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build.

Maintainer:     bacon4...@gmail.com
Last committer: swi...@freebsd.org
Ident:          $FreeBSD: branches/2016Q4/biology/bwa/Makefile 403676 
2015-12-13 16:07:27Z swills $
Log URL:        
http://thunderx1.nyi.freebsd.org/data/110arm64-quarterly/423819/logs/bwa-0.7.9a.log
Build URL:      
http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-quarterly&build=423819
Log:

====>> Building biology/bwa
build started at Fri Oct 14 00:04:11 UTC 2016
port directory: /usr/ports/biology/bwa
building for: FreeBSD 110arm64-quarterly-job-13 11.0-RELEASE-p1 FreeBSD 
11.0-RELEASE-p1 r306420 arm64
maintained by: bacon4...@gmail.com
Makefile ident:      $FreeBSD: branches/2016Q4/biology/bwa/Makefile 403676 
2015-12-13 16:07:27Z swills $
Poudriere version: 3.1.14
Host OSVERSION: 1100121
Jail OSVERSION: 1100122




!!! Jail is newer than host. (Jail: 1100122, Host: 1100121) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
UNAME_v=FreeBSD 11.0-RELEASE-p1 r306420
UNAME_r=11.0-RELEASE-p1
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
OPSYS=FreeBSD
ARCH=aarch64
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/110arm64-quarterly/ref
UID=0
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
_JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=bwa-0.7.9a
OSREL=11.0
_OSRELEASE=11.0-RELEASE-p1
PYTHONBASE=/usr/local
OLDPWD=/
_SMP_CPUS=48
PWD=/usr/local/poudriere/data/.m/110arm64-quarterly/ref/.p/pool
MASTERNAME=110arm64-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
_JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.14
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
CONFIGURE_MAX_CMD_LEN=262144
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
_JAVA_OS_LIST_REGEXP=native\|linux
OSVERSION=1100122
---End Environment---

---Begin OPTIONS List---
---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 
MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES 
PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="cc" CFLAGS="-O2 
-pipe  -msse2 -fno-strict-aliasing"  CPP="cpp" CPPFLAGS=""  LDFLAGS="" LIBS=""  
CXX="c++" CXXFLAGS="-O2 -pipe -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---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
# failed mirror and then fails rather then trying another.  It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
=======================<phase: check-sanity   >============================
===>  License 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-1.8.7_3.txz
[110arm64-quarterly-job-13] Installing pkg-1.8.7_3...
[110arm64-quarterly-job-13] Extracting pkg-1.8.7_3: .......... 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
cc -c -O2 -pipe  -msse2 -fno-strict-aliasing -DHAVE_PTHREAD 
-DUSE_MALLOC_WRAPPERS  utils.c -o utils.o
cc: warning: argument unused during compilation: '-msse2'
cc -c -O2 -pipe  -msse2 -fno-strict-aliasing -DHAVE_PTHREAD 
-DUSE_MALLOC_WRAPPERS  kthread.c -o kthread.o
cc: warning: argument unused during compilation: '-msse2'
cc -c -O2 -pipe  -msse2 -fno-strict-aliasing -DHAVE_PTHREAD 
-DUSE_MALLOC_WRAPPERS  kstring.c -o kstring.o
cc: warning: argument unused during compilation: '-msse2'
cc -c -O2 -pipe  -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:
In file included from /usr/bin/../lib/clang/3.8.0/include/emmintrin.h:27:
In file included from /usr/bin/../lib/clang/3.8.0/include/xmmintrin.h:27:
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:45:12: error: invalid conversion 
between vector type '__m64' (vector of 1 'long long' value) and integer type 
'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:69:12: error: invalid conversion 
between vector type '__m64' (vector of 1 'long long' value) and integer type 
'int' of different size
    return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:75:12: error: invalid conversion 
between vector type '__m64' (vector of 1 'long long' value) and integer type 
'int' of different size
    return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:81:12: error: invalid conversion 
between vector type '__m64' (vector of 1 'long long' value) and integer type 
'int' of different size
    return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:87:12: error: invalid conversion 
between vector type '__m64' (vector of 1 'long long' value) and integer type 
'int' of different size
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:93:12: error: invalid conversion 
between vector type '__m64' (vector of 1 'long long' value) and integer type 
'int' of different size
    return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:99:12: error: invalid conversion 
between vector type '__m64' (vector of 1 'long long' value) and integer type 
'int' of different size
    return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:105:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:111:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:117:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:123:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:129:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:135:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:141:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:147:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:153:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:159:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:165:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/../lib/clang/3.8.0/include/mmintrin.h:171:12: error: invalid 
conversion between vector type '__m64' (vector of 1 'long long' value) and 
integer type 'int' of different size
    return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
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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