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://beefy15.nyi.freebsd.org/data/111armv6-quarterly/460364/logs/hmmer-3.1b2.log
Build URL:      
http://beefy15.nyi.freebsd.org/build.html?mastername=111armv6-quarterly&build=460364
Log:

=>> Building biology/hmmer
build started at Tue Jan 30 03:07:43 UTC 2018
port directory: /usr/ports/biology/hmmer
package name: hmmer-3.1b2
building for: FreeBSD 111armv6-quarterly-job-04 11.1-RELEASE-p6 FreeBSD 
11.1-RELEASE-p6 1101001 arm
maintained by: mz...@niid.go.jp
Makefile ident:      $FreeBSD: branches/2018Q1/biology/hmmer/Makefile 456588 
2017-12-18 04:28:28Z linimon $
Poudriere version: 3.2.4-22-g5aece630
Host OSVERSION: 1200054
Jail OSVERSION: 1101001
Job Id: 04

---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=3.2.4-22-g5aece630
P_PYTHON_MAJOR_VER=2
HOME=/root
USER=root
SCRIPTPREFIX=/usr/local/share/poudriere
MASTERNAME=111armv6-quarterly
PWD=/usr/local/poudriere/data/.m/111armv6-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
OLDPWD=/usr/local/poudriere/data/.m/111armv6-quarterly/ref/.p
POUDRIERE_BUILD_TYPE=bulk
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
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MASTERMNT=/usr/local/poudriere/data/.m/111armv6-quarterly/ref
SAVED_TERM=
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MAIL=/var/mail/root
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UNAME_r=11.1-RELEASE-p6
UNAME_v=FreeBSD 11.1-RELEASE-p6 1101001
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ABI_FILE=/usr/lib/crt1.o
UNAME_m=arm
UNAME_p=armv6
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  -fno-strict-aliasing"  
CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS="" LIBS=""  
CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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=arm
MACHINE_ARCH=armv6
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=armv6
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
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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)  33554432
stack size              (kbytes, -s)  524288
core file size      (512-blocks, -c)  unlimited
max memory size         (kbytes, -m)  unlimited
locked memory           (kbytes, -l)  unlimited
max user processes              (-u)  89999
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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
[111armv6-quarterly-job-04] Installing pkg-1.10.3_1...
[111armv6-quarterly-job-04] 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
[111armv6-quarterly-job-04] Installing gmake-4.2.1_1...
[111armv6-quarterly-job-04] `-- Installing gettext-runtime-0.19.8.1_1...
[111armv6-quarterly-job-04] |   `-- Installing indexinfo-0.3.1...
[111armv6-quarterly-job-04] |   `-- Extracting indexinfo-0.3.1: .... done
[111armv6-quarterly-job-04] `-- Extracting gettext-runtime-0.19.8.1_1: 
.......... done
[111armv6-quarterly-job-04] Extracting gmake-4.2.1_1: .......... done
===>   hmmer-3.1b2 depends on executable: gmake - found
<snip>
fm_general.c:172:42: note: use function 'llabs' instead
  interval->upper  = interval_bk.upper = abs(fm->C[c+1])-1;
                                         ^~~
                                         llabs
fm_general.c:197:21: warning: absolute value function 'abs' given an argument 
of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may 
cause truncation of value [-Wabsolute-value]
  interval->lower = abs(fm->C[(int)c]) + count1;
                    ^
fm_general.c:197:21: note: use function 'llabs' instead
  interval->lower = abs(fm->C[(int)c]) + count1;
                    ^~~
                    llabs
fm_general.c:198:21: warning: absolute value function 'abs' given an argument 
of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may 
cause truncation of value [-Wabsolute-value]
  interval->upper = abs(fm->C[(int)c]) + count2 - 1;
                    ^
fm_general.c:198:21: note: use function 'llabs' instead
  interval->upper = abs(fm->C[(int)c]) + count2 - 1;
                    ^~~
                    llabs
fm_general.c:220:22: warning: absolute value function 'abs' given an argument 
of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may 
cause truncation of value [-Wabsolute-value]
  interval->lower  = abs(fm->C[(int)c]);
                     ^
fm_general.c:220:22: note: use function 'llabs' instead
  interval->lower  = abs(fm->C[(int)c]);
                     ^~~
                     llabs
fm_general.c:221:22: warning: absolute value function 'abs' given an argument 
of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may 
cause truncation of value [-Wabsolute-value]
  interval->upper  = abs(fm->C[(int)c+1])-1;
                     ^
fm_general.c:221:22: note: use function 'llabs' instead
  interval->upper  = abs(fm->C[(int)c+1])-1;
                     ^~~
                     llabs
fm_general.c:572:13: warning: absolute value function 'abs' given an argument 
of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may 
cause truncation of value [-Wabsolute-value]
    prevC = abs(C[i]);
            ^
fm_general.c:572:13: note: use function 'llabs' instead
    prevC = abs(C[i]);
            ^~~
            llabs
9 warnings generated.
/nxb-bin/usr/bin/cc -O2 -pipe  -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 -O2 -pipe  -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
fm_ssv.c:136:10: warning: absolute value function 'abs' given an argument of 
type 'int64_t' (aka 'long long') but has parameter of type 'int' which may 
cause truncation of value [-Wabsolute-value]
    j += abs(fmf->C[c]);
         ^
fm_ssv.c:136:10: note: use function 'llabs' instead
    j += abs(fmf->C[c]);
         ^~~
         llabs
fm_ssv.c:464:65: warning: absolute value function 'abs' given an argument of 
type 'int64_t' (aka 'long long') but has parameter of type 'int' which may 
cause truncation of value [-Wabsolute-value]
    interval_f1.upper = interval_f2.upper = interval_bk.upper = 
abs(fmf->C[i+1])-1;
                                                                ^
fm_ssv.c:464:65: note: use function 'llabs' instead
    interval_f1.upper = interval_f2.upper = interval_bk.upper = 
abs(fmf->C[i+1])-1;
                                                                ^~~
                                                                llabs
2 warnings generated.
/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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -fno-strict-aliasing -D_THREAD_SAFE -pthread 
-fPIC   -DHAVE_CONFIG_H  -I../../easel -I../../easel -I. -I.. -I. -I../../src 
-I./.. -c io.c
io.c:165:12: warning: comparison of array 'hfp->errbuf' not equal to a null 
pointer is always true [-Wtautological-pointer-compare]
  if (hfp->errbuf != NULL) hfp->errbuf[0] = '\0';
      ~~~~~^~~~~~    ~~~~
io.c:278:12: warning: comparison of array 'hfp->errbuf' not equal to a null 
pointer is always true [-Wtautological-pointer-compare]
  if (hfp->errbuf != NULL) hfp->errbuf[0] = '\0';
      ~~~~~^~~~~~    ~~~~
2 warnings generated.
/nxb-bin/usr/bin/cc -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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:671:9: warning: implicit declaration of function 
'p7_oprofile_UpdateVitEmissionScores' is invalid in C99 
[-Wimplicit-function-declaration]
        p7_oprofile_UpdateVitEmissionScores(om, info->bg, info->fwd_emissions, 
info->scores);
        ^
nhmmscan.c:672:9: warning: implicit declaration of function 
'p7_oprofile_UpdateMSVEmissionScores' is invalid in C99 
[-Wimplicit-function-declaration]
        p7_oprofile_UpdateMSVEmissionScores(om, info->bg, info->fwd_emissions, 
info->scores);
        ^
2 warnings generated.
/nxb-bin/usr/bin/cc -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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 -O2 -pipe  -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
makehmmerdb.c:642:33: warning: comparison of constant -1 with expression of 
type 'char' is always false [-Wtautological-constant-out-of-range-compare]
          if (meta->inv_alph[c] == -1) {
              ~~~~~~~~~~~~~~~~~ ^  ~~
makehmmerdb.c:655:38: warning: comparison of constant -1 with expression of 
type 'char' is always false [-Wtautological-constant-out-of-range-compare]
        } else if (meta->inv_alph[c] == -1) {
                   ~~~~~~~~~~~~~~~~~ ^  ~~
2 warnings generated.
/nxb-bin/usr/bin/cc -O2 -pipe  -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 -O2 -pipe  -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
hmmerfm-exactmatch.c:158:12: warning: absolute value function 'abs' given an 
argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' 
which may cause truncation of value [-Wabsolute-value]
      j += abs(fm->C[c]);
           ^
hmmerfm-exactmatch.c:158:12: note: use function 'llabs' instead
      j += abs(fm->C[c]);
           ^~~
           llabs
1 warning generated.
/nxb-bin/usr/bin/cc -O2 -pipe  -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 -I../easel -I../easel -I../src   -I../src -O2 -pipe  
-fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -o 
create-profmark.o -c create-profmark.c          
/nxb-bin/usr/bin/cc -O2 -pipe  -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 -I../easel -I../easel -I../src   -I../src -O2 -pipe  
-fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC  -DHAVE_CONFIG_H -o 
rocplot.o -c rocplot.c          
/nxb-bin/usr/bin/cc -O2 -pipe  -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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