=>> Building biology/stacks build started at Sun Mar 31 08:35:45 BST 2024 port directory: /usr/ports/biology/stacks package name: stacks-2.4_2 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 671 Mar 8 2023 /usr/ports/biology/stacks/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 09 ---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/09/.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 PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/stacks/work/.cache HOME=/wrkdirs/usr/ports/biology/stacks/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/stacks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/stacks/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/stacks/work/.cache HOME=/wrkdirs/usr/ports/biology/stacks/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/stacks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/stacks/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -lpthread -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/stacks" EXAMPLESDIR="share/examples/stacks" DATADIR="share/stacks" WWWDIR="www/stacks" ETCDIR="etc/stacks" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/stacks DOCSDIR=/usr/local/share/doc/stacks EXAMPLESDIR=/usr/local/share/examples/stacks WWWDIR=/usr/local/www/stacks ETCDIR=/usr/local/etc/stacks --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 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 ===> stacks-2.4_2 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 ===> stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of stacks-2.4_2 =========================================================================== =================================================== ===== 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 stacks-2.4_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by stacks-2.4_2 for building => SHA256 Checksum OK for stacks-2.4.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 stacks-2.4_2 for building ===> Extracting for stacks-2.4_2 => SHA256 Checksum OK for stacks-2.4.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 stacks-2.4_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> stacks-2.4_2 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 ===> stacks-2.4_2 depends on package: gmake>=4.4.1 - found ===> Returning to build of stacks-2.4_2 ===> stacks-2.4_2 depends on file: /usr/local/bin/python3.9 - not found ===> Installing existing package /packages/All/python39-3.9.18_1.pkg [pkg-builder.dan.net.uk] Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] `-- Extracting mpdecimal-2.5.1: .......... done [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] `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] Extracting python39-3.9.18_1: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> stacks-2.4_2 depends on file: /usr/local/bin/python3.9 - found ===> Returning to build of stacks-2.4_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for stacks-2.4_2 configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes 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 we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking for style of include used by gmake... GNU checking dependency style of c++... gcc3 checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking dependency style of cc... gcc3 checking whether cc understands -c and -o together... yes checking whether c++ supports C++11 features by default... yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for cc option to support OpenMP... -fopenmp checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking whether closedir returns void... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for floor... no checking for memset... (cached) yes checking for pow... no checking for sqrt... no checking for clock_gettime... (cached) yes checking for functional regular expressions... yes checking for gawk... (cached) /usr/bin/awk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating htslib/Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for stacks-2.4_2 gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' Making all in htslib gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4/htslib' depbase=`echo bcf_sr_sort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT bcf_sr_sort.o -MD -MP -MF $depbase.Tpo -c -o bcf_sr_sort.o bcf_sr_sort.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo bgzf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT bgzf.o -MD -MP -MF $depbase.Tpo -c -o bgzf.o bgzf.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo bgzip.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT bgzip.o -MD -MP -MF $depbase.Tpo -c -o bgzip.o bgzip.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_codecs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram/cram_codecs.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_codecs.o cram/cram_codecs.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_decode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram/cram_decode.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_decode.o cram/cram_decode.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_encode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram/cram_encode.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_encode.o cram/cram_encode.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_external.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram/cram_external.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_external.o cram/cram_external.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_index.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram/cram_index.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_index.o cram/cram_index.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong 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$depbase.Tpo -c -o cram/rANS_static.o cram/rANS_static.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/sam_header.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram/sam_header.o -MD -MP -MF $depbase.Tpo -c -o cram/sam_header.o cram/sam_header.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/string_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT cram/string_alloc.o -MD -MP -MF $depbase.Tpo -c -o cram/string_alloc.o cram/string_alloc.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo errmod.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT errmod.o -MD -MP -MF $depbase.Tpo -c -o errmod.o errmod.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo faidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe 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-fno-strict-aliasing -MT hts_os.o -MD -MP -MF $depbase.Tpo -c -o hts_os.o hts_os.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo htsfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT htsfile.o -MD -MP -MF $depbase.Tpo -c -o htsfile.o htsfile.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo kfunc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT kfunc.o -MD -MP -MF $depbase.Tpo -c -o kfunc.o kfunc.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo knetfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT knetfile.o -MD -MP -MF $depbase.Tpo -c -o knetfile.o knetfile.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo kstring.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT kstring.o -MD -MP -MF $depbase.Tpo -c -o kstring.o kstring.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo md5.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT md5.o -MD -MP -MF $depbase.Tpo -c -o md5.o md5.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo multipart.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT multipart.o -MD -MP -MF $depbase.Tpo -c -o multipart.o multipart.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo os/rand.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT os/rand.o -MD -MP -MF $depbase.Tpo -c -o os/rand.o os/rand.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo probaln.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT probaln.o -MD -MP -MF $depbase.Tpo -c -o probaln.o probaln.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo realn.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT realn.o -MD -MP -MF $depbase.Tpo -c -o realn.o realn.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo regidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT regidx.o -MD -MP -MF $depbase.Tpo -c -o regidx.o regidx.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam.o -MD -MP -MF $depbase.Tpo -c -o sam.o sam.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo synced_bcf_reader.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT synced_bcf_reader.o -MD -MP -MF $depbase.Tpo -c -o synced_bcf_reader.o synced_bcf_reader.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo tabix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT tabix.o -MD -MP -MF $depbase.Tpo -c -o tabix.o tabix.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo tbx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT tbx.o -MD -MP -MF $depbase.Tpo -c -o tbx.o tbx.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo textutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT textutils.o -MD -MP -MF $depbase.Tpo -c -o textutils.o textutils.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo thread_pool.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT thread_pool.o -MD -MP -MF $depbase.Tpo -c -o thread_pool.o thread_pool.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcf.o -MD -MP -MF $depbase.Tpo -c -o vcf.o vcf.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo vcf_sweep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcf_sweep.o -MD -MP -MF $depbase.Tpo -c -o vcf_sweep.o vcf_sweep.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo vcfutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcfutils.o -MD -MP -MF $depbase.Tpo -c -o vcfutils.o vcfutils.c &&\ mv -f $depbase.Tpo $depbase.Po rm -f libhts.a ar cru libhts.a bcf_sr_sort.o bgzf.o bgzip.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o htsfile.o kfunc.o knetfile.o kstring.o md5.o multipart.o os/rand.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o tabix.o tbx.o textutils.o thread_pool.o vcf.o vcf_sweep.o vcfutils.o ranlib libhts.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4/htslib' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' depbase=`echo src/aln_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/aln_utils.o -MD -MP -MF $depbase.Tpo -c -o src/aln_utils.o src/aln_utils.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/BamI.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/BamI.o -MD -MP -MF $depbase.Tpo -c -o src/BamI.o src/BamI.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/catalog_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/catalog_utils.o -MD -MP -MF $depbase.Tpo -c -o src/catalog_utils.o src/catalog_utils.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/cmb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/cmb.o -MD -MP -MF $depbase.Tpo -c -o src/cmb.o src/cmb.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/constants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/constants.o -MD -MP -MF $depbase.Tpo -c -o src/constants.o src/constants.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/DNANSeq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/DNANSeq.o -MD -MP -MF $depbase.Tpo -c -o src/DNANSeq.o src/DNANSeq.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/DNASeq4.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/DNASeq4.o -MD -MP -MF $depbase.Tpo -c -o src/DNASeq4.o src/DNASeq4.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/DNASeq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/DNASeq.o -MD -MP -MF $depbase.Tpo -c -o src/DNASeq.o src/DNASeq.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/gzFasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/gzFasta.o -MD -MP -MF $depbase.Tpo -c -o src/gzFasta.o src/gzFasta.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/input.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/input.o -MD -MP -MF $depbase.Tpo -c -o src/input.o src/input.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/kmers.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/kmers.o -MD -MP -MF $depbase.Tpo -c -o src/kmers.o src/kmers.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/locus.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/locus.o -MD -MP -MF $depbase.Tpo -c -o src/locus.o src/locus.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/log_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/log_utils.o -MD -MP -MF $depbase.Tpo -c -o src/log_utils.o src/log_utils.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/MetaPopInfo.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/MetaPopInfo.o -MD -MP -MF $depbase.Tpo -c -o src/MetaPopInfo.o src/MetaPopInfo.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/models.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/models.o -MD -MP -MF $depbase.Tpo -c -o src/models.o src/models.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/mstack.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/mstack.o -MD -MP -MF $depbase.Tpo -c -o src/mstack.o src/mstack.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/mst.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/mst.o -MD -MP -MF $depbase.Tpo -c -o src/mst.o src/mst.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/nucleotides.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/nucleotides.o -MD -MP -MF $depbase.Tpo -c -o src/nucleotides.o src/nucleotides.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/renz.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/renz.o -MD -MP -MF $depbase.Tpo -c -o src/renz.o src/renz.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/Seq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/Seq.o -MD -MP -MF $depbase.Tpo -c -o src/Seq.o src/Seq.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sql_utilities.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/sql_utilities.o -MD -MP -MF $depbase.Tpo -c -o src/sql_utilities.o src/sql_utilities.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/stacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/stacks.o -MD -MP -MF $depbase.Tpo -c -o src/stacks.o src/stacks.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/utils.o -MD -MP -MF $depbase.Tpo -c -o src/utils.o src/utils.cc &&\ mv -f $depbase.Tpo $depbase.Po src/utils.cc:234:37: warning: implicit conversion from 'long' to 'double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion] if ((errno == ERANGE && (val == LONG_MAX || val == LONG_MIN)) ~~ ^~~~~~~~ /usr/include/sys/limits.h:64:18: note: expanded from macro 'LONG_MAX' #define LONG_MAX __LONG_MAX /* max for a long */ ^~~~~~~~~~ /usr/include/x86/_limits.h:64:20: note: expanded from macro '__LONG_MAX' #define __LONG_MAX 0x7fffffffffffffff /* max for a long */ ^~~~~~~~~~~~~~~~~~ 1 warning generated. depbase=`echo src/Vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/Vcf.o -MD -MP -MF $depbase.Tpo -c -o src/Vcf.o src/Vcf.cc &&\ mv -f $depbase.Tpo $depbase.Po rm -f libcore.a ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o ranlib libcore.a depbase=`echo src/clean.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/clean.o -MD -MP -MF $depbase.Tpo -c -o src/clean.o src/clean.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/file_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/file_io.o -MD -MP -MF $depbase.Tpo -c -o src/file_io.o src/file_io.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/write.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/write.o -MD -MP -MF $depbase.Tpo -c -o src/write.o src/write.cc &&\ mv -f $depbase.Tpo $depbase.Po rm -f libclean.a ar cru libclean.a src/clean.o src/file_io.o src/write.o ranlib libclean.a depbase=`echo src/export_formats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/export_formats.o -MD -MP -MF $depbase.Tpo -c -o src/export_formats.o src/export_formats.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/genotype_dictionaries.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/genotype_dictionaries.o -MD -MP -MF $depbase.Tpo -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/PopSum.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/PopSum.o -MD -MP -MF $depbase.Tpo -c -o src/PopSum.o src/PopSum.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/Hwp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/Hwp.o -MD -MP -MF $depbase.Tpo -c -o src/Hwp.o src/Hwp.cc &&\ mv -f $depbase.Tpo $depbase.Po rm -f libpop.a ar cru libpop.a src/export_formats.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o ranlib libpop.a depbase=`echo src/ustacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/ustacks.o -MD -MP -MF $depbase.Tpo -c -o src/ustacks.o src/ustacks.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o ustacks src/ustacks.o htslib/libhts.a libcore.a -lz -lgomp depbase=`echo src/cstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/cstacks.o -MD -MP -MF $depbase.Tpo -c -o src/cstacks.o src/cstacks.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o cstacks src/cstacks.o htslib/libhts.a libcore.a -lz -lgomp depbase=`echo src/sstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/sstacks.o -MD -MP -MF $depbase.Tpo -c -o src/sstacks.o src/sstacks.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o sstacks src/sstacks.o htslib/libhts.a libcore.a -lz -lgomp depbase=`echo src/process_radtags.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/process_radtags.o -MD -MP -MF $depbase.Tpo -c -o src/process_radtags.o src/process_radtags.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o process_radtags src/process_radtags.o htslib/libhts.a libcore.a libclean.a -lz -lgomp depbase=`echo src/process_shortreads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/process_shortreads.o -MD -MP -MF $depbase.Tpo -c -o src/process_shortreads.o src/process_shortreads.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o process_shortreads src/process_shortreads.o htslib/libhts.a libcore.a libclean.a -lz -lgomp depbase=`echo src/kmer_filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/kmer_filter.o -MD -MP -MF $depbase.Tpo -c -o src/kmer_filter.o src/kmer_filter.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o kmer_filter src/kmer_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp depbase=`echo src/clone_filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/clone_filter.o -MD -MP -MF $depbase.Tpo -c -o src/clone_filter.o src/clone_filter.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o clone_filter src/clone_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp depbase=`echo src/populations.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/populations.o -MD -MP -MF $depbase.Tpo -c -o src/populations.o src/populations.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o populations src/populations.o htslib/libhts.a libcore.a libpop.a -lz -lgomp depbase=`echo src/phasedstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/phasedstacks.o -MD -MP -MF $depbase.Tpo -c -o src/phasedstacks.o src/phasedstacks.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o phasedstacks src/phasedstacks.o htslib/libhts.a libcore.a -lz -lgomp depbase=`echo src/tsv2bam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tsv2bam.o -MD -MP -MF $depbase.Tpo -c -o src/tsv2bam.o src/tsv2bam.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o tsv2bam src/tsv2bam.o htslib/libhts.a libcore.a -lz -lgomp depbase=`echo src/gstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/gstacks.o -MD -MP -MF $depbase.Tpo -c -o src/gstacks.o src/gstacks.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/debruijn.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/debruijn.o -MD -MP -MF $depbase.Tpo -c -o src/debruijn.o src/debruijn.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/SuffixTree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/SuffixTree.o -MD -MP -MF $depbase.Tpo -c -o src/SuffixTree.o src/SuffixTree.cc &&\ mv -f $depbase.Tpo $depbase.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -fstack-protector-strong -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o htslib/libhts.a libcore.a -lz -lgomp gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> stacks-2.4_2 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for stacks-2.4_2 ===> Generating temporary packing list Making install in htslib gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4/htslib' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4/htslib' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4/htslib' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4/htslib' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' /bin/mkdir -p '/wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin' install -s -m 555 ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin' install -m 555 scripts/denovo_map.pl scripts/ref_map.pl scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb '/wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin' gmake install-data-hook gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' sed -e 's,_VERSION_,2.4,' -e 's,_BINDIR_,/usr/local/bin/,g' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl > /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl.subst mv /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl.subst /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl sed -e 's,_VERSION_,2.4,' -e 's,_BINDIR_,/usr/local/bin/,g' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl > /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl.subst mv /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl.subst /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.4,' /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-integrate-alignments rm -f /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-integrate-alignments.bkp chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-integrate-alignments chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-dist-extract chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-gdb gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4' ====> 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=2024-03-31T07:35:45+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' '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 stacks-2.4_2 ===> Building stacks-2.4_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for stacks-2.4_2 build of biology/stacks | stacks-2.4_2 ended at Sun Mar 31 08:42:41 BST 2024 build time: 00:06:56