From owner-freebsd-pkg-fallout@freebsd.org Wed Dec 7 16:13:51 2016 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 7E4AFC6C05B for ; Wed, 7 Dec 2016 16:13:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id 6C18ADD2 for ; Wed, 7 Dec 2016 16:13:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 6B6C4C6C05A; Wed, 7 Dec 2016 16:13:51 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 6B00AC6C059 for ; Wed, 7 Dec 2016 16:13:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy16.nyi.freebsd.org (beefy16.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:e3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 21C61DD1 for ; Wed, 7 Dec 2016 16:13:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy16.nyi.freebsd.org (localhost [127.0.0.1]) by beefy16.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id uB7GDo76013967 for ; Wed, 7 Dec 2016 16:13:50 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy16.nyi.freebsd.org (8.15.2/8.15.2/Submit) id uB7GDoRc013966; Wed, 7 Dec 2016 16:13:50 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 7 Dec 2016 16:13:50 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201612071613.uB7GDoRc013966@beefy16.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 110mips64-quarterly][biology/gmap] Failed for gmap-2015.09.21 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 07 Dec 2016 16:13:51 -0000 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: bacon4000@gmail.com Last committer: swills@FreeBSD.org Ident: $FreeBSD: branches/2016Q4/biology/gmap/Makefile 403676 2015-12-13 16:07:27Z swills $ Log URL: http://beefy16.nyi.freebsd.org/data/110mips64-quarterly/427878/logs/gmap-2015.09.21.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=110mips64-quarterly&build=427878 Log: ====>> Building biology/gmap build started at Wed Dec 7 15:56:18 UTC 2016 port directory: /usr/ports/biology/gmap building for: FreeBSD 110mips64-quarterly-job-27 11.0-RELEASE-p3 FreeBSD 11.0-RELEASE-p3 r309584 mips maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: branches/2016Q4/biology/gmap/Makefile 403676 2015-12-13 16:07:27Z swills $ Poudriere version: 3.1.14 Host OSVERSION: 1200010 Jail OSVERSION: 1100122 Job Id: 27 ---Begin Environment--- SHELL=/bin/csh UNAME_p=mips64 UNAME_m=mips ABI_FILE=/usr/lib/crt1.o UNAME_v=FreeBSD 11.0-RELEASE-p3 r309584 UNAME_r=11.0-RELEASE-p3 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=mips64 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110mips64-quarterly/ref QEMU_EMULATING=1 UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=gmap-2015.09.21 OSREL=11.0 _OSRELEASE=11.0-RELEASE-p3 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=28 PWD=/usr/local/poudriere/data/.m/110mips64-quarterly/ref/.p/pool MASTERNAME=110mips64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1100122 ---End Environment--- ---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--- --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 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" 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-- 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" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 PERL_VER=5.20 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/5.20 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 MACHINE=mips MACHINE_ARCH=mips64 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 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 READELF=/nxb-bin/usr/bin/readelf 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--- =================================================== ===> License GMAP accepted by the user =========================================================================== =================================================== ===> gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.8.txz [110mips64-quarterly-job-27] Installing pkg-1.8.8... [110mips64-quarterly-job-27] Extracting pkg-1.8.8: .......... done ===> gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gmap-2015.09.21 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GMAP accepted by the user ===> Fetching all distfiles required by gmap-2015.09.21 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GMAP accepted by the user ===> Fetching all distfiles required by gmap-2015.09.21 for building ===> Extracting for gmap-2015.09.21 => SHA256 Checksum OK for gmap-gsnap-2015-09-21.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for gmap-2015.09.21 =========================================================================== =================================================== ===> gmap-2015.09.21 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz [110mips64-quarterly-job-27] Installing gmake-4.2.1_1... [110mips64-quarterly-job-27] `-- Installing indexinfo-0.2.5... [110mips64-quarterly-job-27] `-- Extracting indexinfo-0.2.5: .... done [110mips64-quarterly-job-27] `-- Installing gettext-runtime-0.19.8.1... [110mips64-quarterly-job-27] `-- Extracting gettext-runtime-0.19.8.1: .......... done [110mips64-quarterly-job-27] Extracting gmake-4.2.1_1: .......... done ===> gmap-2015.09.21 depends on executable: gmake - found ===> Returning to build of gmap-2015.09.21 ===> gmap-2015.09.21 depends on package: perl5>=5.20<5.21 - not found ===> Installing existing package /packages/All/perl5-5.20.3_15.txz [110mips64-quarterly-job-27] Installing perl5-5.20.3_15... [110mips64-quarterly-job-27] Extracting perl5-5.20.3_15: .......... done Message from perl5-5.20.3_15: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-intron.o -MD -MP -MF .deps/gmapl-intron.Tpo -c -o gmapl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gmapl-intron.Tpo .deps/gmapl-intron.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-maxent.o -MD -MP -MF .deps/gmapl-maxent.Tpo -c -o gmapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gmapl-maxent.Tpo .deps/gmapl-maxent.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-maxent_hr.o -MD -MP -MF .deps/gmapl-maxent_hr.Tpo -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gmapl-maxent_hr.Tpo .deps/gmapl-maxent_hr.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-pair.o -MD -MP -MF .deps/gmapl-pair.Tpo -c -o gmapl-pair.o `test -f 'pair.c' || echo './'`pair.c mv -f .deps/gmapl-pair.Tpo .deps/gmapl-pair.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-pairpool.o -MD -MP -MF .deps/gmapl-pairpool.Tpo -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gmapl-pairpool.Tpo .deps/gmapl-pairpool.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-cellpool.o -MD -MP -MF .deps/gmapl-cellpool.Tpo -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gmapl-cellpool.Tpo .deps/gmapl-cellpool.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-stage2.o -MD -MP -MF .deps/gmapl-stage2.Tpo -c -o gmapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gmapl-stage2.Tpo .deps/gmapl-stage2.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-doublelist.o -MD -MP -MF .deps/gmapl-doublelist.Tpo -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gmapl-doublelist.Tpo .deps/gmapl-doublelist.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-smooth.o -MD -MP -MF .deps/gmapl-smooth.Tpo -c -o gmapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gmapl-smooth.Tpo .deps/gmapl-smooth.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-splicestringpool.o -MD -MP -MF .deps/gmapl-splicestringpool.Tpo -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gmapl-splicestringpool.Tpo .deps/gmapl-splicestringpool.Po /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DTARGET=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -MT gmapl-splicetrie_build.o -MD -MP -MF .deps/gmapl-splicetrie_build.Tpo -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c 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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -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=\"mips64-portbld-freebsd11.0\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -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-o rderstat.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -fno-strict-aliasing -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 -fno-strict-aliasing -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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 -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 -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 -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 -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 -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 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 -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 -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 -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 {standard input}: Assembler messages: {standard input}:2504: Error: unrecognized opcode `bsr $2,$2' {standard input}:2563: Error: unrecognized opcode `bsr $4,$2' {standard input}:2690: Error: unrecognized opcode `bsr $2,$2' {standard input}:2744: Error: unrecognized opcode `bsr $3,$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