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Date:      Tue, 17 Jul 2018 01:19:43 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 111mips-quarterly][biology/freebayes] Failed for freebayes-1.2.0 in build
Message-ID:  <201807170119.w6H1JhMA086311@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: linimon@FreeBSD.org
Ident:          $FreeBSD: branches/2018Q3/biology/freebayes/Makefile 473009 2018-06-21 23:52:37Z linimon $
Log URL:        http://beefy14.nyi.freebsd.org/data/111mips-quarterly/474768/logs/freebayes-1.2.0.log
Build URL:      http://beefy14.nyi.freebsd.org/build.html?mastername=111mips-quarterly&build=474768
Log:

=>> Building biology/freebayes
build started at Tue Jul 17 01:15:46 UTC 2018
port directory: /usr/ports/biology/freebayes
package name: freebayes-1.2.0
building for: FreeBSD 111mips-quarterly-job-08 11.1-RELEASE-p11 FreeBSD 11.1-RELEASE-p11 1101001 mips
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2018Q3/biology/freebayes/Makefile 473009 2018-06-21 23:52:37Z linimon $
Poudriere version: 3.2.7-2-g1cf194be
Host OSVERSION: 1200069
Jail OSVERSION: 1101001
Job Id: 08

---Begin Environment---
POUDRIEREPATH=/usr/local/bin/poudriere
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/111mips-quarterly/ref/.p
SCRIPTPREFIX=/usr/local/share/poudriere
MASTERNAME=111mips-quarterly
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
PWD=/usr/local/poudriere/data/.m/111mips-quarterly/ref/.p/pool
SAVED_TERM=
PACKAGE_BUILDING=yes
POUDRIERE_BUILD_TYPE=bulk
MASTERMNT=/usr/local/poudriere/data/.m/111mips-quarterly/ref
POUDRIERE_VERSION=3.2.7-2-g1cf194be
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=11.1-RELEASE-p11
UNAME_v=FreeBSD 11.1-RELEASE-p11 1101001
OSVERSION=1101001
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---
---End OPTIONS List---

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

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work  HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work  HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/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  --std=c++11"  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--
PORTDOCS="" PORTEXAMPLES="" OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/freebayes"  EXAMPLESDIR="share/examples/freebayes"  DATADIR="share/freebayes"  WWWDIR="www/freebayes"  ETCDIR="etc/freebayes"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/freebayes DOCSDIR=/usr/local/share/doc/freebayes EXAMPLESDIR=/usr/local/share/examples/freebayes  WWWDIR=/usr/local/www/freebayes ETCDIR=/usr/local/etc/freebayes
--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=11.1-RELEASE-p11
OSREL=11.1
OSVERSION=1101001
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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   freebayes-1.2.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_1.txz
[111mips-quarterly-job-08] Installing pkg-1.10.5_1...
[111mips-quarterly-job-08] Extracting pkg-1.10.5_1: .......... done
===>   freebayes-1.2.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of freebayes-1.2.0
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by freebayes-1.2.0 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by freebayes-1.2.0 for building
=> SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz.
=> SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz.
=> SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz.
=> SHA256 Checksum OK for jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz.
=> SHA256 Checksum OK for samtools-htslib-49fdfbd_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-bamtools-e77a43f_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-intervaltree-dbb4c51_GH0.tar.gz.
=> SHA256 Checksum OK for vcflib-vcflib-5e3ce04_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-c68cebb_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz.
=> SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-intervaltree-b704f19_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-multichoose-73d35da_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-smithwaterman-84c08d7_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-tabixpp-80012f8_GH0.tar.gz.
=> SHA256 Checksum OK for samtools-htslib-0f298ce_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by freebayes-1.2.0 for building
===>  Extracting for freebayes-1.2.0
=> SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz.
=> SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz.
=> SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz.
=> SHA256 Checksum OK for jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz.
=> SHA256 Checksum OK for samtools-htslib-49fdfbd_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-bamtools-e77a43f_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-intervaltree-dbb4c51_GH0.tar.gz.
=> SHA256 Checksum OK for vcflib-vcflib-5e3ce04_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-c68cebb_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz.
=> SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-intervaltree-b704f19_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-multichoose-73d35da_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-smithwaterman-84c08d7_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-tabixpp-80012f8_GH0.tar.gz.
=> SHA256 Checksum OK for samtools-htslib-0f298ce_GH0.tar.gz.
/bin/mv -n /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib-temp/* /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib
/bin/mv -n /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib-temp/* /wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for freebayes-1.2.0
===>  Applying FreeBSD patches for freebayes-1.2.0
===========================================================================
=======================<phase: build-depends  >============================
===>   freebayes-1.2.0 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_2.txz
[111mips-quarterly-job-08] Installing gmake-4.2.1_2...
[111mips-quarterly-job-08] `-- Installing gettext-runtime-0.19.8.1_1...
[111mips-quarterly-job-08] |   `-- Installing indexinfo-0.3.1...
[111mips-quarterly-job-08] |   `-- Extracting indexinfo-0.3.1: .... done
[111mips-quarterly-job-08] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[111mips-quarterly-job-08] Extracting gmake-4.2.1_2: .......... done
===>   freebayes-1.2.0 depends on executable: gmake - found
===>   Returning to build of freebayes-1.2.0
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for freebayes-1.2.0
===========================================================================
=======================<phase: build          >============================
===>  Building for freebayes-1.2.0
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0'
cd src && gmake autoversion
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src'
DETECTED_VERSION = v1.0.0
CURRENT_VERSION  = 
Updating version file.
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src'
touch src/version_git.h
# wget -q http://hypervolu.me/freebayes/build/v1.0.0 &
cd src && gmake
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src'
DETECTED_VERSION = v1.0.0
CURRENT_VERSION  = v1.0.0
cd ../SeqLib/htslib && /usr/local/bin/gmake
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/htslib'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o kfunc.o kfunc.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o knetfile.o knetfile.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o kstring.o kstring.c
kstring.c: In function 'kputd':
kstring.c:64: warning: integer constant is too large for 'long' type
kstring.c:91: warning: integer constant is too large for 'long' type
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o bgzf.o bgzf.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o errmod.o errmod.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o faidx.o faidx.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o hfile.o hfile.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.5"' > version.h
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o hts.o hts.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o md5.o md5.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o multipart.o multipart.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o probaln.o probaln.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o realn.o realn.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o regidx.o regidx.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o sam.o sam.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o vcf_sweep.o vcf_sweep.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o tbx.o tbx.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o textutils.o textutils.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o thread_pool.o thread_pool.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o vcf.o vcf.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o vcfutils.o vcfutils.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/cram_external.o cram/cram_external.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/cram_index.o cram/cram_index.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/cram_io.o cram/cram_io.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/files.o cram/files.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/mFILE.o cram/mFILE.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/sam_header.o cram/sam_header.c
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o bgzip.o bgzip.c
/nxb-bin/usr/bin/cc  -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o htsfile.o htsfile.c
/nxb-bin/usr/bin/cc  -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o tabix.o tabix.c
/nxb-bin/usr/bin/cc  -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/hts_endian.o test/hts_endian.c
test/hts_endian.c:105: warning: integer constant is too large for 'long' type
test/hts_endian.c:105: warning: integer constant is too large for 'long' type
/nxb-bin/usr/bin/cc  -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/fieldarith.o test/fieldarith.c
/nxb-bin/usr/bin/cc  -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/hfile.o test/hfile.c
/nxb-bin/usr/bin/cc  -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/sam.o test/sam.c
/nxb-bin/usr/bin/cc  -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/test_bgzf.o test/test_bgzf.c
/nxb-bin/usr/bin/cc  -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/test-regidx.o test/test-regidx.c
/nxb-bin/usr/bin/cc  -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/test_view.o test/test_view.c
/nxb-bin/usr/bin/cc  -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
/nxb-bin/usr/bin/cc  -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
/nxb-bin/usr/bin/cc  -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread
/nxb-bin/usr/bin/cc -O2 -pipe -G0  -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
/nxb-bin/usr/bin/cc  -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/htslib'
cd ../vcflib/tabixpp/ && /usr/local/bin/gmake && cp tabix.hpp ../../src/
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp'
/nxb-bin/usr/bin/c++ -O2 -pipe -G0 -fno-strict-aliasing  --std=c++11 -c tabix.cpp -Ihtslib
cc1plus: error: unrecognized command line option "-std=c++11"
gmake[4]: *** [Makefile:35: tabix.o] Error 1
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp'
gmake[3]: *** [Makefile:22: all-recur] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp'
gmake[2]: *** [Makefile:202: ../vcflib/tabixpp/tabix.o] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src'
gmake[1]: *** [Makefile:2: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0'
*** Error code 1

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



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