce84fb385 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/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/bcf-score/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcf-score/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bcf-score/work/.cache HOME=/wrkdirs/usr/ports/biology/bcf-score/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bcf-score/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bcf-score/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/bcf-score/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcf-score/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bcf-score/work/.cache HOME=/wrkdirs/usr/ports/biology/bcf-score/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bcf-score/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bcf-score/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 -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lcholmod -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -isystem /usr/local/include/suitesparse -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=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 DOCSDIR="share/doc/bcf-score" EXAMPLESDIR="share/examples/bcf-score" DATADIR="share/bcf-score" WWWDIR="www/bcf-score" ETCDIR="etc/bcf-score" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bcf-score DOCSDIR=/usr/local/share/doc/bcf-score EXAMPLESDIR=/usr/local/share/examples/bcf-score WWWDIR=/usr/local/www/bcf-score ETCDIR=/usr/local/etc/bcf-score --End SUB_LIST-- ---Begin make.conf--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 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) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bcf-score-1.20_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> bcf-score-1.20_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bcf-score-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 bcf-score-1.20_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bcf-score-1.20_1 for building => SHA256 Checksum OK for score_1.20-20240505.tar.gz. => SHA256 Checksum OK for samtools-bcftools-1.20-1.21_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 bcf-score-1.20_1 for building ===> Extracting for bcf-score-1.20_1 => SHA256 Checksum OK for score_1.20-20240505.tar.gz. => SHA256 Checksum OK for samtools-bcftools-1.20-1.21_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 bcf-score-1.20_1 ===> Applying FreeBSD patches for bcf-score-1.20_1 from /usr/ports/biology/bcf-score/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bcf-score-1.20_1 depends on package: htslib>=1.21 - not found ===> Installing existing package /packages/All/htslib-1.21.pkg [pkg-builder.dan.net.uk] Installing htslib-1.21... [pkg-builder.dan.net.uk] `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.21: .......... done ===> bcf-score-1.20_1 depends on package: htslib>=1.21 - found ===> Returning to build of bcf-score-1.20_1 ===> bcf-score-1.20_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> bcf-score-1.20_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of bcf-score-1.20_1 ===> bcf-score-1.20_1 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_3: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> bcf-score-1.20_1 depends on package: autoconf>=2.72 - found ===> Returning to build of bcf-score-1.20_1 ===> bcf-score-1.20_1 depends on package: automake>=1.17 - not found ===> Installing existing package /packages/All/automake-1.17.pkg [pkg-builder.dan.net.uk] Installing automake-1.17... [pkg-builder.dan.net.uk] Extracting automake-1.17: .......... done ===> bcf-score-1.20_1 depends on package: automake>=1.17 - found ===> Returning to build of bcf-score-1.20_1 ===> bcf-score-1.20_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] 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. ===> bcf-score-1.20_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of bcf-score-1.20_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bcf-score-1.20_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcf-score-1.20_1 depends on shared library: libcholmod.so - not found ===> Installing existing package /packages/All/suitesparse-cholmod-5.3.2.pkg [pkg-builder.dan.net.uk] Installing suitesparse-cholmod-5.3.2... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.44,1... [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.44,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.2,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.3.0_2: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] `-- Installing openblas-0.3.29_1,2... [pkg-builder.dan.net.uk] `-- Extracting openblas-0.3.29_1,2: .......... done [pkg-builder.dan.net.uk] `-- Installing suitesparse-amd-3.3.3... [pkg-builder.dan.net.uk] | `-- Installing suitesparse-config-7.10.2... [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-config-7.10.2: .......... done [pkg-builder.dan.net.uk] `-- Extracting suitesparse-amd-3.3.3: .......... done [pkg-builder.dan.net.uk] `-- Installing suitesparse-camd-3.3.3... [pkg-builder.dan.net.uk] `-- Extracting suitesparse-camd-3.3.3: .......... done [pkg-builder.dan.net.uk] `-- Installing suitesparse-ccolamd-3.3.4... [pkg-builder.dan.net.uk] `-- Extracting suitesparse-ccolamd-3.3.4: .......... done [pkg-builder.dan.net.uk] `-- Installing suitesparse-colamd-3.3.4... [pkg-builder.dan.net.uk] `-- Extracting suitesparse-colamd-3.3.4: .......... done [pkg-builder.dan.net.uk] Extracting suitesparse-cholmod-5.3.2: .......... done ===== Message from gcc13-13.3.0_2: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> bcf-score-1.20_1 depends on shared library: libcholmod.so - found (/usr/local/lib/libcholmod.so) ===> Returning to build of bcf-score-1.20_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bcf-score-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 bcf-score-1.20_1 echo '#define BCFTOOLS_VERSION "1.21"' > version.h cc -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o main.o main.c cc -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -isystem /usr/local/include/suitesparse -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 -lcholmod -fstack-protector-strong -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 vcfplugin.o -lhts -lm -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -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 -lcholmod -fstack-protector-strong -o test/test-rbuf test/test-rbuf.o -lz -L/usr/local/lib cc -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -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 -lcholmod -fstack-protector-strong -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/GTisec.so version.c plugins/GTisec.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/GTsubset.so version.c plugins/GTsubset.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/allele-length.so version.c plugins/allele-length.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/blup.so version.c plugins/blup.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/contrast.so version.c plugins/contrast.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/counts.so version.c plugins/counts.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/dosage.so version.c plugins/dosage.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -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 -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/fill-tags.so version.c plugins/fill-tags.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/fixref.so version.c plugins/fixref.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/frameshifts.so version.c plugins/frameshifts.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/gvcfz.so version.c plugins/gvcfz.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/impute-info.so version.c plugins/impute-info.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/indel-stats.so version.c plugins/indel-stats.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/liftover.so version.c plugins/liftover.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/mendelian2.so version.c plugins/mendelian2.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/metal.so version.c plugins/metal.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/missing2ref.so version.c plugins/missing2ref.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/munge.so version.c plugins/munge.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/parental-origin.so version.c plugins/parental-origin.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/pgs.so version.c plugins/pgs.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/prune.so version.c plugins/prune.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/scatter.so version.c plugins/scatter.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/score.so version.c plugins/score.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/setGT.so version.c plugins/setGT.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/split-vep.so version.c plugins/split-vep.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/split.so version.c plugins/split.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/tag2tag.so version.c plugins/tag2tag.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/trio-stats.so version.c plugins/trio-stats.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/variant-distance.so version.c plugins/variant-distance.c -L/usr/local/lib cc -fPIC -shared -Wall -O2 -pipe -isystem /usr/local/include/suitesparse -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -lcholmod -fstack-protector-strong -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -L/usr/local/lib =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bcf-score-1.20_1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.37.pkg [pkg-builder.dan.net.uk] Installing bash-5.2.37... [pkg-builder.dan.net.uk] Extracting bash-5.2.37: .......... done ===> bcf-score-1.20_1 depends on executable: bash - found ===> Returning to build of bcf-score-1.20_1 ===> bcf-score-1.20_1 depends on package: bcftools>=1.20 - not found ===> Installing existing package /packages/All/bcftools-1.21.pkg [pkg-builder.dan.net.uk] Installing bcftools-1.21... [pkg-builder.dan.net.uk] `-- Installing gsl-2.7.1_1... [pkg-builder.dan.net.uk] `-- Extracting gsl-2.7.1_1: .......... done [pkg-builder.dan.net.uk] Extracting bcftools-1.21: .......... done ===> bcf-score-1.20_1 depends on package: bcftools>=1.20 - found ===> Returning to build of bcf-score-1.20_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for bcf-score-1.20_1 ===> Generating temporary packing list /bin/mkdir -p /wrkdirs/usr/ports/biology/bcf-score/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.21/plugins/blup.so /wrkdirs/usr/ports/biology/bcf-score/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.21/plugins/liftover.so /wrkdirs/usr/ports/biology/bcf-score/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.21/plugins/metal.so /wrkdirs/usr/ports/biology/bcf-score/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.21/plugins/munge.so /wrkdirs/usr/ports/biology/bcf-score/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.21/plugins/pgs.so /wrkdirs/usr/ports/biology/bcf-score/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.21/plugins/score.so /wrkdirs/usr/ports/biology/bcf-score/work/stage/usr/local/libexec/bcftools (cd /wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.21/bcf-score && /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/bcf-score/work/stage/usr/local/share/bcf-score) ====> 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=2025-05-03T20:09:06+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=8ce84fb385' '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 bcf-score-1.20_1 ===> Building bcf-score-1.20_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bcf-score-1.20_1 build of biology/bcf-score | bcf-score-1.20_1 ended at Sat May 3 21:11:25 BST 2025 build time: 00:02:19