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Date:      Tue, 8 Jan 2019 02:01:48 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 112mips-quarterly][biology/gmap] Failed for gmap-2015.09.21 in build
Message-ID:  <201901080201.x0821mlB090385@beefy14.nyi.freebsd.org>

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You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     jwb@FreeBSD.org
Last committer: jwb@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q1/biology/gmap/Makefile 460452 2018-01-31 01:07:07Z jwb $
Log URL:        http://beefy14.nyi.freebsd.org/data/112mips-quarterly/489634/logs/gmap-2015.09.21.log
Build URL:      http://beefy14.nyi.freebsd.org/build.html?mastername=112mips-quarterly&build=489634
Log:

=>> Building biology/gmap
build started at Tue Jan  8 01:50:38 UTC 2019
port directory: /usr/ports/biology/gmap
package name: gmap-2015.09.21
building for: FreeBSD 112mips-quarterly-job-11 11.2-RELEASE-p7 FreeBSD 11.2-RELEASE-p7 1102000 mips
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q1/biology/gmap/Makefile 460452 2018-01-31 01:07:07Z jwb $
Poudriere version: 3.2.8
Host OSVERSION: 1300002
Jail OSVERSION: 1102000
Job Id: 11

---Begin Environment---
POUDRIEREPATH=/usr/local/bin/poudriere
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/112mips-quarterly/ref/.p
SCRIPTPREFIX=/usr/local/share/poudriere
MASTERNAME=112mips-quarterly
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
PWD=/usr/local/poudriere/data/.m/112mips-quarterly/ref/.p/pool
SAVED_TERM=
PACKAGE_BUILDING=yes
POUDRIERE_BUILD_TYPE=bulk
MASTERMNT=/usr/local/poudriere/data/.m/112mips-quarterly/ref
POUDRIERE_VERSION=3.2.8
LIBEXECPREFIX=/usr/local/libexec/poudriere
USER=root
QEMU_EMULATING=1
LOCALBASE=/usr/local
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
HOME=/root
STATUS=1
MAIL=/var/mail/root
BLOCKSIZE=K
UNAME_r=11.2-RELEASE-p7
UNAME_v=FreeBSD 11.2-RELEASE-p7 1102000
OSVERSION=1102000
ABI_FILE=/usr/lib/crt1.o
UNAME_m=mips
UNAME_p=mips
SHELL=/bin/csh
---End Environment---

---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
===> The following configuration options are available for gmap-2015.09.21:
     SIMD=off: Use CPU-specific optimizations
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--
--disable-builtin-popcount --disable-simd --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl  PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gmap/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gmap/work  HOME=/wrkdirs/usr/ports/biology/gmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--

--MAKE_ENV--
PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gmap/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gmap/work  HOME=/wrkdirs/usr/ports/biology/gmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local  LOCALBASE=/usr/local  CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0  -fno-strict-aliasing "  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS=" " LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -fno-strict-aliasing  "  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 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=11.2 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.1  PERL_VER=5.28  PERL5_MAN1=lib/perl5/site_perl/man/man1  PERL5_MAN3=lib/perl5/site_perl/man/man3  SITE_PERL=lib/perl5/site_perl  SITE_ARCH=lib/perl5/site_perl/mach/5.28 DOCSDIR="share/doc/gmap"  EXAMPLESDIR="share/examples/gmap"  DATADIR="share/gmap"  WWWDIR="www/gmap"  ETCDIR="etc/gmap"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/gmap DOCSDIR=/usr/local/share/doc/gmap EXAMPLESDIR=/usr/local/share/examples/gmap  WWWDIR=/usr/local/www/gmap ETCDIR=/usr/local/etc/gmap
--End SUB_LIST--

---Begin make.conf---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=mips
MACHINE_ARCH=mips
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
# failed mirror and then fails rather then trying another.  It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2

# stable/10 includes src.conf too late but make.conf is in sys.mk
.if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*}
# Disable build of llib now that head no longer has lint(1)
LINT=	true
.endif
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=Using built-in specs. Target: mips-undermydesk-freebsd Configured with: FreeBSD/mips system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-EB" "-EB" "-melf32btsmip_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11"
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11"
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x"
CC_OUTPUT_9d218390_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11"
CC_OUTPUT_9d218390_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14"
CC_OUTPUT_9d218390_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17"
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11"
CC_OUTPUT_9d218390_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14"
CC_OUTPUT_9d218390_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17"
_OBJC_CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
_OBJC_ALTCCVERSION_9d218390=none
ARCH=mips
OPSYS=FreeBSD
_OSRELEASE=11.2-RELEASE-p7
OSREL=11.2
OSVERSION=1102000
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  131072
stack size              (kbytes, -s)  8192
core file size      (512-blocks, -c)  unlimited
max memory size         (kbytes, -m)  unlimited
locked memory           (kbytes, -l)  unlimited
max user processes              (-u)  89999
open files                      (-n)  1024
virtual mem size        (kbytes, -v)  unlimited
swap limit              (kbytes, -w)  unlimited
socket buffer size       (bytes, -b)  unlimited
pseudo-terminals                (-p)  unlimited
kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>  License GMAP accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[112mips-quarterly-job-11] Installing pkg-1.10.5_5...
[112mips-quarterly-job-11] Extracting pkg-1.10.5_5: .......... done
===>   gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gmap-2015.09.21
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GMAP accepted by the user
===> Fetching all distfiles required by gmap-2015.09.21 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GMAP accepted by the user
===> Fetching all distfiles required by gmap-2015.09.21 for building
=> SHA256 Checksum OK for gmap-gsnap-2015-09-21.tar.gz.
===========================================================================
<snip>
mv -f .deps/gmapl-splicetrie_build.Tpo .deps/gmapl-splicetrie_build.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-splicetrie.o -MD -MP -MF .deps/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gmapl-splicetrie.Tpo .deps/gmapl-splicetrie.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-boyer-moore.o -MD -MP -MF .deps/gmapl-boyer-moore.Tpo -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gmapl-boyer-moore.Tpo .deps/gmapl-boyer-moore.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-dynprog.o -MD -MP -MF .deps/gmapl-dynprog.Tpo -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gmapl-dynprog.Tpo .deps/gmapl-dynprog.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-dynprog_simd.o -MD -MP -MF .deps/gmapl-dynprog_simd.Tpo -c -o gmapl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c
mv -f .deps/gmapl-dynprog_simd.Tpo .deps/gmapl-dynprog_simd.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-dynprog_single.o -MD -MP -MF .deps/gmapl-dynprog_single.Tpo -c -o gmapl-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c
mv -f .deps/gmapl-dynprog_single.Tpo .deps/gmapl-dynprog_single.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-dynprog_genome.o -MD -MP -MF .deps/gmapl-dynprog_genome.Tpo -c -o gmapl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c
mv -f .deps/gmapl-dynprog_genome.Tpo .deps/gmapl-dynprog_genome.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-dynprog_cdna.o -MD -MP -MF .deps/gmapl-dynprog_cdna.Tpo -c -o gmapl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c
mv -f .deps/gmapl-dynprog_cdna.Tpo .deps/gmapl-dynprog_cdna.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-dynprog_end.o -MD -MP -MF .deps/gmapl-dynprog_end.Tpo -c -o gmapl-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c
mv -f .deps/gmapl-dynprog_end.Tpo .deps/gmapl-dynprog_end.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-translation.o -MD -MP -MF .deps/gmapl-translation.Tpo -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gmapl-translation.Tpo .deps/gmapl-translation.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-pbinom.o -MD -MP -MF .deps/gmapl-pbinom.Tpo -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gmapl-pbinom.Tpo .deps/gmapl-pbinom.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-changepoint.o -MD -MP -MF .deps/gmapl-changepoint.Tpo -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gmapl-changepoint.Tpo .deps/gmapl-changepoint.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-stage3.o -MD -MP -MF .deps/gmapl-stage3.Tpo -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gmapl-stage3.Tpo .deps/gmapl-stage3.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-request.o -MD -MP -MF .deps/gmapl-request.Tpo -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gmapl-request.Tpo .deps/gmapl-request.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-result.o -MD -MP -MF .deps/gmapl-result.Tpo -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c
mv -f .deps/gmapl-result.Tpo .deps/gmapl-result.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-output.o -MD -MP -MF .deps/gmapl-output.Tpo -c -o gmapl-output.o `test -f 'output.c' || echo './'`output.c
mv -f .deps/gmapl-output.Tpo .deps/gmapl-output.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-inbuffer.o -MD -MP -MF .deps/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gmapl-inbuffer.Tpo .deps/gmapl-inbuffer.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-samheader.o -MD -MP -MF .deps/gmapl-samheader.Tpo -c -o gmapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gmapl-samheader.Tpo .deps/gmapl-samheader.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-outbuffer.o -MD -MP -MF .deps/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gmapl-outbuffer.Tpo .deps/gmapl-outbuffer.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-chimera.o -MD -MP -MF .deps/gmapl-chimera.Tpo -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gmapl-chimera.Tpo .deps/gmapl-chimera.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-datadir.o -MD -MP -MF .deps/gmapl-datadir.Tpo -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gmapl-datadir.Tpo .deps/gmapl-datadir.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-getopt.o -MD -MP -MF .deps/gmapl-getopt.Tpo -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gmapl-getopt.Tpo .deps/gmapl-getopt.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-getopt1.o -MD -MP -MF .deps/gmapl-getopt1.Tpo -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gmapl-getopt1.Tpo .deps/gmapl-getopt1.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapl-gmap.o -MD -MP -MF .deps/gmapl-gmap.Tpo -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
mv -f .deps/gmapl-gmap.Tpo .deps/gmapl-gmap.Po
/bin/sh ../libtool --tag=CC   --mode=link /nxb-bin/usr/bin/cc  -D_THREAD_SAFE -pthread   -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0  -fno-strict-aliasing     -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-filestring.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-popcount.o gmapl-genome128_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-bitpack64-readtwo.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o 
 gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-dynprog_simd.o gmapl-dynprog_single.o gmapl-dynprog_genome.o gmapl-dynprog_cdna.o gmapl-dynprog_end.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-output.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o  -lz -lbz2 -lm 
libtool: link: /nxb-bin/usr/bin/cc -D_THREAD_SAFE -pthread -DTARGET=\"mips-portbld-freebsd11.2\" -DGMAPDB=\"/usr/local/share\" -DLARGE_GENOMES=1 -O2 -pipe -G0 -fno-strict-aliasing -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-filestring.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-popcount.o gmapl-genome128_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-bitpack64-readtwo.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-ord
 erstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-dynprog_simd.o gmapl-dynprog_single.o gmapl-dynprog_genome.o gmapl-dynprog_cdna.o gmapl-dynprog_end.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-output.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o  -lz -lbz2 -lm -pthread
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-except.o -MD -MP -MF .deps/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/get_genome-except.Tpo .deps/get_genome-except.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-assert.o -MD -MP -MF .deps/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/get_genome-assert.Tpo .deps/get_genome-assert.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-mem.o -MD -MP -MF .deps/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-intlist.o -MD -MP -MF .deps/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-list.o -MD -MP -MF .deps/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/get_genome-list.Tpo .deps/get_genome-list.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-littleendian.o -MD -MP -MF .deps/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-bigendian.o -MD -MP -MF .deps/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-univinterval.o -MD -MP -MF .deps/get_genome-univinterval.Tpo -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
mv -f .deps/get_genome-univinterval.Tpo .deps/get_genome-univinterval.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-interval.o -MD -MP -MF .deps/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/get_genome-interval.Tpo .deps/get_genome-interval.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-stopwatch.o -MD -MP -MF .deps/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/get_genome-stopwatch.Tpo .deps/get_genome-stopwatch.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-access.o -MD -MP -MF .deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-filestring.o -MD -MP -MF .deps/get_genome-filestring.Tpo -c -o get_genome-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
mv -f .deps/get_genome-filestring.Tpo .deps/get_genome-filestring.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-iit-read-univ.o -MD -MP -MF .deps/get_genome-iit-read-univ.Tpo -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-iit-read.o -MD -MP -MF .deps/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-md5.o -MD -MP -MF .deps/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-bzip2.o -MD -MP -MF .deps/get_genome-bzip2.Tpo -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/get_genome-bzip2.Tpo .deps/get_genome-bzip2.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-genome.o -MD -MP -MF .deps/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c
mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-genomicpos.o -MD -MP -MF .deps/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-chrom.o -MD -MP -MF .deps/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-chrnum.o -MD -MP -MF .deps/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/get_genome-chrnum.Tpo .deps/get_genome-chrnum.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-datadir.o -MD -MP -MF .deps/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-parserange.o -MD -MP -MF .deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-getopt.o -MD -MP -MF .deps/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/get_genome-getopt.Tpo .deps/get_genome-getopt.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-getopt1.o -MD -MP -MF .deps/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT get_genome-get-genome.o -MD -MP -MF .deps/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c
mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po
/bin/sh ../libtool --tag=CC   --mode=link /nxb-bin/usr/bin/cc  -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing     -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o  -lz -lbz2 -lm 
libtool: link: /nxb-bin/usr/bin/cc -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -G0 -fno-strict-aliasing -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o  -lz -lbz2 -lm -pthread
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-assert.o -MD -MP -MF .deps/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmapindex-assert.Tpo .deps/gmapindex-assert.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-list.o -MD -MP -MF .deps/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmapindex-list.Tpo .deps/gmapindex-list.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-univinterval.o -MD -MP -MF .deps/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-uintlist.o -MD -MP -MF .deps/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-stopwatch.o -MD -MP -MF .deps/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-filestring.o -MD -MP -MF .deps/gmapindex-filestring.Tpo -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
mv -f .deps/gmapindex-filestring.Tpo .deps/gmapindex-filestring.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-iit-read-univ.o -MD -MP -MF .deps/gmapindex-iit-read-univ.Tpo -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-iit-write-univ.o -MD -MP -MF .deps/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c
mv -f .deps/gmapindex-iit-write-univ.Tpo .deps/gmapindex-iit-write-univ.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-iit-read.o -MD -MP -MF .deps/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-md5.o -MD -MP -MF .deps/gmapindex-md5.Tpo -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gmapindex-md5.Tpo .deps/gmapindex-md5.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-bzip2.o -MD -MP -MF .deps/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gmapindex-bzip2.Tpo .deps/gmapindex-bzip2.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-sequence.o -MD -MP -MF .deps/gmapindex-sequence.Tpo -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gmapindex-sequence.Tpo .deps/gmapindex-sequence.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-genome.o -MD -MP -MF .deps/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c
mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-compress-write.o -MD -MP -MF .deps/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c: In function 'nt_unshuffle':
compress-write.c:521: warning: integer constant is too large for 'long' type
compress-write.c:522: warning: integer constant is too large for 'long' type
compress-write.c:523: warning: integer constant is too large for 'long' type
compress-write.c:524: warning: integer constant is too large for 'long' type
mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-compress.o -MD -MP -MF .deps/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmapindex-compress.Tpo .deps/gmapindex-compress.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-popcount.o -MD -MP -MF .deps/gmapindex-popcount.Tpo -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
mv -f .deps/gmapindex-popcount.Tpo .deps/gmapindex-popcount.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-genome128_hr.o -MD -MP -MF .deps/gmapindex-genome128_hr.Tpo -c -o gmapindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
mv -f .deps/gmapindex-genome128_hr.Tpo .deps/gmapindex-genome128_hr.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-bitpack64-read.o -MD -MP -MF .deps/gmapindex-bitpack64-read.Tpo -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
bitpack64-read.c: In function 'Bitpack64_read_one_huge':
bitpack64-read.c:14929: warning: integer constant is too large for 'long' type
bitpack64-read.c:14959: warning: integer constant is too large for 'long' type
bitpack64-read.c:14994: warning: integer constant is too large for 'long' type
bitpack64-read.c:15029: warning: integer constant is too large for 'long' type
bitpack64-read.c: In function 'Bitpack64_block_offsets_huge':
bitpack64-read.c:15367: warning: integer constant is too large for 'long' type
bitpack64-read.c:15373: warning: integer constant is too large for 'long' type
mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-bitpack64-readtwo.o -MD -MP -MF .deps/gmapindex-bitpack64-readtwo.Tpo -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
mv -f .deps/gmapindex-bitpack64-readtwo.Tpo .deps/gmapindex-bitpack64-readtwo.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-bitpack64-access.o -MD -MP -MF .deps/gmapindex-bitpack64-access.Tpo -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/gmapindex-bitpack64-access.Tpo .deps/gmapindex-bitpack64-access.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   -DUTILITYP=1 -O2 -pipe -G0  -fno-strict-aliasing  -MT gmapindex-bitpack64-write.o -MD -MP -MF .deps/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
bitpack64-write.c: In function 'Bitpack64_write_differential_huge':
bitpack64-write.c:5009: warning: integer constant is too large for 'long' type
bitpack64-write.c:5024: warning: integer constant is too large for 'long' type
bitpack64-write.c:5052: warning: integer constant is too large for 'long' type
bitpack64-write.c: In function 'Bitpack64_write_fixed10_huge':
bitpack64-write.c:5177: warning: integer constant is too large for 'long' type
bitpack64-write.c:5194: warning: integer constant is too large for 'long' type
bitpack64-write.c:5226: warning: integer constant is too large for 'long' type
{standard input}: Assembler messages:
{standard input}:2372: Error: unrecognized opcode `bsr $2,$2'
{standard input}:2423: Error: unrecognized opcode `bsr $7,$2'
{standard input}:2526: Error: unrecognized opcode `bsr $2,$2'
{standard input}:2572: Error: unrecognized opcode `bsr $6,$2'
gmake[3]: *** [Makefile:5132: gmapindex-bitpack64-write.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/src'
gmake[2]: *** [Makefile:1195: all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/src'
gmake[1]: *** [Makefile:315: all-recursive] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/gmap



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