------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=5.9 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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="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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/stacks/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=5.9 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500908 OSVERSION=9999999 OSREL=5.9 _OSRELEASE=5.9-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.10.txz Installing /packages/All/ncurses-6.2.20210213.txz Installing /packages/All/readline-8.1.0.txz Installing /packages/All/openssl-1.1.1j_1,1.txz Installing /packages/All/python37-3.7.9_1.txz ===== Message from python37-3.7.9_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 SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by stacks-2.4_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by stacks-2.4_2 for building => SHA256 Checksum OK for stacks-2.4.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found ===> 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. Extracted Memory Use: 54.80M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for stacks-2.4_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> stacks-2.4_2 depends on package: gmake>=4.3 - found ===> stacks-2.4_2 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> stacks-2.4_2 depends on package: gmake>=4.3 - found ===> stacks-2.4_2 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for stacks-2.4_2 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 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 SUCCEEDED 00:00:21 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for stacks-2.4_2 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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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 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-c -o multipart.o multipart.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo probaln.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc 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cram/cram_decode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -pipe -O2 -fno-strict-aliasing -MT cram/cram_index.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_index.o cram/cram_index.c &&\ mv -f 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$depbase.Tpo $depbase.Po depbase=`echo cram/mFILE.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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$||'`;\ cc -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 $depbase.Po rm -f libhts.a ar cru libhts.a bcf_sr_sort.o bgzf.o bgzip.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o htsfile.o kfunc.o knetfile.o kstring.o md5.o multipart.o os/rand.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o tabix.o tbx.o textutils.o thread_pool.o vcf.o vcf_sweep.o vcfutils.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libhts.a gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4/htslib' gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4' depbase=`echo src/aln_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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 $depbase.Po depbase=`echo src/input.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ 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$depbase.Tpo $depbase.Po depbase=`echo src/stacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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$||'`;\ c++ -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/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcore.a rm -f libclean.a ar cru libclean.a src/clean.o src/file_io.o src/write.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libclean.a rm -f libpop.a ar cru libpop.a src/export_formats.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpop.a c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o cstacks src/cstacks.o htslib/libhts.a libcore.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o process_radtags src/process_radtags.o htslib/libhts.a libcore.a libclean.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o process_shortreads src/process_shortreads.o htslib/libhts.a libcore.a libclean.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o clone_filter src/clone_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o ustacks src/ustacks.o htslib/libhts.a libcore.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o kmer_filter src/kmer_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o sstacks src/sstacks.o htslib/libhts.a libcore.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o phasedstacks src/phasedstacks.o htslib/libhts.a libcore.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o populations src/populations.o htslib/libhts.a libcore.a libpop.a -lz -lgomp c++ -pipe -O2 -fno-strict-aliasing -fopenmp -lpthread -o tsv2bam src/tsv2bam.o htslib/libhts.a libcore.a -lz -lgomp c++ -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' SUCCEEDED 00:01:45 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> stacks-2.4_2 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for stacks-2.4_2 ===> stacks-2.4_2 depends on file: /usr/local/bin/python3.7 - found ===> 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 SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for stacks-2.4_2 file sizes/checksums [18]: 0% file sizes/checksums [18]: 100% packing files [18]: 0% packing files [18]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:07 TOTAL TIME 00:02:31