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/bwa/Makefile 403676 2015-12-13 16:07:27Z 
swills $
Log URL:        
http://beefy8.nyi.freebsd.org/data/head-armv6-default/p410528_s296455/logs/bwa-0.7.9a.log
Build URL:      
http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p410528_s296455
Log:

====>> Building biology/bwa
build started at Fri Mar 11 10:20:52 UTC 2016
port directory: /usr/ports/biology/bwa
building for: FreeBSD head-armv6-default-job-12 11.0-CURRENT FreeBSD 
11.0-CURRENT r296455 arm
maintained by: bacon4...@gmail.com
Makefile ident:      $FreeBSD: head/biology/bwa/Makefile 403676 2015-12-13 
16:07:27Z swills $
Poudriere version: 3.1.12
Host OSVERSION: 1100100
Jail OSVERSION: 1100101




!!! Jail is newer than host. (Jail: 1100101, Host: 1100100) !!!
!!! 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 r296455
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=bwa-0.7.9a
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=1100101
---End Environment---

---Begin OPTIONS List---
---End OPTIONS List---

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl 
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work  
HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" SHELL=/bin/sh 
CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work  
HOME=/wrkdirs/usr/ports/biology/bwa/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  -msse2 
-fno-strict-aliasing"  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS="" 
LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -mfloat-abi=softfp 
-msse2 -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/bwa"
EXAMPLESDIR="share/examples/bwa"
DATADIR="share/bwa"
WWWDIR="www/bwa"
ETCDIR="etc/bwa"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/bwa
DOCSDIR=/usr/local/share/doc/bwa
EXAMPLESDIR=/usr/local/share/examples/bwa
WWWDIR=/usr/local/www/bwa
ETCDIR=/usr/local/etc/bwa
--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
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
<snip>
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
MACHINE=arm
MACHINE_ARCH=armv6
ARCH=${MACHINE_ARCH}
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.conf---
=======================<phase: check-sanity   >============================
===>  License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   bwa-0.7.9a depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.6.4_1.txz
[head-armv6-default-job-12] Installing pkg-1.6.4_1...
[head-armv6-default-job-12] Extracting pkg-1.6.4_1: .......... done
===>   bwa-0.7.9a depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of bwa-0.7.9a
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.9a for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.9a for building
=> SHA256 Checksum OK for bwa-0.7.9a.tar.bz2.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.9a for building
===>  Extracting for bwa-0.7.9a
=> SHA256 Checksum OK for bwa-0.7.9a.tar.bz2.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for bwa-0.7.9a
===>  Applying FreeBSD patches for bwa-0.7.9a
===========================================================================
=======================<phase: build-depends  >============================
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for bwa-0.7.9a
===========================================================================
=======================<phase: build          >============================
===>  Building for bwa-0.7.9a
/nxb-bin/usr/bin/cc -c -O2 -pipe -mfloat-abi=softfp  -msse2 
-fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  utils.c -o utils.o
cc: warning: argument unused during compilation: '-msse2'
/nxb-bin/usr/bin/cc -c -O2 -pipe -mfloat-abi=softfp  -msse2 
-fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kthread.c -o 
kthread.o
cc: warning: argument unused during compilation: '-msse2'
/nxb-bin/usr/bin/cc -c -O2 -pipe -mfloat-abi=softfp  -msse2 
-fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kstring.c -o 
kstring.o
cc: warning: argument unused during compilation: '-msse2'
/nxb-bin/usr/bin/cc -c -O2 -pipe -mfloat-abi=softfp  -msse2 
-fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
cc: warning: argument unused during compilation: '-msse2'
In file included from ksw.c:29:
/nxb-bin/usr/bin/../lib/clang/3.7.1/include/emmintrin.h:28:2: error: "SSE2 
instruction set not enabled"
#error "SSE2 instruction set not enabled"
 ^
ksw.c:49:2: error: unknown type name '__m128i'
        __m128i *qp, *H0, *H1, *E, *Hmax;
        ^
ksw.c:72:19: error: expected expression
        q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // 
align memory
                         ^
ksw.c:72:11: error: use of undeclared identifier '__m128i'
        q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // 
align memory
                 ^
ksw.c:115:2: error: use of undeclared identifier '__m128i'
        __m128i zero, oe_del, e_del, oe_ins, e_ins, shift, *H0, *H1, *E, *Hmax;
        ^
ksw.c:131:2: error: use of undeclared identifier 'zero'
        zero = _mm_set1_epi32(0);
        ^
ksw.c:131:9: warning: implicit declaration of function '_mm_set1_epi32' is 
invalid in C99 [-Wimplicit-function-declaration]
        zero = _mm_set1_epi32(0);
               ^
ksw.c:132:2: error: use of undeclared identifier 'oe_del'; did you mean 
'_e_del'?
        oe_del = _mm_set1_epi8(_o_del + _e_del);
        ^~~~~~
        _e_del
ksw.c:111:75: note: '_e_del' declared here
kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int 
_e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e)
                                                                          ^
ksw.c:132:11: warning: implicit declaration of function '_mm_set1_epi8' is 
invalid in C99 [-Wimplicit-function-declaration]
        oe_del = _mm_set1_epi8(_o_del + _e_del);
                 ^
ksw.c:133:2: error: use of undeclared identifier 'e_del'; did you mean '_e_del'?
        e_del = _mm_set1_epi8(_e_del);
        ^~~~~
        _e_del
ksw.c:111:75: note: '_e_del' declared here
kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int 
_e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e)
                                                                          ^
ksw.c:134:2: error: use of undeclared identifier 'oe_ins'; did you mean 
'_e_ins'?
        oe_ins = _mm_set1_epi8(_o_ins + _e_ins);
        ^~~~~~
        _e_ins
ksw.c:111:99: note: '_e_ins' declared here
kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int 
_e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e)
                                                                                
                  ^
ksw.c:135:2: error: use of undeclared identifier 'e_ins'; did you mean '_e_ins'?
        e_ins = _mm_set1_epi8(_e_ins);
        ^~~~~
        _e_ins
ksw.c:111:99: note: '_e_ins' declared here
kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int 
_e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e)
                                                                                
                  ^
ksw.c:136:2: error: use of undeclared identifier 'shift'
        shift = _mm_set1_epi8(q->shift);
        ^
ksw.c:137:2: error: use of undeclared identifier 'H0'
        H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
        ^
ksw.c:137:14: error: use of undeclared identifier 'H1'
        H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
                    ^
ksw.c:137:26: error: use of undeclared identifier 'E'
        H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
                                ^
ksw.c:137:36: error: use of undeclared identifier 'Hmax'; did you mean 'gmax'?
        H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
                                          ^~~~
                                          gmax
ksw.c:113:34: note: 'gmax' declared here
        int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
                                        ^
ksw.c:140:3: warning: implicit declaration of function '_mm_store_si128' is 
invalid in C99 [-Wimplicit-function-declaration]
                _mm_store_si128(E + i, zero);
                ^
ksw.c:140:19: error: use of undeclared identifier 'E'
                _mm_store_si128(E + i, zero);
                                ^
ksw.c:140:26: error: use of undeclared identifier 'zero'; did you mean 'bzero'?
                _mm_store_si128(E + i, zero);
                                       ^~~~
                                       bzero
/usr/include/strings.h:44:7: note: 'bzero' declared here
void     bzero(void *, size_t);                                 /* LEGACY */
         ^
ksw.c:141:19: error: use of undeclared identifier 'H0'
                _mm_store_si128(H0 + i, zero);
                                ^
ksw.c:141:27: error: use of undeclared identifier 'zero'; did you mean 'bzero'?
                _mm_store_si128(H0 + i, zero);
                                        ^~~~
                                        bzero
/usr/include/strings.h:44:7: note: 'bzero' declared here
void     bzero(void *, size_t);                                 /* LEGACY */
         ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
3 warnings and 20 errors generated.
*** Error code 1

Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/bwa/work/bwa-0.7.9a
*** Error code 1

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