=> Building biology/freebayes Started : Wednesday, 6 MAR 2019 at 05:41:34 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-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 XDG_DATA_HOME=/construction/biology/freebayes XDG_CONFIG_HOME=/construction/biology/freebayes HOME=/construction/biology/freebayes TMPDIR="/tmp" PATH=/construction/biology/freebayes/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/freebayes XDG_CONFIG_HOME=/construction/biology/freebayes HOME=/construction/biology/freebayes TMPDIR="/tmp" PATH=/construction/biology/freebayes/.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=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing --std=c++11 " 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/freebayes/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/freebayes" EXAMPLESDIR="share/examples/freebayes" DATADIR="share/freebayes" WWWDIR="www/freebayes" ETCDIR="etc/freebayes" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/freebayes DOCSDIR=/usr/local/share/doc/freebayes EXAMPLESDIR=/usr/local/share/examples/freebayes WWWDIR=/usr/local/www/freebayes ETCDIR=/usr/local/etc/freebayes -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE 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=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> freebayes-1.2.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> freebayes-1.2.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of freebayes-1.2.0_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0_1 for building => SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz. => SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-49fdfbd_GH0.tar.gz. => SHA256 Checksum OK for ekg-bamtools-e77a43f_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-dbb4c51_GH0.tar.gz. => SHA256 Checksum OK for vcflib-vcflib-5e3ce04_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-c68cebb_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz. => SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-b704f19_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-73d35da_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-84c08d7_GH0.tar.gz. => SHA256 Checksum OK for ekg-tabixpp-80012f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-0f298ce_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0_1 for building ===> Extracting for freebayes-1.2.0_1 => SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz. => SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-49fdfbd_GH0.tar.gz. => SHA256 Checksum OK for ekg-bamtools-e77a43f_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-dbb4c51_GH0.tar.gz. => SHA256 Checksum OK for vcflib-vcflib-5e3ce04_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-c68cebb_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz. => SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-b704f19_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-73d35da_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-84c08d7_GH0.tar.gz. => SHA256 Checksum OK for ekg-tabixpp-80012f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-0f298ce_GH0.tar.gz. /bin/mv -n /construction/biology/freebayes/freebayes-1.2.0/SeqLib-temp/* /construction/biology/freebayes/freebayes-1.2.0/SeqLib /bin/mv -n /construction/biology/freebayes/freebayes-1.2.0/vcflib-temp/* /construction/biology/freebayes/freebayes-1.2.0/vcflib -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for freebayes-1.2.0_1 ===> Applying ports patches for freebayes-1.2.0_1 ===> Applying dragonfly patches for freebayes-1.2.0_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> freebayes-1.2.0_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-0.19.8.1_2... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_2: .......... done Extracting gmake-4.2.1_3: .......... done ===> freebayes-1.2.0_1 depends on executable: gmake - found ===> Returning to build of freebayes-1.2.0_1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for freebayes-1.2.0_1 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for freebayes-1.2.0_1 gmake[1]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0' cd src && gmake autoversion gmake[2]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/src' DETECTED_VERSION = v1.0.0 CURRENT_VERSION = Updating version file. gmake[2]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/src' touch src/version_git.h # wget -q http://hypervolu.me/freebayes/build/v1.0.0 & cd src && gmake gmake[2]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/src' DETECTED_VERSION = v1.0.0 CURRENT_VERSION = v1.0.0 cd ../SeqLib/htslib && gmake gmake[3]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/htslib' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o kfunc.o kfunc.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o knetfile.o knetfile.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o kstring.o kstring.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bgzf.o bgzf.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o errmod.o errmod.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o faidx.o faidx.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hfile.o hfile.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.5"' > version.h cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hts.o hts.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o md5.o md5.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o multipart.o multipart.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o probaln.o probaln.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o realn.o realn.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o regidx.o regidx.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o sam.o sam.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcf_sweep.o vcf_sweep.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o tbx.o tbx.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o textutils.o textutils.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o thread_pool.o thread_pool.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcf.o vcf.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcfutils.o vcfutils.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_decode.o cram/cram_decode.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_encode.o cram/cram_encode.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_external.o cram/cram_external.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_index.o cram/cram_index.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_io.o cram/cram_io.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_stats.o cram/cram_stats.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/files.o cram/files.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/mFILE.o cram/mFILE.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/rANS_static.o cram/rANS_static.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/sam_header.o cram/sam_header.c cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.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 ranlib libhts.a cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bgzip.o bgzip.c cc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o htsfile.o htsfile.c cc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o tabix.o tabix.c cc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/hts_endian.o test/hts_endian.c cc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/fieldarith.o test/fieldarith.c cc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/hfile.o test/hfile.c cc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/sam.o test/sam.c cc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test_bgzf.o test/test_bgzf.c cc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-regidx.o test/test-regidx.c cc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test_view.o test/test_view.c cc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c cc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c cc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c cc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gmake[3]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/htslib' cd ../vcflib/tabixpp/ && gmake && cp tabix.hpp ../../src/ gmake[3]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/vcflib/tabixpp' gmake[4]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/vcflib/tabixpp' c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -c tabix.cpp -Ihtslib cd htslib && gmake lib-static gmake[5]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/vcflib/tabixpp/htslib' echo '/* Empty config.h generated by Makefile */' > config.h cc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c cc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c knetfile.c: In function 'socket_wait': knetfile.c:72:8: warning: implicit declaration of function 'select'; did you mean 'exect'? [-Wimplicit-function-declaration] ret = select(fd+1, fdr, fdw, 0, &tv); ^~~~~~ exect cc -g -Wall -O2 -I. -c -o kstring.o kstring.c cc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c cc -g -Wall -O2 -I. -c -o faidx.o faidx.c cc -g -Wall -O2 -I. -c -o hfile.o hfile.c cc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.3.1"' > version.h cc -g -Wall -O2 -I. -c -o hts.o hts.c cc -g -Wall -O2 -I. -c -o md5.o md5.c cc -g -Wall -O2 -I. -c -o regidx.o regidx.c cc -g -Wall -O2 -I. -c -o sam.o sam.c sam.c: In function 'bam_hdr_write': sam.c:230:5: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] strncpy(buf, "BAM\1", 4); ^~~~~~~~~~~~~~~~~~~~~~~~ cc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c cc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c cc -g -Wall -O2 -I. -c -o tbx.o tbx.c cc -g -Wall -O2 -I. -c -o vcf.o vcf.c cc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c cc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c cc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c cc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c cc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c cc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c cc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c: In function 'cram_populate_ref': cram/cram_io.c:2360:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); ^~~~~ cram/cram_io.c:2360:24: note: using the range [0, 4294967295] for directive argument sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); ^~~~~~~~~~~~~~~~~ cram/cram_io.c:2360:24: note: using the range [0, 4294967295] for directive argument cram/cram_io.c:2360:6: note: 'sprintf' output between 11 and 1062 bytes into a destination of size 1024 sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:2252:2: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(path, path2, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'full_path', inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3905:3: cram/cram_io.c:3830:6: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:3822:2: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c cc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c cc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c cc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c cc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c cc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c cc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c cc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c cc -g -Wall -O2 -I. -c -o cram/thread_pool.o cram/thread_pool.c cc -g -Wall -O2 -I. -c -o cram/vlen.o cram/vlen.c cc -g -Wall -O2 -I. -c -o cram/zfio.o cram/zfio.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[5]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/vcflib/tabixpp/htslib' c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -o tabix++ main.cpp tabix.o -Ihtslib -L. -Lhtslib \ -lhts -lpthread -lm -lz gmake[4]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/vcflib/tabixpp' gmake[3]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/vcflib/tabixpp' c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c freebayes.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c BedReader.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c CNV.cpp cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c fastlz.c c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Utility.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Fasta.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Parameters.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Allele.cpp Allele.cpp: In member function 'const string Allele::base() const': Allele.cpp:297:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Sample.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Result.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c AlleleParser.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Genotype.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c DataLikelihood.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Multinomial.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Ewens.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c ResultData.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Dirichlet.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Marginals.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c split.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c LeftAlign.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c IndelAllele.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c Bias.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -c -o Contamination.o Contamination.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c NonCall.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c SegfaultHandler.cpp cd ../vcflib/smithwaterman && gmake gmake[3]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/vcflib/smithwaterman' c++ -O3 -c -o disorder.o disorder.cpp -I. c++ -O3 -c -o smithwaterman.o smithwaterman.cpp -I. c++ -O3 -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I. c++ -O3 -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I. c++ -O3 -c -o LeftAlign.o LeftAlign.cpp -I. c++ -O3 -c -o Repeats.o Repeats.cpp -I. c++ -O3 -c -o IndelAllele.o IndelAllele.cpp -I. c++ -O3 smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -I. -o smithwaterman ld -r BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o -o sw.o -L. #c++ -O3 -c -o smithwaterman.cpp disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -I. gmake[3]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/vcflib/smithwaterman' c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c ../vcflib/src/Variant.cpp ../vcflib/src/Variant.cpp: In member function 'bool vcflib::Variant::getInfoValueBool(std::__cxx11::string&, int)': ../vcflib/src/Variant.cpp:212:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ ../vcflib/src/Variant.cpp: In member function 'bool vcflib::Variant::getSampleValueBool(std::__cxx11::string&, std::__cxx11::string&, int)': ../vcflib/src/Variant.cpp:334:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ ../vcflib/src/Variant.cpp: In member function 'std::__cxx11::string vcflib::Variant::getSampleValueString(std::__cxx11::string&, std::__cxx11::string&, int)': ../vcflib/src/Variant.cpp:368:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ ../vcflib/src/Variant.cpp: In member function 'double vcflib::Variant::getSampleValueFloat(std::__cxx11::string&, std::__cxx11::string&, int)': ../vcflib/src/Variant.cpp:406:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ cd ../SeqLib && ./configure && gmake checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /construction/biology/freebayes/freebayes-1.2.0/SeqLib/missing: Unknown `--is-lightweight' option Try `/construction/biology/freebayes/freebayes-1.2.0/SeqLib/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no 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 make... 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 whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gzopen... none required checking for library containing lzma_code... none required checking for library containing BZ2_bzBuffToBuffDecompress... none required checking for library containing clock_gettime... none required checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/seqtools/Makefile config.status: creating config.h config.status: executing depfiles commands gmake[3]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib' gmake all-recursive gmake[4]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib' Making all in bwa gmake[5]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/bwa' cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o ar -csru libbwa.a utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o is.o bwtindex.o rope.o rle.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread gmake[5]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/bwa' Making all in htslib gmake[5]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/htslib' gmake[5]: Nothing to be done for 'all'. gmake[5]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/htslib' Making all in fermi-lite gmake[5]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/fermi-lite' cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 kthread.c -o kthread.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 misc.c -o misc.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 bseq.c -o bseq.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 htab.c -o htab.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 bfc.c -o bfc.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 rle.c -o rle.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 rope.c -o rope.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 mrope.c -o mrope.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 rld0.c -o rld0.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 unitig.c -o unitig.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 mag.c -o mag.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 bubble.c -o bubble.o cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 f_ksw.c -o f_ksw.o ar -csru libfml.a kthread.o misc.o bseq.o htab.o bfc.o rle.o rope.o mrope.o rld0.o unitig.o mag.o bubble.o f_ksw.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') cc -c -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 example.c -o example.o cc -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 libfml.a example.o -o fml-asm -L. -lfml -lm -lz -lpthread gmake[5]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/fermi-lite' Making all in src gmake[5]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/src' c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-FastqReader.o -MD -MP -MF .deps/libseqlib_a-FastqReader.Tpo -c -o libseqlib_a-FastqReader.o `test -f 'FastqReader.cpp' || echo './'`FastqReader.cpp mv -f .deps/libseqlib_a-FastqReader.Tpo .deps/libseqlib_a-FastqReader.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-BFC.o -MD -MP -MF .deps/libseqlib_a-BFC.Tpo -c -o libseqlib_a-BFC.o `test -f 'BFC.cpp' || echo './'`BFC.cpp mv -f .deps/libseqlib_a-BFC.Tpo .deps/libseqlib_a-BFC.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-ReadFilter.o -MD -MP -MF .deps/libseqlib_a-ReadFilter.Tpo -c -o libseqlib_a-ReadFilter.o `test -f 'ReadFilter.cpp' || echo './'`ReadFilter.cpp mv -f .deps/libseqlib_a-ReadFilter.Tpo .deps/libseqlib_a-ReadFilter.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-SeqPlot.o -MD -MP -MF .deps/libseqlib_a-SeqPlot.Tpo -c -o libseqlib_a-SeqPlot.o `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp mv -f .deps/libseqlib_a-SeqPlot.Tpo .deps/libseqlib_a-SeqPlot.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-jsoncpp.o -MD -MP -MF .deps/libseqlib_a-jsoncpp.Tpo -c -o libseqlib_a-jsoncpp.o `test -f 'jsoncpp.cpp' || echo './'`jsoncpp.cpp mv -f .deps/libseqlib_a-jsoncpp.Tpo .deps/libseqlib_a-jsoncpp.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-ssw_cpp.o -MD -MP -MF .deps/libseqlib_a-ssw_cpp.Tpo -c -o libseqlib_a-ssw_cpp.o `test -f 'ssw_cpp.cpp' || echo './'`ssw_cpp.cpp mv -f .deps/libseqlib_a-ssw_cpp.Tpo .deps/libseqlib_a-ssw_cpp.Po cc -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -MT libseqlib_a-ssw.o -MD -MP -MF .deps/libseqlib_a-ssw.Tpo -c -o libseqlib_a-ssw.o `test -f 'ssw.c' || echo './'`ssw.c mv -f .deps/libseqlib_a-ssw.Tpo .deps/libseqlib_a-ssw.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-GenomicRegion.o -MD -MP -MF .deps/libseqlib_a-GenomicRegion.Tpo -c -o libseqlib_a-GenomicRegion.o `test -f 'GenomicRegion.cpp' || echo './'`GenomicRegion.cpp mv -f .deps/libseqlib_a-GenomicRegion.Tpo .deps/libseqlib_a-GenomicRegion.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-RefGenome.o -MD -MP -MF .deps/libseqlib_a-RefGenome.Tpo -c -o libseqlib_a-RefGenome.o `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp mv -f .deps/libseqlib_a-RefGenome.Tpo .deps/libseqlib_a-RefGenome.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-BamWriter.o -MD -MP -MF .deps/libseqlib_a-BamWriter.Tpo -c -o libseqlib_a-BamWriter.o `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp mv -f .deps/libseqlib_a-BamWriter.Tpo .deps/libseqlib_a-BamWriter.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-BamReader.o -MD -MP -MF .deps/libseqlib_a-BamReader.Tpo -c -o libseqlib_a-BamReader.o `test -f 'BamReader.cpp' || echo './'`BamReader.cpp mv -f .deps/libseqlib_a-BamReader.Tpo .deps/libseqlib_a-BamReader.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-BWAWrapper.o -MD -MP -MF .deps/libseqlib_a-BWAWrapper.Tpo -c -o libseqlib_a-BWAWrapper.o `test -f 'BWAWrapper.cpp' || echo './'`BWAWrapper.cpp mv -f .deps/libseqlib_a-BWAWrapper.Tpo .deps/libseqlib_a-BWAWrapper.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-BamRecord.o -MD -MP -MF .deps/libseqlib_a-BamRecord.Tpo -c -o libseqlib_a-BamRecord.o `test -f 'BamRecord.cpp' || echo './'`BamRecord.cpp mv -f .deps/libseqlib_a-BamRecord.Tpo .deps/libseqlib_a-BamRecord.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-FermiAssembler.o -MD -MP -MF .deps/libseqlib_a-FermiAssembler.Tpo -c -o libseqlib_a-FermiAssembler.o `test -f 'FermiAssembler.cpp' || echo './'`FermiAssembler.cpp mv -f .deps/libseqlib_a-FermiAssembler.Tpo .deps/libseqlib_a-FermiAssembler.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -pipe -O2 -fno-strict-aliasing --std=c++11 -MT libseqlib_a-BamHeader.o -MD -MP -MF .deps/libseqlib_a-BamHeader.Tpo -c -o libseqlib_a-BamHeader.o `test -f 'BamHeader.cpp' || echo './'`BamHeader.cpp mv -f .deps/libseqlib_a-BamHeader.Tpo .deps/libseqlib_a-BamHeader.Po rm -f libseqlib.a ar cru libseqlib.a libseqlib_a-FastqReader.o libseqlib_a-BFC.o libseqlib_a-ReadFilter.o libseqlib_a-SeqPlot.o libseqlib_a-jsoncpp.o libseqlib_a-ssw_cpp.o libseqlib_a-ssw.o libseqlib_a-GenomicRegion.o libseqlib_a-RefGenome.o libseqlib_a-BamWriter.o libseqlib_a-BamReader.o libseqlib_a-BWAWrapper.o libseqlib_a-BamRecord.o libseqlib_a-FermiAssembler.o libseqlib_a-BamHeader.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqlib.a gmake[5]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib/src' gmake[5]: Entering directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib' gmake[5]: Nothing to be done for 'all-am'. gmake[5]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib' gmake[4]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib' gmake[3]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/SeqLib' c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib freebayes.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o ../vcflib/tabixpp/tabix.o ../vcflib/smithwaterman/SmithWatermanGotoh.o ../vcflib/smithwaterman/disorder.cpp ../vcflib/smithwaterman/LeftAlign.o ../vcflib/smithwaterman/Repeats.o ../vcflib/smithwaterman/IndelAllele.o Variant.o ../SeqLib/src/libseqlib.a ../SeqLib/bwa/libbwa.a ../SeqLib/fermi-lite/libfml.a ../SeqLib/htslib/libhts.a -o ../bin/freebayes -lz -llzma -lbz2 -lm -lpthread -lexecinfo c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib -c bamleftalign.cpp c++ -pipe -O2 -fno-strict-aliasing --std=c++11 -I../src -I../ttmath -I../vcflib/src/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/fastahack/ -I../SeqLib/htslib -I../SeqLib bamleftalign.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o ../vcflib/tabixpp/tabix.o ../vcflib/smithwaterman/SmithWatermanGotoh.o ../vcflib/smithwaterman/disorder.cpp ../vcflib/smithwaterman/LeftAlign.o ../vcflib/smithwaterman/Repeats.o ../vcflib/smithwaterman/IndelAllele.o Variant.o ../SeqLib/src/libseqlib.a ../SeqLib/bwa/libbwa.a ../SeqLib/fermi-lite/libfml.a ../SeqLib/htslib/libhts.a -o ../bin/bamleftalign -lz -llzma -lbz2 -lm -lpthread -lexecinfo gmake[2]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0/src' gmake[1]: Leaving directory '/construction/biology/freebayes/freebayes-1.2.0' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for freebayes-1.2.0_1 ===> Generating temporary packing list install -s -m 555 /construction/biology/freebayes/freebayes-1.2.0/bin/* /construction/biology/freebayes/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for freebayes-1.2.0_1 file sizes/checksums [5]: . done packing files [5]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 6 MAR 2019 at 05:51:03 UTC Duration: 00:09:28