=>> Building biology/samtools build started at Thu Mar 28 06:09:12 GMT 2024 port directory: /usr/ports/biology/samtools package name: samtools-1.17_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 577 Mar 7 22:02 /usr/ports/biology/samtools/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 01064ce0bd Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 17 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-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/13-amd64-default-dan/17/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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=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/python3.9" 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=/ccache/libexec/ccache:/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" CCACHE_DIR="/root/.ccache" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 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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 mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/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 --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-1.17_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> samtools-1.17_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of samtools-1.17_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 samtools-1.17_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by samtools-1.17_1 for building => SHA256 Checksum OK for samtools-samtools-1.17_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-1.17_1 for building ===> Extracting for samtools-1.17_1 => SHA256 Checksum OK for samtools-samtools-1.17_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-1.17_1 ===> Applying FreeBSD patches for samtools-1.17_1 from /usr/ports/biology/samtools/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> samtools-1.17_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-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> samtools-1.17_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of samtools-1.17_1 ===> samtools-1.17_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_1... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_1: .......... 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-1.17_1 depends on package: autoconf>=2.72 - found ===> Returning to build of samtools-1.17_1 ===> samtools-1.17_1 depends on package: automake>=1.16.5 - not found ===> Installing existing package /packages/All/automake-1.16.5_1.pkg [pkg-builder.dan.net.uk] Installing automake-1.16.5_1... [pkg-builder.dan.net.uk] Extracting automake-1.16.5_1: .......... done ===> samtools-1.17_1 depends on package: automake>=1.16.5 - found ===> Returning to build of samtools-1.17_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> samtools-1.17_1 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.17_1.pkg [pkg-builder.dan.net.uk] Installing htslib-1.17_1... [pkg-builder.dan.net.uk] `-- Installing curl-8.6.0... [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 libidn2-2.3.7... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.2... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.7: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.60.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.60.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing librtmp-2.4.20190330_1... [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting librtmp-2.4.20190330_1: ......... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.0_1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.0_1,3: .......... done [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.6.0: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.19... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.19: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.17_1: .......... done ===> samtools-1.17_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of samtools-1.17_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for samtools-1.17_1 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-1.17_1 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 "1.17"' > 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-1.17_1 ===> 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=2024-03-28T06:09:12+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=01064ce0bd' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for samtools-1.17_1 ===> Building samtools-1.17_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for samtools-1.17_1 build of biology/samtools | samtools-1.17_1 ended at Thu Mar 28 06:10:08 GMT 2024 build time: 00:00:57