You are receiving this mail as a port that you maintain
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Please investigate the failure and submit a PR to fix
build.

Maintainer:     mz...@niid.go.jp
Last committer: lini...@freebsd.org
Ident:          $FreeBSD: branches/2018Q1/biology/hmmer/Makefile 456588 
2017-12-18 04:28:28Z linimon $
Log URL:        
http://beefy14.nyi.freebsd.org/data/111mips-quarterly/460130/logs/hmmer-3.1b2.log
Build URL:      
http://beefy14.nyi.freebsd.org/build.html?mastername=111mips-quarterly&build=460130
Log:

=>> Building biology/hmmer
build started at Sun Jan 28 02:08:17 UTC 2018
port directory: /usr/ports/biology/hmmer
package name: hmmer-3.1b2
building for: FreeBSD 111mips-quarterly-job-23 11.1-RELEASE-p6 FreeBSD 
11.1-RELEASE-p6 1101001 mips
maintained by: mz...@niid.go.jp
Makefile ident:      $FreeBSD: branches/2018Q1/biology/hmmer/Makefile 456588 
2017-12-18 04:28:28Z linimon $
Poudriere version: 3.2.4-20-g3ab5fc55
Host OSVERSION: 1200054
Jail OSVERSION: 1101001
Job Id: 23

---Begin Environment---
POUDRIEREPATH=/usr/local/bin/poudriere
PACKAGE_BUILDING=yes
LOCALBASE=/usr/local
LIBEXECPREFIX=/usr/local/libexec/poudriere
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIERE_VERSION=3.2.4-20-g3ab5fc55
P_PYTHON_MAJOR_VER=2
HOME=/root
USER=root
SCRIPTPREFIX=/usr/local/share/poudriere
MASTERNAME=111mips-quarterly
PWD=/usr/local/poudriere/data/.m/111mips-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
OLDPWD=/usr/local/poudriere/data/.m/111mips-quarterly/ref/.p
POUDRIERE_BUILD_TYPE=bulk
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
QEMU_EMULATING=1
MASTERMNT=/usr/local/poudriere/data/.m/111mips-quarterly/ref
SAVED_TERM=
STATUS=1
MAIL=/var/mail/root
BLOCKSIZE=K
UNAME_r=11.1-RELEASE-p6
UNAME_v=FreeBSD 11.1-RELEASE-p6 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---
===> The following configuration options are available for hmmer-3.1b2:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
     TEST=off: Build and/or run tests
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
mz...@niid.go.jp
--End MAINTAINER--

--CONFIGURE_ARGS--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hmmer/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hmmer/work  
HOME=/wrkdirs/usr/ports/biology/hmmer/work TMPDIR="/tmp" 
PATH=/wrkdirs/usr/ports/biology/hmmer/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--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hmmer/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hmmer/work  
HOME=/wrkdirs/usr/ports/biology/hmmer/work TMPDIR="/tmp" 
PATH=/wrkdirs/usr/ports/biology/hmmer/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  LIBDIR="/usr/lib"  
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=11.1 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local PORTDOCS="" 
PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/hmmer"  
EXAMPLESDIR="share/examples/hmmer"  DATADIR="share/hmmer"  WWWDIR="www/hmmer"  
ETCDIR="etc/hmmer"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/hmmer 
DOCSDIR=/usr/local/share/doc/hmmer EXAMPLESDIR=/usr/local/share/examples/hmmer  
WWWDIR=/usr/local/www/hmmer ETCDIR=/usr/local/etc/hmmer
--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
#### /usr/ports/Mk/Scripts/ports_env.sh ####
ARCH=mips
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=11.1
OSVERSION=1101001
PYTHONBASE=/usr/local
UID=0
_OSRELEASE=11.1-RELEASE-p6
#### Misc Poudriere ####
GID=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 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   hmmer-3.1b2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.3_1.txz
[111mips-quarterly-job-23] Installing pkg-1.10.3_1...
[111mips-quarterly-job-23] Extracting pkg-1.10.3_1: .......... done
===>   hmmer-3.1b2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of hmmer-3.1b2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by hmmer-3.1b2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by hmmer-3.1b2 for building
=> SHA256 Checksum OK for hmmer-3.1b2.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by hmmer-3.1b2 for building
===>  Extracting for hmmer-3.1b2
=> SHA256 Checksum OK for hmmer-3.1b2.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for hmmer-3.1b2
===>  Applying FreeBSD patches for hmmer-3.1b2
===========================================================================
=======================<phase: build-depends  >============================
===>   hmmer-3.1b2 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_1.txz
[111mips-quarterly-job-23] Installing gmake-4.2.1_1...
[111mips-quarterly-job-23] `-- Installing gettext-runtime-0.19.8.1_1...
[111mips-quarterly-job-23] |   `-- Installing indexinfo-0.3.1...
[111mips-quarterly-job-23] |   `-- Extracting indexinfo-0.3.1: .... done
[111mips-quarterly-job-23] `-- Extracting gettext-runtime-0.19.8.1_1: 
.......... done
[111mips-quarterly-job-23] Extracting gmake-4.2.1_1: .......... done
===>   hmmer-3.1b2 depends on executable: gmake - found
<snip>
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-mask esl-mask.o 
-leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-reformat.o -c esl-reformat.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-reformat 
esl-reformat.o -leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-selectn.o -c esl-selectn.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-selectn 
esl-selectn.o -leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-seqrange.o -c esl-seqrange.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-seqrange 
esl-seqrange.o -leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-seqstat.o -c esl-seqstat.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-seqstat 
esl-seqstat.o -leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-sfetch.o -c esl-sfetch.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-sfetch esl-sfetch.o 
-leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-shuffle.o -c esl-shuffle.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-shuffle 
esl-shuffle.o -leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-ssdraw.o -c esl-ssdraw.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-ssdraw esl-ssdraw.o 
-leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-stranslate.o -c esl-stranslate.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-stranslate 
esl-stranslate.o -leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o 
esl-weight.o -c esl-weight.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L.. -o esl-weight esl-weight.o 
-leasel    -lm
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/easel/miniapps'
gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/easel'
gmake -C libdivsufsort       all
gmake[2]: Entering directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/libdivsufsort'
/nxb-bin/usr/bin/cc -std=gnu99 -I. -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -o divsufsort.o -c divsufsort.c
/usr/bin/ar rc libdivsufsort.a divsufsort.o 
gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/libdivsufsort'
gmake -C src            all
gmake[2]: Entering directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src'
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o alimask.o -c alimask.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o build.o -c build.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o cachedb.o -c cachedb.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o emit.o -c emit.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o errors.o -c errors.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o evalues.o -c evalues.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o eweight.o -c eweight.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_decoding.o -c generic_decoding.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_fwdback.o -c generic_fwdback.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_fwdback_chk.o -c generic_fwdback_chk.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_fwdback_banded.o -c generic_fwdback_banded.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_null2.o -c generic_null2.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_msv.o -c generic_msv.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_optacc.o -c generic_optacc.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_stotrace.o -c generic_stotrace.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_viterbi.o -c generic_viterbi.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o generic_vtrace.o -c generic_vtrace.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o h2_io.o -c h2_io.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o heatmap.o -c heatmap.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmlogo.o -c hmmlogo.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmdmstr.o -c hmmdmstr.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmdwrkr.o -c hmmdwrkr.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmdutils.o -c hmmdutils.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmer.o -c hmmer.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o logsum.o -c logsum.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o modelconfig.o -c modelconfig.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o modelstats.o -c modelstats.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o mpisupport.o -c mpisupport.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o seqmodel.o -c seqmodel.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o tracealign.o -c tracealign.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_alidisplay.o -c p7_alidisplay.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_bg.o -c p7_bg.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_builder.o -c p7_builder.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_domaindef.o -c p7_domaindef.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_gbands.o -c p7_gbands.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_gmx.o -c p7_gmx.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_gmxb.o -c p7_gmxb.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_gmxchk.o -c p7_gmxchk.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_hmm.o -c p7_hmm.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_hmmcache.o -c p7_hmmcache.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_hmmfile.o -c p7_hmmfile.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_hmmwindow.o -c p7_hmmwindow.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_null3.o -c p7_null3.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_pipeline.o -c p7_pipeline.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_prior.o -c p7_prior.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_profile.o -c p7_profile.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_spensemble.o -c p7_spensemble.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_tophits.o -c p7_tophits.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_trace.o -c p7_trace.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o p7_scoredata.o -c p7_scoredata.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmpgmd2msa.o -c hmmpgmd2msa.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o fm_alphabet.o -c fm_alphabet.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o fm_general.o -c fm_general.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o fm_sse.o -c fm_sse.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o fm_ssv.o -c fm_ssv.c
/usr/bin/ar  -r libhmmer.a build.o cachedb.o emit.o errors.o evalues.o 
eweight.o generic_decoding.o generic_fwdback.o generic_fwdback_chk.o 
generic_fwdback_banded.o generic_null2.o generic_msv.o generic_optacc.o 
generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o 
hmmlogo.o hmmdmstr.o hmmdwrkr.o hmmdutils.o hmmer.o logsum.o modelconfig.o 
modelstats.o mpisupport.o seqmodel.o tracealign.o p7_alidisplay.o p7_bg.o 
p7_builder.o p7_domaindef.o p7_gbands.o p7_gmx.o p7_gmxb.o p7_gmxchk.o p7_hmm.o 
p7_hmmcache.o p7_hmmfile.o p7_hmmwindow.o p7_null3.o p7_pipeline.o p7_prior.o 
p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o p7_scoredata.o 
hmmpgmd2msa.o fm_alphabet.o fm_general.o fm_sse.o fm_ssv.o > /dev/null 2>&1 
/usr/local/bin/gmake -C impl_dummy  libhmmer-impl.stamp
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src/impl_dummy'
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c decoding.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c fwdback.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c io.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c msvfilter.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c null2.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c optacc.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c stotrace.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c vitfilter.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c p7_omx.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c p7_oprofile.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel 
-I. -I.. -I. -I../../src -I./.. -c mpi.c
/usr/bin/ar  -r ../libhmmer.a decoding.o fwdback.o io.o msvfilter.o null2.o 
optacc.o stotrace.o vitfilter.o p7_omx.o p7_oprofile.o mpi.o > /dev/null 2>&1
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src/impl_dummy'
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o alimask alimask.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmalign.o -c hmmalign.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmalign hmmalign.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmbuild.o -c hmmbuild.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmbuild hmmbuild.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmconvert.o -c hmmconvert.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmconvert hmmconvert.o  -lhmmer -leasel -ldivsufsort 
    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmemit.o -c hmmemit.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmemit hmmemit.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmfetch.o -c hmmfetch.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmfetch hmmfetch.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmlogo hmmlogo.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmpress.o -c hmmpress.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmpress hmmpress.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmscan.o -c hmmscan.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmscan hmmscan.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmsearch hmmsearch.o  -lhmmer -leasel -ldivsufsort   
  -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmsim.o -c hmmsim.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmsim hmmsim.o  -lhmmer -leasel -ldivsufsort     -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmstat.o -c hmmstat.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmstat hmmstat.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o jackhmmer jackhmmer.o  -lhmmer -leasel -ldivsufsort   
  -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o phmmer.o -c phmmer.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o phmmer phmmer.o  -lhmmer -leasel -ldivsufsort     -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o nhmmer.o -c nhmmer.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o nhmmer nhmmer.o  -lhmmer -leasel -ldivsufsort     -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o nhmmscan.o -c nhmmscan.c
nhmmscan.c: In function 'serial_loop':
nhmmscan.c:671: warning: implicit declaration of function 
'p7_oprofile_UpdateVitEmissionScores'
nhmmscan.c:672: warning: implicit declaration of function 
'p7_oprofile_UpdateMSVEmissionScores'
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o nhmmscan nhmmscan.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmpgmd.o -c hmmpgmd.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmpgmd hmmpgmd.o  -lhmmer -leasel -ldivsufsort     
-lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmc2.o -c hmmc2.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmc2 hmmc2.o  -lhmmer -leasel -ldivsufsort     -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o  -lhmmer -leasel 
-ldivsufsort     -lm
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -I../easel -I../libdivsufsort 
-I../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H  -L../easel -L./impl_dummy 
-L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o  -lhmmer 
-leasel -ldivsufsort     -lm
gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src'
gmake -C profmark       all
gmake[2]: Entering directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/profmark'
/nxb-bin/usr/bin/cc -std=gnu99 -I../easel -I../easel -I../src   -I../src -O2 
-pipe -G0  -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H 
-o create-profmark.o -c create-profmark.c           
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H  -L../easel -L../src -o 
create-profmark create-profmark.o -lhmmer -leasel    -lm
/nxb-bin/usr/bin/cc -std=gnu99 -I../easel -I../easel -I../src   -I../src -O2 
-pipe -G0  -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H 
-o rocplot.o -c rocplot.c           
/nxb-bin/usr/bin/cc -std=gnu99 -O2 -pipe -G0  -fno-strict-aliasing 
-D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H  -L../easel -L../src -o rocplot 
rocplot.o -lhmmer -leasel    -lm
gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/profmark'
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2'
===========================================================================
=======================<phase: run-depends    >============================
===========================================================================
=======================<phase: stage          >============================
===>  Staging for hmmer-3.1b2
===>   Generating temporary packing list
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2'
/usr/bin/install -c -d /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/bin
/usr/bin/install -c -d /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/lib
/usr/bin/install -c -d 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include
/usr/bin/install -c -d 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/man/man1
/usr/bin/install -c -d 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/share/doc/hmmer
gmake -C src            install
gmake[2]: Entering directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src'
/usr/local/bin/gmake -C impl_dummy  install
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src/impl_dummy'
for file in impl_dummy.h; do \
   /usr/bin/install -c -m 0644 ./$file 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include/ ;\
done
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src/impl_dummy'
for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo 
hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan 
hmmpgmd hmmc2 makehmmerdb hmmerfm-exactmatch; do \
   /usr/bin/install -c -m 0755 $file 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/bin/ ;\
done
/usr/bin/install -c -m 0755 libhmmer.a 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/lib/
for file in hmmer.h cachedb.h p7_gbands.h p7_gmxb.h p7_gmxchk.h p7_hmmcache.h; 
do \
   /usr/bin/install -c -m 0644 ./$file 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include/ ;\
done
/usr/bin/install -c -m 0644 p7_config.h 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include/ ;\

gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src'
gmake -C documentation  install
gmake[2]: Entering directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/documentation'
/usr/local/bin/gmake -C man        install
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/documentation/man'
for file in hmmer hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd 
hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer 
nhmmscan alimask; do \
   /usr/bin/install -c -m 0755 ./$file.man 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/man/man1/${file}.1 ;\
done
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/documentation/man'
gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/documentation'
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2'
install  -m 0644 /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/COPYRIGHT 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/Userguide.pdf 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/share/doc/hmmer
install  -m 0644 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/7LESS_DROME 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/HBB_HUMAN 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/MADE1.hmm 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/MADE1.out 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/MADE1.sto 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/Pkinase.hmm 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/Pkinase.sto 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/dna_target.fa 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/fn3.hmm 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/fn3.out 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/fn3.sto 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/globins4.hmm 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/globins4.out 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/globins4.sto /w
 rkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/globins45.fa 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam.h3f 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam.h3i 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam.h3m 
/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam.h3p 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/share/examples/hmmer
====> Compressing man pages (compress-man)
===========================================================================
=======================<phase: package        >============================
===>  Building package for hmmer-3.1b2
pkg-static: Unable to access file 
/wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include/impl_sse.h:No 
such file or directory
*** Error code 1

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