Date: Sat, 18 Feb 2017 12:51:33 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110armv6-quarterly][biology/gmap] Failed for gmap-2015.09.21 in build Message-ID: <201702181251.v1ICpXL4072786@beefy15.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: bacon4000@gmail.com Last committer: linimon@FreeBSD.org Ident: $FreeBSD: branches/2017Q1/biology/gmap/Makefile 425758 2016-11-08 19:29:56Z linimon $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/434324/logs/gmap-2015.09.21.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=434324 Log: ====>> Building biology/gmap build started at Sat Feb 18 12:48:53 UTC 2017 port directory: /usr/ports/biology/gmap building for: FreeBSD 110armv6-quarterly-job-06 11.0-RELEASE-p5 FreeBSD 11.0-RELEASE-p5 r309692 arm maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: branches/2017Q1/biology/gmap/Makefile 425758 2016-11-08 19:29:56Z linimon $ Poudriere version: 3.1.14 Host OSVERSION: 1200018 Jail OSVERSION: 1100122 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p5 r309692 UNAME_r=11.0-RELEASE-p5 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=gmap-2015.09.21 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool MASTERNAME=110armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---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 -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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=5.24.1 PERL_VER=5.24 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/5.24 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=arm MACHINE_ARCH=armv6 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 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=armv6 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native\|linux _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ _OSRELEASE=11.0-RELEASE-p5 _SMP_CPUS=28 #### Misc Poudriere #### 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--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 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 sbsize (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtxp (-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-1.9.4_1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-06] Installing pkg-1.9.4_1... [110armv6-quarterly-job-06] Extracting pkg-1.9.4_1: .......... 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. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> 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. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for gmap-2015.09.21 =========================================================================== =======================<phase: build-depends >============================ ===> gmap-2015.09.21 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended <snip> /nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -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 -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 -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 -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 -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 -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 -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 -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 access.c:686:17: warning: format specifies type 'unsigned long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] filename,*len); ^~~~ access.c:862:18: warning: format specifies type 'intmax_t' (aka 'long long') but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:933:8: warning: format specifies type 'intmax_t' (aka 'long long') but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] *len,length,errno,strerror(errno)); ^~~~ access.c:1000:15: warning: format specifies type 'intmax_t' (aka 'long long') but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:1087:8: warning: format specifies type 'intmax_t' (aka 'long long') but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] *len,length,errno,strerror(errno)); ^~~~ 5 warnings generated. 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 parserange.c:188:8: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~~~~~~~~~~~~~~~~~~~~~~~ parserange.c:188:35: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~ parserange.c:188:40: warning: format specifies type 'unsigned long' but the argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat] Univinterval_low(interval),left,*genomicstart); ^~~~~~~~~~~~~ 3 warnings generated. 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 access.c:686:17: warning: format specifies type 'unsigned long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] filename,*len); ^~~~ access.c:862:18: warning: format specifies type 'intmax_t' (aka 'long long') but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] fd,offset,length,errno,strerror(errno)); ^~~~~~ access.c:933:8: warning: format specifies type 'intmax_t' (aka 'long long') but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] *len,length,errno,strerror(errno)); ^~~~ access.c:1000:15: warning: format specifies type 'intmax_t' (aka 'long long') but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] offset,length,errno,strerror(errno)); ^~~~~~ access.c:1087:8: warning: format specifies type 'intmax_t' (aka 'long long') but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] *len,length,errno,strerror(errno)); ^~~~ 5 warnings generated. 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 genome-write.c:567:30: warning: comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] if ((c = fgetc(input)) != EOF && c != '\n') { ~~~~~~~~~~~~~~~~~~ ^ ~~~ 1 warning generated. 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 -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 -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 -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 -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 -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 -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 -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:4462:9: error: invalid instruction asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr r1,r0 ^~~ bitpack64-write.c:4504:9: error: invalid instruction asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr r0,r0 ^~~ bitpack64-write.c:4504:9: error: invalid instruction asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr r0,r0 ^~~ bitpack64-write.c:4554:9: error: invalid instruction asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr r1,r0 ^~~ bitpack64-write.c:5336:9: error: invalid instruction asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr r0,r0 ^~~ bitpack64-write.c:5336:9: error: invalid instruction asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr r6,r0 ^~~ 6 errors generated. 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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