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:     bacon4...@gmail.com
Last committer: swi...@freebsd.org
Ident:          $FreeBSD: head/biology/gmap/Makefile 403676 2015-12-13 
16:07:27Z swills $
Log URL:        
http://beefy8.nyi.freebsd.org/data/head-armv6-default/p413605_s298221/logs/gmap-2015.09.21.log
Build URL:      
http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p413605_s298221
Log:

====>> Building biology/gmap
build started at Sat Apr 23 23:14:43 UTC 2016
port directory: /usr/ports/biology/gmap
building for: FreeBSD head-armv6-default-job-18 11.0-CURRENT FreeBSD 
11.0-CURRENT r298221 arm
maintained by: bacon4...@gmail.com
Makefile ident:      $FreeBSD: head/biology/gmap/Makefile 403676 2015-12-13 
16:07:27Z swills $
Poudriere version: 3.1.12
Host OSVERSION: 1100102
Jail OSVERSION: 1100105




!!! Jail is newer than host. (Jail: 1100105, Host: 1100102) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
UNAME_v=FreeBSD 11.0-CURRENT r298221
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
OPSYS=FreeBSD
ARCH=armv6
LINUX_OSRELEASE=2.6.32
SAVED_TERM=screen
QEMU_EMULATING=1
MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/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-CURRENT
PYTHONBASE=/usr/local
OLDPWD=/
_SMP_CPUS=24
PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool
MASTERNAME=head-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
_JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.12
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=1100105
---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 
WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES 
PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  
CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -mfloat-abi=softfp  
-fno-strict-aliasing"  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS="" 
LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -mfloat-abi=softfp 
-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---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
<snip>
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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-fno-strict-aliasing -MT get_genome-access.o -MD -MP -MF 
.deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || 
echo './'`access.c
access.c:686:17: warning: format specifies type 'unsigned long' but the 
argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              filename,*len);
                       ^~~~
access.c:862:18: warning: format specifies type 'intmax_t' (aka 'long long') 
but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                        ^~~~~~
access.c:933:8: warning: format specifies type 'intmax_t' (aka 'long long') but 
the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              *len,length,errno,strerror(errno));
              ^~~~
access.c:1000:15: warning: format specifies type 'intmax_t' (aka 'long long') 
but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              offset,length,errno,strerror(errno));
                     ^~~~~~
access.c:1087:8: warning: format specifies type 'intmax_t' (aka 'long long') 
but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              *len,length,errno,strerror(errno));
              ^~~~
5 warnings generated.
mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread 
-DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-fno-strict-aliasing -MT get_genome-parserange.o -MD -MP -MF 
.deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 
'parserange.c' || echo './'`parserange.c
parserange.c:188:8: warning: format specifies type 'unsigned long' but the 
argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~
parserange.c:188:35: warning: format specifies type 'unsigned long' but the 
argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
                                         ^~~~
parserange.c:188:40: warning: format specifies type 'unsigned long' but the 
argument has type 'Univcoord_T' (aka 'unsigned long long') [-Wformat]
              Univinterval_low(interval),left,*genomicstart);
                                              ^~~~~~~~~~~~~
3 warnings generated.
mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread 
-DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 -mfloat-abi=softfp  
-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 
-mfloat-abi=softfp  -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 -mfloat-abi=softfp 
-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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -fno-strict-aliasing -MT 
gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o 
gmapindex-access.o `test -f 'access.c' || echo './'`access.c
access.c:686:17: warning: format specifies type 'unsigned long' but the 
argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              filename,*len);
                       ^~~~
access.c:862:18: warning: format specifies type 'intmax_t' (aka 'long long') 
but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              fd,offset,length,errno,strerror(errno));
                        ^~~~~~
access.c:933:8: warning: format specifies type 'intmax_t' (aka 'long long') but 
the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              *len,length,errno,strerror(errno));
              ^~~~
access.c:1000:15: warning: format specifies type 'intmax_t' (aka 'long long') 
but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              offset,length,errno,strerror(errno));
                     ^~~~~~
access.c:1087:8: warning: format specifies type 'intmax_t' (aka 'long long') 
but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
              *len,length,errno,strerror(errno));
              ^~~~
5 warnings generated.
mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   
-DUTILITYP=1 -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -fno-strict-aliasing -MT 
gmapindex-compress-write.o -MD -MP -MF .deps/gmapindex-compress-write.Tpo -c -o 
gmapindex-compress-write.o `test -f 'compress-write.c' || echo 
'./'`compress-write.c
mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   
-DUTILITYP=1 -O2 -pipe -mfloat-abi=softfp  -fno-strict-aliasing -MT 
gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o 
gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
genome-write.c:567:30: warning: comparison of constant -1 with expression of 
type 'char' is always true [-Wtautological-constant-out-of-range-compare]
      if ((c = fgetc(input)) != EOF && c != '\n') {
          ~~~~~~~~~~~~~~~~~~ ^  ~~~
1 warning generated.
mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   
-DUTILITYP=1 -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -fno-strict-aliasing -MT 
gmapindex-bitpack64-read.o -MD -MP -MF .deps/gmapindex-bitpack64-read.Tpo -c -o 
gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo 
'./'`bitpack64-read.c
mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I.     -D_THREAD_SAFE -pthread   
-DUTILITYP=1 -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -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 -mfloat-abi=softfp  -fno-strict-aliasing -MT 
gmapindex-bitpack64-write.o -MD -MP -MF .deps/gmapindex-bitpack64-write.Tpo -c 
-o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo 
'./'`bitpack64-write.c
bitpack64-write.c:4462:9: error: invalid instruction
    asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff));
        ^
<inline asm>:1:2: note: instantiated into assembly here
        bsr r1,r0
        ^~~
bitpack64-write.c:4504:9: error: invalid instruction
    asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff));
        ^
<inline asm>:1:2: note: instantiated into assembly here
        bsr r0,r0
        ^~~
bitpack64-write.c:4504:9: error: invalid instruction
    asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff));
        ^
<inline asm>:1:2: note: instantiated into assembly here
        bsr r0,r0
        ^~~
bitpack64-write.c:4554:9: error: invalid instruction
    asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff));
        ^
<inline asm>:1:2: note: instantiated into assembly here
        bsr r1,r0
        ^~~
bitpack64-write.c:5336:9: error: invalid instruction
    asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue));
        ^
<inline asm>:1:2: note: instantiated into assembly here
        bsr r0,r0
        ^~~
bitpack64-write.c:5336:9: error: invalid instruction
    asm("bsr %1,%0" : "=r"(msb) : "r"(maxvalue));
        ^
<inline asm>:1:2: note: instantiated into assembly here
        bsr r6,r0
        ^~~
6 errors generated.
Makefile:5132: recipe for target 'gmapindex-bitpack64-write.o' failed
gmake[3]: *** [gmapindex-bitpack64-write.o] Error 1
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/src'
Makefile:1195: recipe for target 'all' failed
gmake[2]: *** [all] Error 2
gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/src'
Makefile:315: recipe for target 'all-recursive' failed
gmake[1]: *** [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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