=>> Building biology/samtools build started at Thu May 1 12:44:31 BST 2025 port directory: /usr/ports/biology/samtools package name: samtools-1.21 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 604 Dec 29 14:16 /usr/ports/biology/samtools/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 02 ---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/02/.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/samtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/samtools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/samtools/work/.cache HOME=/wrkdirs/usr/ports/biology/samtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/samtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/samtools/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/samtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/samtools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/samtools/work/.cache HOME=/wrkdirs/usr/ports/biology/samtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/samtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/samtools/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=" -fstack-protector-strong " 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=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/samtools" EXAMPLESDIR="share/examples/samtools" DATADIR="share/samtools" WWWDIR="www/samtools" ETCDIR="etc/samtools" --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/samtools DOCSDIR=/usr/local/share/doc/samtools EXAMPLESDIR=/usr/local/share/examples/samtools WWWDIR=/usr/local/www/samtools ETCDIR=/usr/local/etc/samtools --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 ===> samtools-1.21 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 ===> samtools-1.21 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of samtools-1.21 =========================================================================== =================================================== ===== 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 samtools-1.21 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by samtools-1.21 for building => SHA256 Checksum OK for samtools-samtools-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 samtools-1.21 for building ===> Extracting for samtools-1.21 => SHA256 Checksum OK for samtools-samtools-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 samtools-1.21 ===> Applying FreeBSD patches for samtools-1.21 from /usr/ports/biology/samtools/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> samtools-1.21 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 ===> samtools-1.21 depends on package: htslib>=1.21 - found ===> Returning to build of samtools-1.21 ===> samtools-1.21 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 ===> samtools-1.21 depends on package: gmake>=4.4.1 - found ===> Returning to build of samtools-1.21 ===> samtools-1.21 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. ===> samtools-1.21 depends on package: autoconf>=2.72 - found ===> Returning to build of samtools-1.21 ===> samtools-1.21 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 ===> samtools-1.21 depends on package: automake>=1.17 - found ===> Returning to build of samtools-1.21 ===> samtools-1.21 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. ===> samtools-1.21 depends on file: /usr/local/bin/ccache - found ===> Returning to build of samtools-1.21 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> samtools-1.21 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for samtools-1.21 configure.ac:64: 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:64: the top level configure: loading site script /usr/ports/Templates/config.site checking for gawk... (cached) /usr/bin/awk 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 for NcursesW wide-character library... yes checking for working ncursesw/curses.h... no checking for working ncursesw.h... no checking for working ncurses.h... yes checking for library containing cbreak... none required 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 samtools-1.21 cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_aux.o bam_aux.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_index.o bam_index.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_plcmd.o bam_plcmd.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o sam_view.o sam_view.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_fastq.o bam_fastq.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_cat.o bam_cat.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_md.o bam_md.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_plbuf.o bam_plbuf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_reheader.o bam_reheader.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_sort.o bam_sort.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_rmdup.o bam_rmdup.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_rmdupse.o bam_rmdupse.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_mate.o bam_mate.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_stat.o bam_stat.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.21"' > version.h echo '#define SAMTOOLS_CC "cc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-isystem /usr/local/include"' >> version.h echo '#define SAMTOOLS_CFLAGS "-Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing "' >> version.h echo '#define SAMTOOLS_LDFLAGS "-fstack-protector-strong "' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS "-L/usr/local/lib"' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bamtk.o bamtk.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -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. -I./lz4 -isystem /usr/local/include -c -o sample.o sample.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o cut_target.o cut_target.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o phase.o phase.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam2depth.o bam2depth.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o coverage.o coverage.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o padding.o padding.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bedcov.o bedcov.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bamshuf.o bamshuf.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o faidx.o faidx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o dict.o dict.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o stats.o stats.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o stats_isize.o stats_isize.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_flags.o bam_flags.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_split.o bam_split.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_tview.o bam_tview.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_tview_curses.o bam_tview_curses.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_tview_html.o bam_tview_html.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_lpileup.o bam_lpileup.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_quickcheck.o bam_quickcheck.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_addrprg.o bam_addrprg.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_markdup.o bam_markdup.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o tmp_file.o tmp_file.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_ampliconclip.o bam_ampliconclip.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o amplicon_stats.o amplicon_stats.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_import.o bam_import.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_samples.o bam_samples.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam_consensus.o bam_consensus.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o consensus_pileup.o consensus_pileup.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o reference.o reference.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o reset.o reset.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o cram_size.o cram_size.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o lz4/lz4.o lz4/lz4.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o sam_opts.o sam_opts.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o sam_utils.o sam_utils.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bedidx.o bedidx.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o bam.o bam.c ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o cc -L./lz4 -fstack-protector-strong -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o misc/ace2sam.o misc/ace2sam.c cc -L./lz4 -fstack-protector-strong -o misc/ace2sam misc/ace2sam.o -lhts -lz -L/usr/local/lib cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DMAQ_LONGREADS -I. -I./lz4 -isystem /usr/local/include -c -o misc/maq2sam-long.o misc/maq2sam.c cc -fstack-protector-strong -o misc/maq2sam-long misc/maq2sam-long.o -lz -L/usr/local/lib cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o misc/maq2sam-short.o misc/maq2sam.c cc -fstack-protector-strong -o misc/maq2sam-short misc/maq2sam-short.o -lz -L/usr/local/lib cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o misc/md5fa.o misc/md5fa.c cc -L./lz4 -fstack-protector-strong -o misc/md5fa misc/md5fa.o -lhts -lz -L/usr/local/lib cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc -L./lz4 -fstack-protector-strong -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -L/usr/local/lib cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o misc/wgsim.o misc/wgsim.c cc -L./lz4 -fstack-protector-strong -o misc/wgsim misc/wgsim.o -lm -lhts -lz -L/usr/local/lib cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/test.o test/test.c cc -L./lz4 -fstack-protector-strong -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc -L./lz4 -fstack-protector-strong -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc -L./lz4 -fstack-protector-strong -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc -L./lz4 -fstack-protector-strong -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc -L./lz4 -fstack-protector-strong -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc -L./lz4 -fstack-protector-strong -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc -L./lz4 -fstack-protector-strong -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -L/usr/local/lib -lpthread cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -I./lz4 -isystem /usr/local/include -c -o test/vcf-miniview.o test/vcf-miniview.c cc -L./lz4 -fstack-protector-strong -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -L/usr/local/lib -lpthread =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for samtools-1.21 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/share/man/man1 install -s -m 555 samtools /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin install -s -m 555 misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin install -m 555 misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin install -m 444 doc/samtools*.1 misc/wgsim.1 /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/share/man/man1 ====> 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=2025-05-01T11:44:31+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' '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 samtools-1.21 ===> Building samtools-1.21 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for samtools-1.21 build of biology/samtools | samtools-1.21 ended at Thu May 1 12:47:24 BST 2025 build time: 00:02:57