=> Building biology/stacks Started : Thursday, 30 AUG 2018 at 13:01:31 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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/python2.7" 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=gcc50 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=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -lpthread" LIBS="" CXX="c++" 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 -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.3 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> stacks-1.48 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> stacks-1.48 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of stacks-1.48 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by stacks-1.48 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by stacks-1.48 for building => SHA256 Checksum OK for stacks-1.48.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by stacks-1.48 for building ===> Extracting for stacks-1.48 => SHA256 Checksum OK for stacks-1.48.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for stacks-1.48 ===> Applying ports patches for stacks-1.48 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> stacks-1.48 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_2: .......... done ===> stacks-1.48 depends on executable: gmake - found ===> Returning to build of stacks-1.48 ===> stacks-1.48 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.15.txz Installing python27-2.7.15... `-- Installing expat-2.2.5... `-- Extracting expat-2.2.5: .......... done `-- Installing libffi-3.2.1_2... `-- Extracting libffi-3.2.1_2: .......... done `-- Installing libressl-2.7.4... `-- Extracting libressl-2.7.4: .......... done `-- Installing ncurses-6.0.0s20171223_1... `-- Extracting ncurses-6.0.0s20171223_1: .......... done `-- Installing readline-7.0.3_1... `-- Extracting readline-7.0.3_1: .......... done Extracting python27-2.7.15: .......... done Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> stacks-1.48 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of stacks-1.48 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for stacks-1.48 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 for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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... no checking whether c++ supports C++11 features with -std=gnu++11... yes 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 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 functional regular expressions... yes checking for gawk... (cached) /usr/bin/awk configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for stacks-1.48 gmake[1]: Entering directory '/construction/biology/stacks/stacks-1.48' gmake all-recursive gmake[2]: Entering directory '/construction/biology/stacks/stacks-1.48' Making all in htslib gmake[3]: Entering directory '/construction/biology/stacks/stacks-1.48/htslib' echo '/* Empty config.h generated by Makefile */' > config.h echo '#define HTS_VERSION "1.3.1"' > version.h cc -pipe -O2 -fno-strict-aliasing -I. -c -o md5.o md5.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o regidx.o regidx.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o sam.o sam.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o synced_bcf_reader.o synced_bcf_reader.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o vcf_sweep.o vcf_sweep.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o tbx.o tbx.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o vcf.o vcf.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o vcfutils.o vcfutils.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/cram_codecs.o cram/cram_codecs.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/cram_decode.o cram/cram_decode.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/cram_encode.o cram/cram_encode.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/cram_external.o cram/cram_external.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/cram_index.o cram/cram_index.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/cram_io.o cram/cram_io.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/cram_samtools.o cram/cram_samtools.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/cram_stats.o cram/cram_stats.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/files.o cram/files.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/mFILE.o cram/mFILE.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/open_trace_file.o cram/open_trace_file.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/rANS_static.o cram/rANS_static.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/sam_header.o cram/sam_header.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/string_alloc.o cram/string_alloc.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/thread_pool.o cram/thread_pool.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/vlen.o cram/vlen.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o cram/zfio.o cram/zfio.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o kfunc.o kfunc.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o knetfile.o knetfile.c knetfile.c: In function 'socket_wait': knetfile.c:72:8: warning: implicit declaration of function 'select' [-Wimplicit-function-declaration] ret = select(fd+1, fdr, fdw, 0, &tv); ^ cc -pipe -O2 -fno-strict-aliasing -I. -c -o kstring.o kstring.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o bgzf.o bgzf.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o faidx.o faidx.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o hfile.o hfile.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o hfile_net.o hfile_net.c cc -pipe -O2 -fno-strict-aliasing -I. -c -o hts.o hts.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.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 cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a gmake[3]: Leaving directory '/construction/biology/stacks/stacks-1.48/htslib' Making all in . gmake[3]: Entering directory '/construction/biology/stacks/stacks-1.48' c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/ustacks-ustacks.o -MD -MP -MF src/.deps/ustacks-ustacks.Tpo -c -o src/ustacks-ustacks.o `test -f 'src/ustacks.cc' || echo './'`src/ustacks.cc c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/ustacks-stacks.o -MD -MP -MF src/.deps/ustacks-stacks.Tpo -c -o src/ustacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/ustacks-constants.o -MD -MP -MF src/.deps/ustacks-constants.Tpo -c -o src/ustacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/ustacks-mstack.o -MD -MP -MF src/.deps/ustacks-mstack.Tpo -c -o src/ustacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp 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'src/models.cc' || echo './'`src/models.cc c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/ustacks-utils.o -MD -MP -MF src/.deps/ustacks-utils.Tpo -c -o src/ustacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/ustacks-kmers.o -MD -MP -MF src/.deps/ustacks-kmers.Tpo -c -o src/ustacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/ustacks-aln_utils.o -MD -MP -MF src/.deps/ustacks-aln_utils.Tpo -c -o src/ustacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc mv -f src/.deps/ustacks-DNASeq.Tpo src/.deps/ustacks-DNASeq.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/ustacks-input.o -MD -MP -MF src/.deps/ustacks-input.Tpo -c -o src/ustacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc mv -f src/.deps/ustacks-DNANSeq.Tpo src/.deps/ustacks-DNANSeq.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -MT src/pstacks-pstacks.o -MD -MP -MF src/.deps/pstacks-pstacks.Tpo -c -o src/pstacks-pstacks.o `test -f 'src/pstacks.cc' || echo './'`src/pstacks.cc mv -f src/.deps/ustacks-utils.Tpo src/.deps/ustacks-utils.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -MT src/pstacks-stacks.o -MD -MP -MF src/.deps/pstacks-stacks.Tpo -c -o src/pstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc mv -f src/.deps/ustacks-input.Tpo src/.deps/ustacks-input.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -MT src/pstacks-constants.o -MD -MP -MF src/.deps/pstacks-constants.Tpo -c -o src/pstacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc mv -f src/.deps/ustacks-aln_utils.Tpo src/.deps/ustacks-aln_utils.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -MT src/pstacks-mstack.o -MD -MP -MF src/.deps/pstacks-mstack.Tpo -c -o src/pstacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc mv -f src/.deps/ustacks-mstack.Tpo src/.deps/ustacks-mstack.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -MT src/pstacks-log_utils.o -MD -MP -MF src/.deps/pstacks-log_utils.Tpo -c -o src/pstacks-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc mv -f src/.deps/ustacks-models.Tpo src/.deps/ustacks-models.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -MT src/pstacks-DNANSeq.o -MD -MP -MF src/.deps/pstacks-DNANSeq.Tpo -c -o src/pstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc mv -f src/.deps/ustacks-stacks.Tpo src/.deps/ustacks-stacks.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -I./htslib/htslib -pipe -O2 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'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc mv -f src/.deps/genotypes-genotype_dictionaries.Tpo src/.deps/genotypes-genotype_dictionaries.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/populations-renz.o -MD -MP -MF src/.deps/populations-renz.Tpo -c -o src/populations-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc mv -f src/.deps/genotypes-MetaPopInfo.Tpo src/.deps/genotypes-MetaPopInfo.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/populations-export_formats.o -MD -MP -MF src/.deps/populations-export_formats.Tpo -c -o src/populations-export_formats.o `test -f 'src/export_formats.cc' || echo './'`src/export_formats.cc mv -f src/.deps/populations-input.Tpo src/.deps/populations-input.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/populations-MetaPopInfo.o -MD -MP -MF src/.deps/populations-MetaPopInfo.Tpo -c -o src/populations-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc mv -f src/.deps/populations-aln_utils.Tpo src/.deps/populations-aln_utils.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/populations-Vcf.o -MD -MP -MF src/.deps/populations-Vcf.Tpo -c -o src/populations-Vcf.o `test -f 'src/Vcf.cc' || echo './'`src/Vcf.cc mv -f src/.deps/genotypes-catalog_utils.Tpo src/.deps/genotypes-catalog_utils.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks-phasedstacks.o -MD -MP -MF src/.deps/phasedstacks-phasedstacks.Tpo -c -o src/phasedstacks-phasedstacks.o `test -f 'src/phasedstacks.cc' || echo './'`src/phasedstacks.cc mv -f src/.deps/populations-locus.Tpo src/.deps/populations-locus.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks-constants.o -MD -MP -MF src/.deps/phasedstacks-constants.Tpo -c -o src/phasedstacks-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc mv -f src/.deps/populations-renz.Tpo src/.deps/populations-renz.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks-locus.o -MD -MP -MF src/.deps/phasedstacks-locus.Tpo -c -o src/phasedstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc mv -f src/.deps/populations-sql_utilities.Tpo src/.deps/populations-sql_utilities.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks-input.o -MD -MP -MF src/.deps/phasedstacks-input.Tpo -c -o src/phasedstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc mv -f src/.deps/genotypes-genotypes.Tpo src/.deps/genotypes-genotypes.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks-sql_utilities.o -MD -MP -MF src/.deps/phasedstacks-sql_utilities.Tpo -c -o src/phasedstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc mv -f src/.deps/phasedstacks-input.Tpo src/.deps/phasedstacks-input.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks-log_utils.o -MD -MP -MF src/.deps/phasedstacks-log_utils.Tpo -c -o src/phasedstacks-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc mv -f src/.deps/populations-constants.Tpo src/.deps/populations-constants.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks-utils.o -MD -MP -MF src/.deps/phasedstacks-utils.Tpo -c -o src/phasedstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc mv -f src/.deps/phasedstacks-locus.Tpo src/.deps/phasedstacks-locus.Po c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -fopenmp -pipe -O2 -fno-strict-aliasing -MT src/phasedstacks-catalog_utils.o -MD -MP -MF src/.deps/phasedstacks-catalog_utils.Tpo -c -o src/phasedstacks-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc mv -f src/.deps/populations-MetaPopInfo.Tpo src/.deps/populations-MetaPopInfo.Po c++ -std=gnu++11 -fopenmp -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o ustacks src/ustacks-ustacks.o src/ustacks-stacks.o src/ustacks-constants.o src/ustacks-mstack.o src/ustacks-mst.o src/ustacks-cmb.o src/ustacks-DNASeq.o src/ustacks-DNANSeq.o src/ustacks-models.o src/ustacks-utils.o src/ustacks-kmers.o src/ustacks-aln_utils.o src/ustacks-input.o -lz -lgomp c++ -std=gnu++11 -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o pstacks src/pstacks-pstacks.o src/pstacks-stacks.o src/pstacks-constants.o src/pstacks-mstack.o src/pstacks-log_utils.o src/pstacks-DNANSeq.o src/pstacks-DNASeq.o src/pstacks-models.o src/pstacks-utils.o src/pstacks-aln_utils.o src/pstacks-input.o ./htslib/libhts.a -lz -lgomp c++ -std=gnu++11 -fopenmp -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o cstacks src/cstacks-cstacks.o src/cstacks-constants.o src/cstacks-stacks.o src/cstacks-locus.o src/cstacks-kmers.o src/cstacks-utils.o src/cstacks-aln_utils.o src/cstacks-DNASeq.o src/cstacks-DNANSeq.o src/cstacks-input.o src/cstacks-sql_utilities.o src/cstacks-MetaPopInfo.o -lz -lgomp mv -f src/.deps/populations-genotype_dictionaries.Tpo src/.deps/populations-genotype_dictionaries.Po c++ -std=gnu++11 -fopenmp -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o sstacks src/sstacks-sstacks.o src/sstacks-constants.o src/sstacks-stacks.o src/sstacks-locus.o src/sstacks-kmers.o src/sstacks-aln_utils.o src/sstacks-DNASeq.o src/sstacks-DNANSeq.o src/sstacks-utils.o src/sstacks-input.o src/sstacks-sql_utilities.o src/sstacks-catalog_utils.o src/sstacks-MetaPopInfo.o -lz -lgomp c++ -std=gnu++11 -fopenmp -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o rxstacks src/rxstacks-rxstacks.o src/rxstacks-constants.o src/rxstacks-stacks.o src/rxstacks-locus.o src/rxstacks-DNANSeq.o src/rxstacks-DNASeq.o src/rxstacks-mst.o src/rxstacks-models.o src/rxstacks-aln_utils.o src/rxstacks-utils.o src/rxstacks-input.o src/rxstacks-sql_utilities.o src/rxstacks-catalog_utils.o src/rxstacks-MetaPopInfo.o -lz -lgomp c++ -std=gnu++11 -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o process_radtags src/process_radtags-process_radtags.o src/process_radtags-constants.o src/process_radtags-utils.o src/process_radtags-log_utils.o src/process_radtags-write.o src/process_radtags-clean.o src/process_radtags-file_io.o src/process_radtags-input.o src/process_radtags-renz.o ./htslib/libhts.a -lz -lgomp c++ -std=gnu++11 -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o process_shortreads src/process_shortreads-process_shortreads.o src/process_shortreads-constants.o src/process_shortreads-clean.o src/process_shortreads-file_io.o src/process_shortreads-utils.o src/process_shortreads-log_utils.o src/process_shortreads-write.o src/process_shortreads-kmers.o src/process_shortreads-input.o ./htslib/libhts.a -lz -lgomp c++ -std=gnu++11 -fopenmp -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o kmer_filter src/kmer_filter-kmer_filter.o src/kmer_filter-constants.o src/kmer_filter-utils.o src/kmer_filter-write.o src/kmer_filter-kmers.o src/kmer_filter-input.o -lz -lgomp c++ -std=gnu++11 -fopenmp -I./htslib/htslib -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o clone_filter src/clone_filter-clone_filter.o src/clone_filter-constants.o src/clone_filter-kmers.o src/clone_filter-utils.o src/clone_filter-write.o src/clone_filter-clean.o src/clone_filter-file_io.o src/clone_filter-input.o ./htslib/libhts.a -lz -lgomp c++ -std=gnu++11 -fopenmp -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o genotypes src/genotypes-genotypes.o src/genotypes-constants.o src/genotypes-utils.o src/genotypes-catalog_utils.o src/genotypes-log_utils.o src/genotypes-stacks.o src/genotypes-locus.o src/genotypes-DNASeq.o src/genotypes-DNANSeq.o src/genotypes-aln_utils.o src/genotypes-genotype_dictionaries.o src/genotypes-input.o src/genotypes-sql_utilities.o src/genotypes-renz.o src/genotypes-MetaPopInfo.o -lz -lgomp mv -f src/.deps/populations-Vcf.Tpo src/.deps/populations-Vcf.Po mv -f src/.deps/phasedstacks-utils.Tpo src/.deps/phasedstacks-utils.Po mv -f src/.deps/phasedstacks-sql_utilities.Tpo src/.deps/phasedstacks-sql_utilities.Po mv -f src/.deps/phasedstacks-log_utils.Tpo src/.deps/phasedstacks-log_utils.Po mv -f src/.deps/phasedstacks-constants.Tpo src/.deps/phasedstacks-constants.Po mv -f src/.deps/populations-catalog_utils.Tpo src/.deps/populations-catalog_utils.Po mv -f src/.deps/phasedstacks-phasedstacks.Tpo src/.deps/phasedstacks-phasedstacks.Po mv -f src/.deps/phasedstacks-catalog_utils.Tpo src/.deps/phasedstacks-catalog_utils.Po c++ -std=gnu++11 -fopenmp -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o phasedstacks src/phasedstacks-phasedstacks.o src/phasedstacks-constants.o src/phasedstacks-locus.o src/phasedstacks-input.o src/phasedstacks-sql_utilities.o src/phasedstacks-log_utils.o src/phasedstacks-utils.o src/phasedstacks-catalog_utils.o -lz -lgomp mv -f src/.deps/populations-export_formats.Tpo src/.deps/populations-export_formats.Po mv -f src/.deps/populations-populations.Tpo src/.deps/populations-populations.Po c++ -std=gnu++11 -fopenmp -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o populations src/populations-populations.o src/populations-constants.o src/populations-utils.o src/populations-catalog_utils.o src/populations-log_utils.o src/populations-stacks.o src/populations-locus.o src/populations-DNASeq.o src/populations-DNANSeq.o src/populations-aln_utils.o src/populations-genotype_dictionaries.o src/populations-input.o src/populations-sql_utilities.o src/populations-renz.o src/populations-export_formats.o src/populations-MetaPopInfo.o src/populations-Vcf.o -lz -lgomp gmake[3]: Leaving directory '/construction/biology/stacks/stacks-1.48' gmake[2]: Leaving directory '/construction/biology/stacks/stacks-1.48' gmake[1]: Leaving directory '/construction/biology/stacks/stacks-1.48' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> stacks-1.48 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for stacks-1.48 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/stacks/stacks-1.48' Making install in htslib gmake[2]: Entering directory '/construction/biology/stacks/stacks-1.48/htslib' gmake[2]: Nothing to be done for 'install'. gmake[2]: Leaving directory '/construction/biology/stacks/stacks-1.48/htslib' Making install in . gmake[2]: Entering directory '/construction/biology/stacks/stacks-1.48' gmake[3]: Entering directory '/construction/biology/stacks/stacks-1.48' test -z "/usr/local/bin" || /bin/mkdir -p "/construction/biology/stacks/stage/usr/local/bin" install -s -m 555 ustacks pstacks cstacks sstacks rxstacks process_radtags process_shortreads kmer_filter clone_filter genotypes populations phasedstacks '/construction/biology/stacks/stage/usr/local/bin' test -z "/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/export_sql.pl scripts/sort_read_pairs.pl scripts/exec_velvet.pl scripts/load_sequences.pl scripts/index_radtags.pl scripts/load_radtags.pl scripts/stacks_export_notify.pl scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py '/construction/biology/stacks/stage/usr/local/bin' test -z "/usr/local/share/stacks" || /bin/mkdir -p "/construction/biology/stacks/stage/usr/local/share/stacks" /bin/mkdir -p '/construction/biology/stacks/stage/usr/local/share/stacks/php' install -m 0644 php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php php/stacks_functions.php php/view_sequence.php php/sequence_blast.php php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css '/construction/biology/stacks/stage/usr/local/share/stacks/php' /bin/mkdir -p '/construction/biology/stacks/stage/usr/local/share/stacks/sql' install -m 0644 sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql '/construction/biology/stacks/stage/usr/local/share/stacks/sql' /bin/mkdir -p '/construction/biology/stacks/stage/usr/local/share/stacks/php/images' install -m 0644 php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png php/images/stacks_logo_rev_small.png '/construction/biology/stacks/stage/usr/local/share/stacks/php/images' gmake install-data-hook gmake[4]: Entering directory '/construction/biology/stacks/stacks-1.48' sed -e 's,_VERSION_,1.48,' -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_,1.48,' -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 -e 's,_VERSION_,1.48,' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /construction/biology/stacks/stage/usr/local/bin/export_sql.pl > /construction/biology/stacks/stage/usr/local/bin/export_sql.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/export_sql.pl.subst /construction/biology/stacks/stage/usr/local/bin/export_sql.pl chmod +x /construction/biology/stacks/stage/usr/local/bin/export_sql.pl sed -e 's,_VERSION_,1.48,' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /construction/biology/stacks/stage/usr/local/bin/index_radtags.pl > /construction/biology/stacks/stage/usr/local/bin/index_radtags.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/index_radtags.pl.subst /construction/biology/stacks/stage/usr/local/bin/index_radtags.pl chmod +x /construction/biology/stacks/stage/usr/local/bin/index_radtags.pl sed -e 's,_VERSION_,1.48,' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /construction/biology/stacks/stage/usr/local/bin/load_radtags.pl > /construction/biology/stacks/stage/usr/local/bin/load_radtags.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/load_radtags.pl.subst /construction/biology/stacks/stage/usr/local/bin/load_radtags.pl chmod +x /construction/biology/stacks/stage/usr/local/bin/load_radtags.pl sed -e 's,_VERSION_,1.48,' /construction/biology/stacks/stage/usr/local/bin/sort_read_pairs.pl > /construction/biology/stacks/stage/usr/local/bin/sort_read_pairs.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/sort_read_pairs.pl.subst /construction/biology/stacks/stage/usr/local/bin/sort_read_pairs.pl chmod +x /construction/biology/stacks/stage/usr/local/bin/sort_read_pairs.pl sed -e 's,_VERSION_,1.48,' /construction/biology/stacks/stage/usr/local/bin/exec_velvet.pl > /construction/biology/stacks/stage/usr/local/bin/exec_velvet.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/exec_velvet.pl.subst /construction/biology/stacks/stage/usr/local/bin/exec_velvet.pl chmod +x /construction/biology/stacks/stage/usr/local/bin/exec_velvet.pl sed -e 's,_VERSION_,1.48,' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /construction/biology/stacks/stage/usr/local/bin/load_sequences.pl > /construction/biology/stacks/stage/usr/local/bin/load_sequences.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/load_sequences.pl.subst /construction/biology/stacks/stage/usr/local/bin/load_sequences.pl chmod +x /construction/biology/stacks/stage/usr/local/bin/load_sequences.pl sed -e 's,_VERSION_,1.48,' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' -e 's,_BINDIR_,/usr/local/bin/,g' \ /construction/biology/stacks/stage/usr/local/bin/stacks_export_notify.pl > /construction/biology/stacks/stage/usr/local/bin/stacks_export_notify.pl.subst mv /construction/biology/stacks/stage/usr/local/bin/stacks_export_notify.pl.subst /construction/biology/stacks/stage/usr/local/bin/stacks_export_notify.pl chmod +x /construction/biology/stacks/stage/usr/local/bin/stacks_export_notify.pl sed -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' -e 's,_BINDIR_,/usr/local/bin/,g' \ /construction/biology/stacks/stage/usr/local/share/stacks/php/constants.php.dist > /construction/biology/stacks/stage/usr/local/share/stacks/php/constants.php.dist.subst mv /construction/biology/stacks/stage/usr/local/share/stacks/php/constants.php.dist.subst /construction/biology/stacks/stage/usr/local/share/stacks/php/constants.php.dist echo 1.48 > /construction/biology/stacks/stage/usr/local/share/stacks/php/version.php /bin/sh /construction/biology/stacks/stacks-1.48/config/install-sh -d -m 755 /construction/biology/stacks/stage/usr/local/share/stacks/php/export gmake[4]: Leaving directory '/construction/biology/stacks/stacks-1.48' gmake[3]: Leaving directory '/construction/biology/stacks/stacks-1.48' gmake[2]: Leaving directory '/construction/biology/stacks/stacks-1.48' gmake[1]: Leaving directory '/construction/biology/stacks/stacks-1.48' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for stacks-1.48 file sizes/checksums [72]: . done packing files [72]: . done packing directories [1]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:03:56 UTC Duration: 00:02:24