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:     y...@freebsd.org
Last committer: y...@freebsd.org
Ident:          $FreeBSD: head/biology/abyss/Makefile 522851 2020-01-13 
04:06:14Z yuri $
Log URL:        
http://beefy10.nyi.freebsd.org/data/113i386-default/522982/logs/abyss-2.2.3.log
Build URL:      
http://beefy10.nyi.freebsd.org/build.html?mastername=113i386-default&build=522982
Log:

=>> Building biology/abyss
build started at Tue Jan 14 16:42:19 UTC 2020
port directory: /usr/ports/biology/abyss
package name: abyss-2.2.3
building for: FreeBSD 113i386-default-job-15 11.3-RELEASE-p5 FreeBSD 
11.3-RELEASE-p5 i386
maintained by: y...@freebsd.org
Makefile ident:      $FreeBSD: head/biology/abyss/Makefile 522851 2020-01-13 
04:06:14Z yuri $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300062
Jail OSVERSION: 1103000
Job Id: 15

---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1103000
UNAME_v=FreeBSD 11.3-RELEASE-p5
UNAME_r=11.3-RELEASE-p5
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-5-gc81843e5
MASTERMNT=/usr/local/poudriere/data/.m/113i386-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/113i386-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=113i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/113i386-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---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 abyss-2.2.3:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
y...@freebsd.org
--End MAINTAINER--

--CONFIGURE_ARGS--
--without-sparsehash --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work  
HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" 
PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
 SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" 
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/abyss/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work  
HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" 
PATH=/wrkdirs/usr/ports/biology/abyss/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="cc" CFLAGS="-O2 -pipe  
-fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing "  
CPP="cpp" CPPFLAGS="-isystem /usr/local/include"  LDFLAGS=" 
-fstack-protector-strong -L/usr/local/lib " LIBS=""  CXX="c++" CXXFLAGS="-O2 
-pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing 
 -isystem /usr/local/include "  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="" OSREL=11.3 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local 
LIB32DIR=lib DOCSDIR="share/doc/abyss"  EXAMPLESDIR="share/examples/abyss"  
DATADIR="share/abyss"  WWWDIR="www/abyss"  ETCDIR="etc/abyss"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/abyss 
DOCSDIR=/usr/local/share/doc/abyss EXAMPLESDIR=/usr/local/share/examples/abyss  
WWWDIR=/usr/local/www/abyss ETCDIR=/usr/local/etc/abyss
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
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 ####
_CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) 
(based on LLVM 8.0.0) Target: i386-unknown-freebsd11.3 Thread model: posix 
InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 
356365) (based on LLVM 8.0.0) Target: i386-unknown-freebsd11.3 Thread model: 
posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" 
"/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" 
"elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" 
"/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" 
"--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" 
"--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 
356365) (based on LLVM 8.0.0) Target: i386-unknown-freebsd11.3 Thread model: 
posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=11.3-RELEASE-p5
OSREL=11.3
OSVERSION=1103000
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---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  524288
stack size              (kbytes, -s)  65536
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    >============================
===>   abyss-2.2.3 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.12.0.txz
[113i386-default-job-15] Installing pkg-1.12.0...
[113i386-default-job-15] Extracting pkg-1.12.0: .......... done
===>   abyss-2.2.3 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of abyss-2.2.3
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
=> bcgsc-abyss-2.2.3_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch 
https://codeload.github.com/bcgsc/abyss/tar.gz/2.2.3?dummy=/bcgsc-abyss-2.2.3_GH0.tar.gz
fetch: 
https://codeload.github.com/bcgsc/abyss/tar.gz/2.2.3?dummy=/bcgsc-abyss-2.2.3_GH0.tar.gz:
 size unknown
fetch: 
https://codeload.github.com/bcgsc/abyss/tar.gz/2.2.3?dummy=/bcgsc-abyss-2.2.3_GH0.tar.gz:
 size of remote file is not known
bcgsc-abyss-2.2.3_GH0.tar.gz                          1175 kB 6220 kBps    01s
===> Fetching all distfiles required by abyss-2.2.3 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.2.3 for building
=> SHA256 Checksum OK for bcgsc-abyss-2.2.3_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.2.3 for building
===>  Extracting for abyss-2.2.3
=> SHA256 Checksum OK for bcgsc-abyss-2.2.3_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for abyss-2.2.3
===>  Applying FreeBSD patches for abyss-2.2.3
===========================================================================
=======================<phase: build-depends  >============================
===>   abyss-2.2.3 depends on file: /usr/local/include/boost/version.hpp - not 
found
===>   Installing existing package /packages/All/boost-libs-1.72.0.txz
[113i386-default-job-15] Installing boost-libs-1.72.0...
[113i386-default-job-15] `-- Installing icu-65.1,1...
[113i386-default-job-15] `-- Extracting icu-65.1,1: .......... done
[113i386-default-job-15] Extracting boost-libs-1.72.0: .......... done
=====
<snip>
checking for PTHREAD_PRIO_INHERIT... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... no
checking for sqrt in -lm... yes
checking for pow... yes
checking for sqrt... yes
checking for ceilf... yes
checking for dlsym in -ldl... yes
checking how to run the C++ preprocessor... c++ -std=c++11 -E
checking functional usability... yes
checking functional presence... yes
checking for functional... yes
checking tr1/functional usability... yes
checking tr1/functional presence... yes
checking for tr1/functional... yes
checking boost/functional/hash.hpp usability... yes
checking boost/functional/hash.hpp presence... yes
checking for boost/functional/hash.hpp... yes
checking boost/property_map/property_map.hpp usability... yes
checking boost/property_map/property_map.hpp presence... yes
checking for boost/property_map/property_map.hpp... yes
checking google/sparse_hash_map usability... no
checking google/sparse_hash_map presence... no
checking for google/sparse_hash_map... no
checking unordered_map usability... yes
checking unordered_map presence... yes
checking for unordered_map... yes
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking unordered_set usability... yes
checking unordered_set presence... yes
checking for unordered_set... yes
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking boost/unordered_set.hpp usability... yes
checking boost/unordered_set.hpp presence... yes
checking for boost/unordered_set.hpp... yes
checking sqlite3.h usability... yes
checking sqlite3.h presence... yes
checking for sqlite3.h... yes
checking for main in -lsqlite3... yes
checking for c++ -std=c++11 option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating PairedDBG/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Sealer/Makefile
config.status: creating vendor/gtest-1.7.0/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating BloomDBG/Makefile
config.status: creating DataBase/Makefile
config.status: creating vendor/Makefile
config.status: creating vendor/nthash/Makefile
config.status: creating config.h
config.status: executing depfiles commands
===========================================================================
=======================<phase: build          >============================
===>  Building for abyss-2.2.3
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3'
gmake  all-recursive
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3'
Making all in bin
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/bin'
cp ../bin/abyss-nompi ABYSS-P
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/bin'
Making all in doc
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/doc'
gmake[3]: Nothing to be done for 'all'.
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/doc'
Making all in Common
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Common'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-ContigID.o 
-MD -MP -MF .deps/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test 
-f 'ContigID.cpp' || echo './'`ContigID.cpp
mv -f .deps/libcommon_a-ContigID.Tpo .deps/libcommon_a-ContigID.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-Fcontrol.o 
-MD -MP -MF .deps/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test 
-f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-Histogram.o 
-MD -MP -MF .deps/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test 
-f 'Histogram.cpp' || echo './'`Histogram.cpp
mv -f .deps/libcommon_a-Histogram.Tpo .deps/libcommon_a-Histogram.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-Kmer.o -MD 
-MP -MF .deps/libcommon_a-Kmer.Tpo -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' 
|| echo './'`Kmer.cpp
mv -f .deps/libcommon_a-Kmer.Tpo .deps/libcommon_a-Kmer.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-Log.o -MD 
-MP -MF .deps/libcommon_a-Log.Tpo -c -o libcommon_a-Log.o `test -f 'Log.cpp' || 
echo './'`Log.cpp
mv -f .deps/libcommon_a-Log.Tpo .deps/libcommon_a-Log.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-Options.o 
-MD -MP -MF .deps/libcommon_a-Options.Tpo -c -o libcommon_a-Options.o `test -f 
'Options.cpp' || echo './'`Options.cpp
mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-Sequence.o 
-MD -MP -MF .deps/libcommon_a-Sequence.Tpo -c -o libcommon_a-Sequence.o `test 
-f 'Sequence.cpp' || echo './'`Sequence.cpp
mv -f .deps/libcommon_a-Sequence.Tpo .deps/libcommon_a-Sequence.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT 
libcommon_a-SignalHandler.o -MD -MP -MF .deps/libcommon_a-SignalHandler.Tpo -c 
-o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo 
'./'`SignalHandler.cpp
mv -f .deps/libcommon_a-SignalHandler.Tpo .deps/libcommon_a-SignalHandler.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-Timer.o -MD 
-MP -MF .deps/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.o `test -f 
'Timer.cpp' || echo './'`Timer.cpp
mv -f .deps/libcommon_a-Timer.Tpo .deps/libcommon_a-Timer.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-Uncompress.o 
-MD -MP -MF .deps/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o 
`test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libcommon_a-city.o -MD 
-MP -MF .deps/libcommon_a-city.Tpo -c -o libcommon_a-city.o `test -f 'city.cc' 
|| echo './'`city.cc
mv -f .deps/libcommon_a-city.Tpo .deps/libcommon_a-city.Po
rm -f libcommon.a
ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o 
libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o 
libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o 
libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o 
ranlib libcommon.a
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Common'
Making all in Graph
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Graph'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_gc-gc.o -MD -MP 
-MF .deps/abyss_gc-gc.Tpo -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo 
'./'`gc.cc
mv -f .deps/abyss_gc-gc.Tpo .deps/abyss_gc-gc.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong 
-isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   
-fstack-protector-strong -L/usr/local/lib  -o abyss-gc abyss_gc-gc.o 
../Common/libcommon.a -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_todot-todot.o -MD 
-MP -MF .deps/abyss_todot-todot.Tpo -c -o abyss_todot-todot.o `test -f 
'todot.cc' || echo './'`todot.cc
mv -f .deps/abyss_todot-todot.Tpo .deps/abyss_todot-todot.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong 
-isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  
-L. -fstack-protector-strong -L/usr/local/lib  -o abyss-todot 
abyss_todot-todot.o ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Graph'
Making all in DataLayer
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/DataLayer'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_fac-fac.o -MD -MP 
-MF .deps/abyss_fac-fac.Tpo -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo 
'./'`fac.cc
mv -f .deps/abyss_fac-fac.Tpo .deps/abyss_fac-fac.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT 
libdatalayer_a-FastaReader.o -MD -MP -MF .deps/libdatalayer_a-FastaReader.Tpo 
-c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo 
'./'`FastaReader.cpp
mv -f .deps/libdatalayer_a-FastaReader.Tpo .deps/libdatalayer_a-FastaReader.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT 
libdatalayer_a-FastaWriter.o -MD -MP -MF .deps/libdatalayer_a-FastaWriter.Tpo 
-c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo 
'./'`FastaWriter.cpp
mv -f .deps/libdatalayer_a-FastaWriter.Tpo .deps/libdatalayer_a-FastaWriter.Po
rm -f libdatalayer.a
ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o 
ranlib libdatalayer.a
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong 
-isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   
-fstack-protector-strong -L/usr/local/lib  -o abyss-fac abyss_fac-fac.o 
libdatalayer.a ../Common/libcommon.a -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT 
abyss_tofastq-abyss-tofastq.o -MD -MP -MF .deps/abyss_tofastq-abyss-tofastq.Tpo 
-c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo 
'./'`abyss-tofastq.cc
mv -f .deps/abyss_tofastq-abyss-tofastq.Tpo .deps/abyss_tofastq-abyss-tofastq.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong 
-isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   
-fstack-protector-strong -L/usr/local/lib  -o abyss-tofastq 
abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/DataLayer'
Making all in DataBase
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/DataBase'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_db_csv-DB.o -MD 
-MP -MF .deps/abyss_db_csv-DB.Tpo -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || 
echo './'`DB.cc
mv -f .deps/abyss_db_csv-DB.Tpo .deps/abyss_db_csv-DB.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_db_csv-db-csv.o 
-MD -MP -MF .deps/abyss_db_csv-db-csv.Tpo -c -o abyss_db_csv-db-csv.o `test -f 
'db-csv.cc' || echo './'`db-csv.cc
mv -f .deps/abyss_db_csv-db-csv.Tpo .deps/abyss_db_csv-db-csv.Po
c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong 
-isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   
-fstack-protector-strong -L/usr/local/lib  -o abyss-db-csv abyss_db_csv-DB.o 
abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT libdb_a-DB.o -MD -MP -MF 
.deps/libdb_a-DB.Tpo -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
mv -f .deps/libdb_a-DB.Tpo .deps/libdb_a-DB.Po
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ranlib libdb.a
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/DataBase'
Making all in FMIndex
gmake[3]: Entering directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/FMIndex'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common 
-I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3     -isystem 
/usr/local/include 
-isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall 
-Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include 
-fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_count-count.o -MD 
-MP -MF .deps/abyss_count-count.Tpo -c -o abyss_count-count.o `test -f 
'count.cc' || echo './'`count.cc
In file included from count.cc:2:
In file included from ./DAWG.h:5:
./FMIndex.h:547:11: error: result of comparison of constant 
18446744073709551615 with expression of type 'size_t' (aka 'unsigned int') is 
always true [-Werror,-Wtautological-constant-out-of-range-compare]
        assert(n < std::numeric_limits<size_type>::max());
               ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/assert.h:54:21: note: expanded from macro 'assert'
#define assert(e)       ((e) ? (void)0 : __assert(__func__, __FILE__, \
                          ^
In file included from count.cc:2:
In file included from ./DAWG.h:5:
./FMIndex.h:555:11: error: result of comparison of constant 
18446744073709551615 with expression of type 'size_t' (aka 'unsigned int') is 
always true [-Werror,-Wtautological-constant-out-of-range-compare]
        assert(n < std::numeric_limits<size_type>::max());
               ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/assert.h:54:21: note: expanded from macro 'assert'
#define assert(e)       ((e) ? (void)0 : __assert(__func__, __FILE__, \
                          ^
2 errors generated.
gmake[3]: *** [Makefile:438: abyss_count-count.o] Error 1
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/FMIndex'
gmake[2]: *** [Makefile:486: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3'
gmake[1]: *** [Makefile:406: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3'
*** Error code 1

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