Date: Wed, 26 Aug 2020 23:31:45 GMT From: pkg-fallout@FreeBSD.org To: jwb@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-amd64-default][biology/gmap] Failed for gmap-2015.09.21 in build Message-ID: <202008262331.07QNVjP9077902@beefy18.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Last committer: linimon@FreeBSD.org Ident: $FreeBSD: head/biology/gmap/Makefile 504785 2019-06-21 11:15:08Z linimon $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p546132_s364744/logs/gmap-2015.09.21.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p546132_s364744 Log: =>> Building biology/gmap build started at Wed Aug 26 23:28:25 UTC 2020 port directory: /usr/ports/biology/gmap package name: gmap-2015.09.21 building for: FreeBSD head-amd64-default-job-06 13.0-CURRENT FreeBSD 13.0-CURRENT 1300111 amd64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/gmap/Makefile 504785 2019-06-21 11:15:08Z linimon $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300111 Job Id: 06 !!! Jail is newer than host. (Jail: 1300111, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300111 UNAME_v=FreeBSD 13.0-CURRENT 1300111 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for gmap-2015.09.21: SIMD=off: Use CPU-specific optimizations ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --disable-builtin-popcount --disable-simd --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gmap/work HOME=/wrkdirs/usr/ports/biology/gmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gmap/work HOME=/wrkdirs/usr/ports/biology/gmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.0 PERL_VER=5.32 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/5.32 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300111 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.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 socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GMAP accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-amd64-default-job-06] Installing pkg-1.14.7... [head-amd64-default-job-06] Extracting pkg-1.14.7: .......... 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 package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.txz [head-amd64-default-job-06] Installing gmake-4.3_2... [head-amd64-default-job-06] `-- Installing gettext-runtime-0.21... [head-amd64-default-job-06] | `-- Installing indexinfo-0.3.1... [head-amd64-default-job-06] | `-- Extracting indexinfo-0.3.1: .... done [head-amd64-default-job-06] `-- Extracting gettext-runtime-0.21: .......... done [head-amd64-default-job-06] Extracting gmake-4.3_2: .......... done <snip> cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c mv -f .deps/atoiindex-genomicpos.Tpo .deps/atoiindex-genomicpos.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-univinterval.o -MD -MP -MF .deps/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/atoiindex-univinterval.Tpo .deps/atoiindex-univinterval.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-interval.o -MD -MP -MF .deps/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-filestring.o -MD -MP -MF .deps/atoiindex-filestring.Tpo -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c mv -f .deps/atoiindex-interval.Tpo .deps/atoiindex-interval.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-iit-read-univ.o -MD -MP -MF .deps/atoiindex-iit-read-univ.Tpo -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/atoiindex-filestring.Tpo .deps/atoiindex-filestring.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-iit-read.o -MD -MP -MF .deps/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/atoiindex-iit-read-univ.Tpo .deps/atoiindex-iit-read-univ.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-compress.o -MD -MP -MF .deps/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/atoiindex-compress.Tpo .deps/atoiindex-compress.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-compress-write.o -MD -MP -MF .deps/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c mv -f .deps/atoiindex-compress-write.Tpo .deps/atoiindex-compress-write.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-popcount.o -MD -MP -MF .deps/atoiindex-popcount.Tpo -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c mv -f .deps/atoiindex-popcount.Tpo .deps/atoiindex-popcount.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-genome128_hr.o -MD -MP -MF .deps/atoiindex-genome128_hr.Tpo -c -o atoiindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bitpack64-read.o -MD -MP -MF .deps/atoiindex-bitpack64-read.Tpo -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/atoiindex-bitpack64-read.Tpo .deps/atoiindex-bitpack64-read.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bitpack64-readtwo.o -MD -MP -MF .deps/atoiindex-bitpack64-readtwo.Tpo -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c mv -f .deps/atoiindex-genome128_hr.Tpo .deps/atoiindex-genome128_hr.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bitpack64-write.o -MD -MP -MF .deps/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c mv -f .deps/atoiindex-bitpack64-readtwo.Tpo .deps/atoiindex-bitpack64-readtwo.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-indexdb-write.o -MD -MP -MF .deps/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c:1189:67: warning: format specifies type 'intmax_t' (aka 'long') but the argument has type 'Positionsptr_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(unsigned char),offset); ~~~ ^~~ %u indexdb-write.c:1201:67: warning: format specifies type 'intmax_t' (aka 'long') but the argument has type 'Positionsptr_T' (aka 'unsigned int') [-Wformat] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(UINT4),offset); ~~~ ^~~ %u indexdb-write.c:2328:22: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat] positionsfile_high,totalcounts*sizeof(unsigned char),filesize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb-write.c:2343:24: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat] positionsfile_high,totalcounts*sizeof(unsigned char),filesize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb-write.c:2350:21: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat] positionsfile_low,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~~~~~~~~~~~~~~~~~~ indexdb-write.c:2365:23: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat] positionsfile_low,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~~~~~~~~~~~~~~~~~~ indexdb-write.c:2408:21: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat] positionsfile_low,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~~~~~~~~~~~~~~~~~~ indexdb-write.c:2423:23: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat] positionsfile_low,totalcounts*sizeof(UINT4),filesize); ^~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/atoiindex-bitpack64-write.Tpo .deps/atoiindex-bitpack64-write.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-atoi.o -MD -MP -MF .deps/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c 8 warnings generated. mv -f .deps/atoiindex-indexdb-write.Tpo .deps/atoiindex-indexdb-write.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-md5.o -MD -MP -MF .deps/atoiindex-md5.Tpo -c -o atoiindex-md5.o `test -f 'md5.c' || echo './'`md5.c mv -f .deps/atoiindex-md5.Tpo .deps/atoiindex-md5.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bzip2.o -MD -MP -MF .deps/atoiindex-bzip2.Tpo -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/atoiindex-bzip2.Tpo .deps/atoiindex-bzip2.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-sequence.o -MD -MP -MF .deps/atoiindex-sequence.Tpo -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/atoiindex-atoi.Tpo .deps/atoiindex-atoi.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-genome.o -MD -MP -MF .deps/atoiindex-genome.Tpo -c -o atoiindex-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/atoiindex-sequence.Tpo .deps/atoiindex-sequence.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-uintlist.o -MD -MP -MF .deps/atoiindex-uintlist.Tpo -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/atoiindex-uintlist.Tpo .deps/atoiindex-uintlist.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-intlist.o -MD -MP -MF .deps/atoiindex-intlist.Tpo -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/atoiindex-intlist.Tpo .deps/atoiindex-intlist.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-saca-k.o -MD -MP -MF .deps/atoiindex-saca-k.Tpo -c -o atoiindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c mv -f .deps/atoiindex-saca-k.Tpo .deps/atoiindex-saca-k.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-uint8list.o -MD -MP -MF .deps/atoiindex-uint8list.Tpo -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c:268:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u,",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu uint8list.c:271:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu uint8list.c:277:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u,",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu uint8list.c:280:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat] sprintf(Buffer,"%u",Uint8list_head(p)); ~~ ^~~~~~~~~~~~~~~~~ %llu 4 warnings generated. mv -f .deps/atoiindex-uint8list.Tpo .deps/atoiindex-uint8list.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bytecoding.o -MD -MP -MF .deps/atoiindex-bytecoding.Tpo -c -o atoiindex-bytecoding.o `test -f 'bytecoding.c' || echo './'`bytecoding.c mv -f .deps/atoiindex-bytecoding.Tpo .deps/atoiindex-bytecoding.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-sarray-write.o -MD -MP -MF .deps/atoiindex-sarray-write.Tpo -c -o atoiindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c sarray-write.c:530:65: warning: format specifies type 'unsigned int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ~~ ^~~~~~~~~ %llu sarray-write.c:530:75: warning: format specifies type 'unsigned int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ~~ ^~~~~~~~~~ %llu sarray-write.c:634:65: warning: format specifies type 'unsigned int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ~~ ^~~~~~~~~ %llu sarray-write.c:634:75: warning: format specifies type 'unsigned int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ~~ ^~~~~~~~~~ %llu sarray-write.c:2273:62: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] Genome_fill_buffer_simple(genomecomp,/*left*/0,/*length*/n,gbuffer); ^~~~~~~ ./genome.h:49:77: note: passing argument to parameter 'gbuffer1' here Genome_fill_buffer_simple (T this, Univcoord_T left, Chrpos_T length, char *gbuffer1); ^ sarray-write.c:2391:62: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign] Genome_fill_buffer_simple(genomecomp,/*left*/0,/*length*/n,gbuffer); ^~~~~~~ ./genome.h:49:77: note: passing argument to parameter 'gbuffer1' here Genome_fill_buffer_simple (T this, Univcoord_T left, Chrpos_T length, char *gbuffer1); ^ 6 warnings generated. mv -f .deps/atoiindex-sarray-write.Tpo .deps/atoiindex-sarray-write.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-list.o -MD -MP -MF .deps/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/atoiindex-genome.Tpo .deps/atoiindex-genome.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-datadir.o -MD -MP -MF .deps/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/atoiindex-list.Tpo .deps/atoiindex-list.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-getopt.o -MD -MP -MF .deps/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/atoiindex-datadir.Tpo .deps/atoiindex-datadir.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-getopt1.o -MD -MP -MF .deps/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/atoiindex-getopt1.Tpo .deps/atoiindex-getopt1.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-atoiindex.o -MD -MP -MF .deps/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c mv -f .deps/atoiindex-getopt.Tpo .deps/atoiindex-getopt.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-except.o -MD -MP -MF .deps/sam_sort-except.Tpo -c -o sam_sort-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/sam_sort-except.Tpo .deps/sam_sort-except.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-assert.o -MD -MP -MF .deps/sam_sort-assert.Tpo -c -o sam_sort-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/sam_sort-assert.Tpo .deps/sam_sort-assert.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-mem.o -MD -MP -MF .deps/sam_sort-mem.Tpo -c -o sam_sort-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/sam_sort-mem.Tpo .deps/sam_sort-mem.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-littleendian.o -MD -MP -MF .deps/sam_sort-littleendian.Tpo -c -o sam_sort-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/sam_sort-littleendian.Tpo .deps/sam_sort-littleendian.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-bigendian.o -MD -MP -MF .deps/sam_sort-bigendian.Tpo -c -o sam_sort-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/sam_sort-bigendian.Tpo .deps/sam_sort-bigendian.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-intlist.o -MD -MP -MF .deps/sam_sort-intlist.Tpo -c -o sam_sort-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/atoiindex-atoiindex.Tpo .deps/atoiindex-atoiindex.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-list.o -MD -MP -MF .deps/sam_sort-list.Tpo -c -o sam_sort-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/sam_sort-list.Tpo .deps/sam_sort-list.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-stopwatch.o -MD -MP -MF .deps/sam_sort-stopwatch.Tpo -c -o sam_sort-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/sam_sort-intlist.Tpo .deps/sam_sort-intlist.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-access.o -MD -MP -MF .deps/sam_sort-access.Tpo -c -o sam_sort-access.o `test -f 'access.c' || echo './'`access.c mv -f .deps/sam_sort-stopwatch.Tpo .deps/sam_sort-stopwatch.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-univinterval.o -MD -MP -MF .deps/sam_sort-univinterval.Tpo -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/sam_sort-univinterval.Tpo .deps/sam_sort-univinterval.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-interval.o -MD -MP -MF .deps/sam_sort-interval.Tpo -c -o sam_sort-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/sam_sort-access.Tpo .deps/sam_sort-access.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-uintlist.o -MD -MP -MF .deps/sam_sort-uintlist.Tpo -c -o sam_sort-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/sam_sort-interval.Tpo .deps/sam_sort-interval.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-filestring.o -MD -MP -MF .deps/sam_sort-filestring.Tpo -c -o sam_sort-filestring.o `test -f 'filestring.c' || echo './'`filestring.c mv -f .deps/sam_sort-uintlist.Tpo .deps/sam_sort-uintlist.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-iit-read-univ.o -MD -MP -MF .deps/sam_sort-iit-read-univ.Tpo -c -o sam_sort-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/sam_sort-filestring.Tpo .deps/sam_sort-filestring.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-iit-read.o -MD -MP -MF .deps/sam_sort-iit-read.Tpo -c -o sam_sort-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/sam_sort-iit-read-univ.Tpo .deps/sam_sort-iit-read-univ.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-samheader.o -MD -MP -MF .deps/sam_sort-samheader.Tpo -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/sam_sort-samheader.Tpo .deps/sam_sort-samheader.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-samread.o -MD -MP -MF .deps/sam_sort-samread.Tpo -c -o sam_sort-samread.o `test -f 'samread.c' || echo './'`samread.c mv -f .deps/sam_sort-samread.Tpo .deps/sam_sort-samread.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-datadir.o -MD -MP -MF .deps/sam_sort-datadir.Tpo -c -o sam_sort-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/sam_sort-datadir.Tpo .deps/sam_sort-datadir.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-getopt.o -MD -MP -MF .deps/sam_sort-getopt.Tpo -c -o sam_sort-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/sam_sort-getopt.Tpo .deps/sam_sort-getopt.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-getopt1.o -MD -MP -MF .deps/sam_sort-getopt1.Tpo -c -o sam_sort-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/sam_sort-getopt1.Tpo .deps/sam_sort-getopt1.Po cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-sam_sort.o -MD -MP -MF .deps/sam_sort-sam_sort.Tpo -c -o sam_sort-sam_sort.o `test -f 'sam_sort.c' || echo './'`sam_sort.c mv -f .deps/sam_sort-iit-read.Tpo .deps/sam_sort-iit-read.Po /bin/sh ../libtool --tag=CC --mode=link cc -D_THREAD_SAFE -pthread -DTARGET=\"amd64-portbld-freebsd13.0\" -DGMAPDB=\"/usr/local/share\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-filestring.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-order stat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm libtool: link: cc -D_THREAD_SAFE -pthread -DTARGET=\"amd64-portbld-freebsd13.0\" -DGMAPDB=\"/usr/local/share\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-filestring.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-in tron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm -pthread ld: error: duplicate symbol: homopolymerp >>> defined at dynprog_single.c >>> gmap-dynprog_single.o:(homopolymerp) >>> defined at dynprog_end.c >>> gmap-dynprog_end.o:(.bss+0x38) cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[3]: *** [Makefile:1300: gmap] Error 1 gmake[3]: *** Waiting for unfinished jobs.... mv -f .deps/sam_sort-sam_sort.Tpo .deps/sam_sort-sam_sort.Po 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' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/gmap
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