=> Building biology/stacks Started : Sunday, 22 DEC 2019 at 07:46:17 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.1191.g9d275-DEVELOPMENT #19: Sun Dec 22 10:53:59 PST 2019 root@sting.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.7-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.7-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/construction/biology/stacks XDG_CONFIG_HOME=/construction/biology/stacks HOME=/construction/biology/stacks TMPDIR="/tmp" PATH=/construction/biology/stacks/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/stacks XDG_CONFIG_HOME=/construction/biology/stacks HOME=/construction/biology/stacks TMPDIR="/tmp" PATH=/construction/biology/stacks/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="gcc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -lpthread " LIBS="" CXX="g++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/stacks/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=5.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/stacks" EXAMPLESDIR="share/examples/stacks" DATADIR="share/stacks" WWWDIR="www/stacks" ETCDIR="etc/stacks" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=15 DPORTS_BUILDER= yes DISABLE_LICENSES= yes DEFAULT_VERSIONS= ssl=openssl FORCE_PACKAGE= yes DEVELOPER= yes HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.30.0 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500709 OSVERSION=9999999 OSREL=5.7 _OSRELEASE=5.7-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> stacks-2.4_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz Installing pkg-1.12.0... Extracting pkg-1.12.0: .......... done ===> stacks-2.4_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of stacks-2.4_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- => stacks-2.4.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch http://catchenlab.life.illinois.edu/stacks/source/stacks-2.4.tar.gz stacks-2.4.tar.gz 10 MB 3312 kBps 04s ===> Fetching all distfiles required by stacks-2.4_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by stacks-2.4_1 for building => SHA256 Checksum OK for stacks-2.4.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by stacks-2.4_1 for building ===> Extracting for stacks-2.4_1 => SHA256 Checksum OK for stacks-2.4.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for stacks-2.4_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> stacks-2.4_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: . done `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> stacks-2.4_1 depends on executable: gmake - found ===> Returning to build of stacks-2.4_1 ===> stacks-2.4_1 depends on file: /usr/local/bin/python3.7 - not found ===> Installing existing package /packages/All/python37-3.7.5_1.txz Installing python37-3.7.5_1... `-- Installing expat-2.2.8... `-- Extracting expat-2.2.8: .......... done `-- Installing libffi-3.2.1_3... `-- Extracting libffi-3.2.1_3: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done `-- Installing openssl-1.0.2u,1... `-- Extracting openssl-1.0.2u,1: .......... done `-- Installing readline-8.0.0_1... `-- Extracting readline-8.0.0_1: .......... done Extracting python37-3.7.5_1: .......... done ===== Message from openssl-1.0.2u,1: -- Edit /usr/local/openssl/openssl.cnf to fit your needs. ===== Message from python37-3.7.5_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 ===> stacks-2.4_1 depends on file: /usr/local/bin/python3.7 - found ===> Returning to build of stacks-2.4_1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for stacks-2.4_1 configure: loading site script /xports/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 g++ accepts -g... yes checking for style of include used by gmake... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking whether gcc and cc understand -c and -o together... yes checking whether g++ 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 gcc 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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for stacks-2.4_1 gmake[1]: Entering directory '/construction/biology/stacks/stacks-2.4' gmake all-recursive gmake[2]: Entering directory '/construction/biology/stacks/stacks-2.4' Making all in htslib gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4/htslib' depbase=`echo bcf_sr_sort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT bgzip.o -MD -MP -MF $depbase.Tpo -c -o bgzip.o bgzip.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo errmod.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT faidx.o -MD -MP -MF $depbase.Tpo -c -o faidx.o faidx.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo hfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT hfile.o -MD -MP -MF $depbase.Tpo -c -o hfile.o hfile.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo hfile_net.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT hfile_net.o -MD -MP -MF $depbase.Tpo -c -o hfile_net.o hfile_net.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo hts.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT hts.o -MD -MP -MF $depbase.Tpo -c -o hts.o hts.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo hts_os.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT multipart.o -MD -MP -MF $depbase.Tpo -c -o multipart.o multipart.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo probaln.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT vcfutils.o -MD -MP -MF $depbase.Tpo -c -o vcfutils.o vcfutils.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_codecs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/cram_io.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_io.o cram/cram_io.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_samtools.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/cram_samtools.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_samtools.o cram/cram_samtools.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/cram_stats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/cram_stats.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_stats.o cram/cram_stats.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/files.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/files.o -MD -MP -MF $depbase.Tpo -c -o cram/files.o cram/files.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/mFILE.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/mFILE.o -MD -MP -MF $depbase.Tpo -c -o cram/mFILE.o cram/mFILE.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/open_trace_file.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/open_trace_file.o -MD -MP -MF $depbase.Tpo -c -o cram/open_trace_file.o cram/open_trace_file.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/pooled_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/pooled_alloc.o -MD -MP -MF $depbase.Tpo -c -o cram/pooled_alloc.o cram/pooled_alloc.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cram/rANS_static.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/rANS_static.o -MD -MP -MF $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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -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 $depbase.Po depbase=`echo os/rand.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT os/rand.o -MD -MP -MF $depbase.Tpo -c -o os/rand.o os/rand.c &&\ mv -f $depbase.Tpo $depbase.Po rm -f libhts.a ar cru libhts.a bcf_sr_sort.o bgzf.o bgzip.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o htsfile.o kfunc.o knetfile.o kstring.o md5.o multipart.o os/rand.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o tabix.o tbx.o textutils.o thread_pool.o vcf.o vcf_sweep.o vcfutils.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libhts.a gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4/htslib' gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4' depbase=`echo src/aln_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/gzFasta.o -MD -MP -MF $depbase.Tpo -c -o src/gzFasta.o src/gzFasta.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/input.o | sed 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| sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/utils.o -MD -MP -MF $depbase.Tpo -c -o src/utils.o src/utils.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/Vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/Vcf.o -MD -MP -MF $depbase.Tpo -c -o src/Vcf.o src/Vcf.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/clean.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/write.o -MD -MP -MF $depbase.Tpo -c -o src/write.o src/write.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/export_formats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/Hwp.o -MD -MP -MF $depbase.Tpo -c -o src/Hwp.o src/Hwp.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/ustacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/ustacks.o -MD -MP -MF $depbase.Tpo -c -o src/ustacks.o src/ustacks.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/cstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/cstacks.o -MD -MP -MF $depbase.Tpo -c -o src/cstacks.o src/cstacks.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/sstacks.o -MD -MP -MF $depbase.Tpo -c -o src/sstacks.o src/sstacks.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/process_radtags.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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 $depbase.Po depbase=`echo src/process_shortreads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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 $depbase.Po depbase=`echo src/kmer_filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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 $depbase.Po depbase=`echo src/clone_filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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 $depbase.Po depbase=`echo src/populations.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/populations.o -MD -MP -MF $depbase.Tpo -c -o src/populations.o src/populations.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/phasedstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks.o -MD -MP -MF $depbase.Tpo -c -o src/phasedstacks.o src/phasedstacks.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tsv2bam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -fno-strict-aliasing -MT src/tsv2bam.o -MD -MP -MF $depbase.Tpo -c -o src/tsv2bam.o src/tsv2bam.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/gstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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$||'`;\ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -pipe -O2 -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 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 /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') rm -f libclean.a ranlib libcore.a ar cru libclean.a src/clean.o src/file_io.o src/write.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libclean.a g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o process_shortreads src/process_shortreads.o htslib/libhts.a libcore.a libclean.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o kmer_filter src/kmer_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o clone_filter src/clone_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp rm -f libpop.a ar cru libpop.a src/export_formats.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpop.a g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o phasedstacks src/phasedstacks.o htslib/libhts.a libcore.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o process_radtags src/process_radtags.o htslib/libhts.a libcore.a libclean.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o sstacks src/sstacks.o htslib/libhts.a libcore.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o ustacks src/ustacks.o htslib/libhts.a libcore.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o cstacks src/cstacks.o htslib/libhts.a libcore.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o tsv2bam src/tsv2bam.o htslib/libhts.a libcore.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o populations src/populations.o htslib/libhts.a libcore.a libpop.a -lz -lgomp g++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o htslib/libhts.a libcore.a -lz -lgomp gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4' gmake[2]: Leaving directory '/construction/biology/stacks/stacks-2.4' gmake[1]: Leaving directory '/construction/biology/stacks/stacks-2.4' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> stacks-2.4_1 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for stacks-2.4_1 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/stacks/stacks-2.4' Making install in htslib gmake[2]: Entering directory '/construction/biology/stacks/stacks-2.4/htslib' gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4/htslib' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4/htslib' gmake[2]: Leaving directory '/construction/biology/stacks/stacks-2.4/htslib' gmake[2]: Entering directory '/construction/biology/stacks/stacks-2.4' gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4' /bin/mkdir -p '/construction/biology/stacks/stage/usr/local/bin' install -s -m 555 ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/construction/biology/stacks/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/stacks/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 '/construction/biology/stacks/stage/usr/local/bin' gmake install-data-hook gmake[4]: Entering directory '/construction/biology/stacks/stacks-2.4' sed -e 's,_VERSION_,2.4,' -e 's,_BINDIR_,/usr/local/bin/,g' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl > /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl.subst /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl chmod +x /construction/biology/stacks/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' /construction/biology/stacks/stage/usr/local/bin/ref_map.pl > /construction/biology/stacks/stage/usr/local/bin/ref_map.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/ref_map.pl.subst /construction/biology/stacks/stage/usr/local/bin/ref_map.pl chmod +x /construction/biology/stacks/stage/usr/local/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.4,' /construction/biology/stacks/stage/usr/local/bin/stacks-integrate-alignments rm -f /construction/biology/stacks/stage/usr/local/bin/stacks-integrate-alignments.bkp chmod +x /construction/biology/stacks/stage/usr/local/bin/stacks-integrate-alignments chmod +x /construction/biology/stacks/stage/usr/local/bin/stacks-dist-extract chmod +x /construction/biology/stacks/stage/usr/local/bin/stacks-gdb gmake[4]: Leaving directory '/construction/biology/stacks/stacks-2.4' gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4' gmake[2]: Leaving directory '/construction/biology/stacks/stacks-2.4' gmake[1]: Leaving directory '/construction/biology/stacks/stacks-2.4' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for stacks-2.4_1 file sizes/checksums [18]: . done packing files [18]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 22 DEC 2019 at 07:49:19 UTC Duration: 00:03:01