Date: Sat, 19 Jan 2019 09:41:50 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120mips-quarterly][biology/gmap] Failed for gmap-2015.09.21 in build Message-ID: <201901190941.x0J9foMP001766@beefy14.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Last committer: jwb@FreeBSD.org Ident: $FreeBSD: branches/2019Q1/biology/gmap/Makefile 460452 2018-01-31 01:07:07Z jwb $ Log URL: http://beefy14.nyi.freebsd.org/data/120mips-quarterly/490693/logs/gmap-2015.09.21.log Build URL: http://beefy14.nyi.freebsd.org/build.html?mastername=120mips-quarterly&build=490693 Log: =>> Building biology/gmap build started at Sat Jan 19 09:29:49 UTC 2019 port directory: /usr/ports/biology/gmap package name: gmap-2015.09.21 building for: FreeBSD 120mips-quarterly-job-21 12.0-RELEASE-p2 FreeBSD 12.0-RELEASE-p2 1200086 mips maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q1/biology/gmap/Makefile 460452 2018-01-31 01:07:07Z jwb $ Poudriere version: 3.2.8 Host OSVERSION: 1300002 Jail OSVERSION: 1200086 Job Id: 21 ---Begin Environment--- SHELL=/bin/csh UNAME_p=mips UNAME_m=mips ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p2 1200086 UNAME_r=12.0-RELEASE-p2 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/120mips-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120mips-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120mips-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120mips-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for gmap-2015.09.21: SIMD=off: Use CPU-specific optimizations ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --disable-builtin-popcount --disable-simd --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gmap/work HOME=/wrkdirs/usr/ports/biology/gmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gmap/work HOME=/wrkdirs/usr/ports/biology/gmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -EB -mabi=32 " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -EB -mabi=32 -msoft-float -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" --End MAKE_ENV-- --PLIST_SUB-- OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.1 PERL_VER=5.28 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.28 DOCSDIR="share/doc/gmap" EXAMPLESDIR="share/examples/gmap" DATADIR="share/gmap" WWWDIR="www/gmap" ETCDIR="etc/gmap" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gmap DOCSDIR=/usr/local/share/doc/gmap EXAMPLESDIR=/usr/local/share/examples/gmap WWWDIR=/usr/local/www/gmap ETCDIR=/usr/local/etc/gmap --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=mips MACHINE_ARCH=mips ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=Using built-in specs. Target: mips-undermydesk-freebsd Configured with: FreeBSD/mips system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-EB" "-EB" "-melf32btsmip_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_9d218390_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_9d218390_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_9d218390_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_9d218390_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_9d218390_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_9d218390=none ARCH=mips OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p2 OSREL=12.0 OSVERSION=1200086 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 131072 stack size (kbytes, -s) 8192 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GMAP accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120mips-quarterly-job-21] Installing pkg-1.10.5_5... [120mips-quarterly-job-21] Extracting pkg-1.10.5_5: .......... done ===> gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gmap-2015.09.21 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GMAP accepted by the user ===> Fetching all distfiles required by gmap-2015.09.21 for building =========================================================================== =======================<phase: checksum >============================ ===> License GMAP accepted by the user ===> Fetching all distfiles required by gmap-2015.09.21 for building => SHA256 Checksum OK for gmap-gsnap-2015-09-21.tar.gz. =========================================================================== <snip> mv -f .deps/gmapl-splicetrie_build.Tpo .deps/gmapl-splicetrie_build.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-splicetrie.o -MD -MP -MF .deps/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gmapl-splicetrie.Tpo .deps/gmapl-splicetrie.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-boyer-moore.o -MD -MP -MF .deps/gmapl-boyer-moore.Tpo -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gmapl-boyer-moore.Tpo .deps/gmapl-boyer-moore.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-dynprog.o -MD -MP -MF .deps/gmapl-dynprog.Tpo -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gmapl-dynprog.Tpo .deps/gmapl-dynprog.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-dynprog_simd.o -MD -MP -MF .deps/gmapl-dynprog_simd.Tpo -c -o gmapl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c mv -f .deps/gmapl-dynprog_simd.Tpo .deps/gmapl-dynprog_simd.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-dynprog_single.o -MD -MP -MF .deps/gmapl-dynprog_single.Tpo -c -o gmapl-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c mv -f .deps/gmapl-dynprog_single.Tpo .deps/gmapl-dynprog_single.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-dynprog_genome.o -MD -MP -MF .deps/gmapl-dynprog_genome.Tpo -c -o gmapl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c mv -f .deps/gmapl-dynprog_genome.Tpo .deps/gmapl-dynprog_genome.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-dynprog_cdna.o -MD -MP -MF .deps/gmapl-dynprog_cdna.Tpo -c -o gmapl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c mv -f .deps/gmapl-dynprog_cdna.Tpo .deps/gmapl-dynprog_cdna.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-dynprog_end.o -MD -MP -MF .deps/gmapl-dynprog_end.Tpo -c -o gmapl-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c mv -f .deps/gmapl-dynprog_end.Tpo .deps/gmapl-dynprog_end.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-translation.o -MD -MP -MF .deps/gmapl-translation.Tpo -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gmapl-translation.Tpo .deps/gmapl-translation.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-pbinom.o -MD -MP -MF .deps/gmapl-pbinom.Tpo -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gmapl-pbinom.Tpo .deps/gmapl-pbinom.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-changepoint.o -MD -MP -MF .deps/gmapl-changepoint.Tpo -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gmapl-changepoint.Tpo .deps/gmapl-changepoint.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-stage3.o -MD -MP -MF .deps/gmapl-stage3.Tpo -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gmapl-stage3.Tpo .deps/gmapl-stage3.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-request.o -MD -MP -MF .deps/gmapl-request.Tpo -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gmapl-request.Tpo .deps/gmapl-request.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-result.o -MD -MP -MF .deps/gmapl-result.Tpo -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c mv -f .deps/gmapl-result.Tpo .deps/gmapl-result.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-output.o -MD -MP -MF .deps/gmapl-output.Tpo -c -o gmapl-output.o `test -f 'output.c' || echo './'`output.c mv -f .deps/gmapl-output.Tpo .deps/gmapl-output.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-inbuffer.o -MD -MP -MF .deps/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gmapl-inbuffer.Tpo .deps/gmapl-inbuffer.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-samheader.o -MD -MP -MF .deps/gmapl-samheader.Tpo -c -o gmapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gmapl-samheader.Tpo .deps/gmapl-samheader.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-outbuffer.o -MD -MP -MF .deps/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gmapl-outbuffer.Tpo .deps/gmapl-outbuffer.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-chimera.o -MD -MP -MF .deps/gmapl-chimera.Tpo -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gmapl-chimera.Tpo .deps/gmapl-chimera.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-datadir.o -MD -MP -MF .deps/gmapl-datadir.Tpo -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gmapl-datadir.Tpo .deps/gmapl-datadir.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-getopt.o -MD -MP -MF .deps/gmapl-getopt.Tpo -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gmapl-getopt.Tpo .deps/gmapl-getopt.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-getopt1.o -MD -MP -MF .deps/gmapl-getopt1.Tpo -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gmapl-getopt1.Tpo .deps/gmapl-getopt1.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapl-gmap.o -MD -MP -MF .deps/gmapl-gmap.Tpo -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c mv -f .deps/gmapl-gmap.Tpo .deps/gmapl-gmap.Po /bin/sh ../libtool --tag=CC --mode=link /nxb-bin/usr/bin/cc -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -EB -mabi=32 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-filestring.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-popcount.o gmapl-genome128_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-bitpack64-readtwo.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl- stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-dynprog_simd.o gmapl-dynprog_single.o gmapl-dynprog_genome.o gmapl-dynprog_cdna.o gmapl-dynprog_end.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-output.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm libtool: link: /nxb-bin/usr/bin/cc -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd12.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -EB -mabi=32 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-filestring.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-popcount.o gmapl-genome128_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-bitpack64-readtwo.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpoo l.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-dynprog_simd.o gmapl-dynprog_single.o gmapl-dynprog_genome.o gmapl-dynprog_cdna.o gmapl-dynprog_end.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-output.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm -pthread /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-except.o -MD -MP -MF .deps/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/get_genome-except.Tpo .deps/get_genome-except.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-assert.o -MD -MP -MF .deps/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/get_genome-assert.Tpo .deps/get_genome-assert.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-mem.o -MD -MP -MF .deps/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-intlist.o -MD -MP -MF .deps/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-list.o -MD -MP -MF .deps/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/get_genome-list.Tpo .deps/get_genome-list.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-littleendian.o -MD -MP -MF .deps/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-bigendian.o -MD -MP -MF .deps/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-univinterval.o -MD -MP -MF .deps/get_genome-univinterval.Tpo -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/get_genome-univinterval.Tpo .deps/get_genome-univinterval.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-interval.o -MD -MP -MF .deps/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/get_genome-interval.Tpo .deps/get_genome-interval.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-stopwatch.o -MD -MP -MF .deps/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/get_genome-stopwatch.Tpo .deps/get_genome-stopwatch.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-access.o -MD -MP -MF .deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-filestring.o -MD -MP -MF .deps/get_genome-filestring.Tpo -c -o get_genome-filestring.o `test -f 'filestring.c' || echo './'`filestring.c mv -f .deps/get_genome-filestring.Tpo .deps/get_genome-filestring.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-iit-read-univ.o -MD -MP -MF .deps/get_genome-iit-read-univ.Tpo -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-iit-read.o -MD -MP -MF .deps/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-md5.o -MD -MP -MF .deps/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-bzip2.o -MD -MP -MF .deps/get_genome-bzip2.Tpo -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/get_genome-bzip2.Tpo .deps/get_genome-bzip2.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-genome.o -MD -MP -MF .deps/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-genomicpos.o -MD -MP -MF .deps/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-chrom.o -MD -MP -MF .deps/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-chrnum.o -MD -MP -MF .deps/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/get_genome-chrnum.Tpo .deps/get_genome-chrnum.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-datadir.o -MD -MP -MF .deps/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-parserange.o -MD -MP -MF .deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-getopt.o -MD -MP -MF .deps/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/get_genome-getopt.Tpo .deps/get_genome-getopt.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-getopt1.o -MD -MP -MF .deps/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT get_genome-get-genome.o -MD -MP -MF .deps/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po /bin/sh ../libtool --tag=CC --mode=link /nxb-bin/usr/bin/cc -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -EB -mabi=32 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm libtool: link: /nxb-bin/usr/bin/cc -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -EB -mabi=32 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm -pthread /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-assert.o -MD -MP -MF .deps/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmapindex-assert.Tpo .deps/gmapindex-assert.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-list.o -MD -MP -MF .deps/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmapindex-list.Tpo .deps/gmapindex-list.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-univinterval.o -MD -MP -MF .deps/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-uintlist.o -MD -MP -MF .deps/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-stopwatch.o -MD -MP -MF .deps/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-filestring.o -MD -MP -MF .deps/gmapindex-filestring.Tpo -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c mv -f .deps/gmapindex-filestring.Tpo .deps/gmapindex-filestring.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-iit-read-univ.o -MD -MP -MF .deps/gmapindex-iit-read-univ.Tpo -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-iit-write-univ.o -MD -MP -MF .deps/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c mv -f .deps/gmapindex-iit-write-univ.Tpo .deps/gmapindex-iit-write-univ.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-iit-read.o -MD -MP -MF .deps/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-md5.o -MD -MP -MF .deps/gmapindex-md5.Tpo -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/gmapindex-md5.Tpo .deps/gmapindex-md5.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-bzip2.o -MD -MP -MF .deps/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmapindex-bzip2.Tpo .deps/gmapindex-bzip2.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-sequence.o -MD -MP -MF .deps/gmapindex-sequence.Tpo -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmapindex-sequence.Tpo .deps/gmapindex-sequence.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-genome.o -MD -MP -MF .deps/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-compress-write.o -MD -MP -MF .deps/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c: In function 'nt_unshuffle': compress-write.c:521: warning: integer constant is too large for 'long' type compress-write.c:522: warning: integer constant is too large for 'long' type compress-write.c:523: warning: integer constant is too large for 'long' type compress-write.c:524: warning: integer constant is too large for 'long' type mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-compress.o -MD -MP -MF .deps/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmapindex-compress.Tpo .deps/gmapindex-compress.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-popcount.o -MD -MP -MF .deps/gmapindex-popcount.Tpo -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c mv -f .deps/gmapindex-popcount.Tpo .deps/gmapindex-popcount.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-genome128_hr.o -MD -MP -MF .deps/gmapindex-genome128_hr.Tpo -c -o gmapindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c mv -f .deps/gmapindex-genome128_hr.Tpo .deps/gmapindex-genome128_hr.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-bitpack64-read.o -MD -MP -MF .deps/gmapindex-bitpack64-read.Tpo -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c bitpack64-read.c: In function 'Bitpack64_read_one_huge': bitpack64-read.c:14929: warning: integer constant is too large for 'long' type bitpack64-read.c:14959: warning: integer constant is too large for 'long' type bitpack64-read.c:14994: warning: integer constant is too large for 'long' type bitpack64-read.c:15029: warning: integer constant is too large for 'long' type bitpack64-read.c: In function 'Bitpack64_block_offsets_huge': bitpack64-read.c:15367: warning: integer constant is too large for 'long' type bitpack64-read.c:15373: warning: integer constant is too large for 'long' type mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-bitpack64-readtwo.o -MD -MP -MF .deps/gmapindex-bitpack64-readtwo.Tpo -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c mv -f .deps/gmapindex-bitpack64-readtwo.Tpo .deps/gmapindex-bitpack64-readtwo.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-bitpack64-access.o -MD -MP -MF .deps/gmapindex-bitpack64-access.Tpo -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/gmapindex-bitpack64-access.Tpo .deps/gmapindex-bitpack64-access.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DUTILITYP=1 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -MT gmapindex-bitpack64-write.o -MD -MP -MF .deps/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c: In function 'Bitpack64_write_differential_huge': bitpack64-write.c:5009: warning: integer constant is too large for 'long' type bitpack64-write.c:5024: warning: integer constant is too large for 'long' type bitpack64-write.c:5052: warning: integer constant is too large for 'long' type bitpack64-write.c: In function 'Bitpack64_write_fixed10_huge': bitpack64-write.c:5177: warning: integer constant is too large for 'long' type bitpack64-write.c:5194: warning: integer constant is too large for 'long' type bitpack64-write.c:5226: warning: integer constant is too large for 'long' type {standard input}: Assembler messages: {standard input}:2372: Error: unrecognized opcode `bsr $2,$2' {standard input}:2423: Error: unrecognized opcode `bsr $7,$2' {standard input}:2526: Error: unrecognized opcode `bsr $2,$2' {standard input}:2572: Error: unrecognized opcode `bsr $6,$2' gmake[3]: *** [Makefile:5132: gmapindex-bitpack64-write.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/src' gmake[2]: *** [Makefile:1195: all] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/src' gmake[1]: *** [Makefile:315: all-recursive] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21' *** Error code 1 Stop. make: stopped in /usr/ports/biology/gmap
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