Date: Tue, 25 Oct 2016 06:34:17 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110arm64-quarterly][biology/gmap] Failed for gmap-2015.09.21 in build Message-ID: <201610250634.u9P6YH7h092386@thunderx1.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: swills@FreeBSD.org Ident: $FreeBSD: branches/2016Q4/biology/gmap/Makefile 403676 2015-12-13 16:07:27Z swills $ Log URL: http://thunderx1.nyi.freebsd.org/data/110arm64-quarterly/424582/logs/gmap-2015.09.21.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-quarterly&build=424582 Log: ====>> Building biology/gmap build started at Tue Oct 25 06:22:25 UTC 2016 port directory: /usr/ports/biology/gmap building for: FreeBSD 110arm64-quarterly-job-18 11.0-RELEASE-p1 FreeBSD 11.0-RELEASE-p1 r306420 arm64 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: 1100121 Jail OSVERSION: 1100122 !!! Jail is newer than host. (Jail: 1100122, Host: 1100121) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_v=FreeBSD 11.0-RELEASE-p1 r306420 UNAME_r=11.0-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=aarch64 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110arm64-quarterly/ref 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-p1 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=48 PWD=/usr/local/poudriere/data/.m/110arm64-quarterly/ref/.p/pool MASTERNAME=110arm64-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="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="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=5.20.3 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /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--- =======================<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-1.8.7_3.txz [110arm64-quarterly-job-18] Installing pkg-1.8.7_3... [110arm64-quarterly-job-18] Extracting pkg-1.8.7_3: .......... 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 [110arm64-quarterly-job-18] Installing gmake-4.2.1_1... [110arm64-quarterly-job-18] `-- Installing indexinfo-0.2.5... [110arm64-quarterly-job-18] `-- Extracting indexinfo-0.2.5: .... done [110arm64-quarterly-job-18] `-- Installing gettext-runtime-0.19.8.1... [110arm64-quarterly-job-18] `-- Extracting gettext-runtime-0.19.8.1: .......... done [110arm64-quarterly-job-18] 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 [110arm64-quarterly-job-18] Installing perl5-5.20.3_15... [110arm64-quarterly-job-18] 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 The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> gmap-2015.09.21 depends on package: perl5>=5.20<5.21 - found ===> Returning to build of gmap-2015.09.21 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for gmap-2015.09.21 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/config/libtool.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/configure configure: loading site script /usr/ports/Templates/config.site checking package version... 2015-09-21 really loading site script /usr/ports/Templates/config.site: file was found checking CFLAGS... -O2 -pipe -fno-strict-aliasing checking MPI_CFLAGS... checking build system type... aarch64-portbld-freebsd11.0 checking host system type... aarch64-portbld-freebsd11.0 <snip> 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 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 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 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 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 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 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 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 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 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 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 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: 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 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 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 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 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 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 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 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 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 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 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 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 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 mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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:4462:39: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ bitpack64-write.c:4462:14: note: use constraint modifier "w" asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^~ %w1 bitpack64-write.c:4462:28: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ bitpack64-write.c:4462:17: note: use constraint modifier "w" asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^~ %w0 bitpack64-write.c:4504:39: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ bitpack64-write.c:4504:14: note: use constraint modifier "w" asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^~ %w1 bitpack64-write.c:4504:28: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ bitpack64-write.c:4504:17: note: use constraint modifier "w" asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^~ %w0 bitpack64-write.c:4554:39: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ bitpack64-write.c:4554:14: note: use constraint modifier "w" asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^~ %w1 bitpack64-write.c:4554:28: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ bitpack64-write.c:4554:17: note: use constraint modifier "w" asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^~ %w0 bitpack64-write.c:5336:39: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue)); ^ bitpack64-write.c:5336:14: note: use constraint modifier "w" asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue)); ^~ %w1 bitpack64-write.c:5336:28: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue)); ^ bitpack64-write.c:5336:17: note: use constraint modifier "w" asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue)); ^~ %w0 bitpack64-write.c:4462:9: error: unrecognized instruction mnemonic asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr x8,x8 ^ bitpack64-write.c:4504:9: error: unrecognized instruction mnemonic asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr x8,x8 ^ bitpack64-write.c:4504:9: error: unrecognized instruction mnemonic asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr x8,x8 ^ bitpack64-write.c:4554:9: error: unrecognized instruction mnemonic asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr x8,x8 ^ bitpack64-write.c:5336:9: error: unrecognized instruction mnemonic asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr x8,x8 ^ bitpack64-write.c:5336:9: error: unrecognized instruction mnemonic asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue)); ^ <inline asm>:1:2: note: instantiated into assembly here bsr x8,x8 ^ 8 warnings and 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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