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://beefy18.nyi.freebsd.org/data/head-amd64-default/p522982_s356710/logs/abyss-2.2.3.log
Build URL:      
http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p522982_s356710
Log:

=>> Building biology/abyss
build started at Tue Jan 14 10:28:42 UTC 2020
port directory: /usr/ports/biology/abyss
package name: abyss-2.2.3
building for: FreeBSD head-amd64-default-job-05 13.0-CURRENT FreeBSD 
13.0-CURRENT 1300076 amd64
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: 1300076
Job Id: 05




!!! Jail is newer than host. (Jail: 1300076, Host: 1300062) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
OSVERSION=1300076
UNAME_v=FreeBSD 13.0-CURRENT 1300076
UNAME_r=13.0-CURRENT
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/head-amd64-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=head-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-amd64-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=13.0 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
#### /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 9.0.1 
(g...@github.com:llvm/llvm-project.git 
c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: 
x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 9.0.1 
(g...@github.com:llvm/llvm-project.git 
c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: 
x86_64-unknown-freebsd13.0 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" "-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 9.0.1 
(g...@github.com:llvm/llvm-project.git 
c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: 
x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=amd64
OPSYS=FreeBSD
_OSRELEASE=13.0-CURRENT
OSREL=13.0
OSVERSION=1300076
PYTHONBASE=/usr/local
HAVE_COMPAT_IA32_KERN=YES
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
---End make.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
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
[head-amd64-default-job-05] Installing pkg-1.12.0...
[head-amd64-default-job-05] 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 6995 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
<snip>
checking for vfork... (cached) yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... (cached) yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... (cached) yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... no
checking build system type... amd64-portbld-freebsd13.0
checking host system type... amd64-portbld-freebsd13.0
checking if compiler needs -Werror to reject unknown flags... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
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
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-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-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-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-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-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-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-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-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-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-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-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-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
mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.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
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
In file included from todot.cc:8:
./Graph/ContigGraphAlgorithms.h:219:15: error: 'mem_fun_ref<bool, ContigNode>' 
is deprecated [-Werror,-Wdeprecated-declarations]
                                not1(std::mem_fun_ref(&ContigNode::ambiguous)));
                                          ^
/usr/include/c++/v1/functional:1256:1: note: 'mem_fun_ref<bool, ContigNode>' 
has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/usr/include/c++/v1/__config:945:39: note: expanded from macro 
'_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/usr/include/c++/v1/__config:934:48: note: expanded from macro 
'_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from todot.cc:8:
./Graph/ContigGraphAlgorithms.h:289:9: error: 'mem_fun_ref<ContigID, 
ContigNode>' is deprecated [-Werror,-Wdeprecated-declarations]
                        std::mem_fun_ref(&ContigNode::contigIndex));
                             ^
/usr/include/c++/v1/functional:1256:1: note: 'mem_fun_ref<ContigID, 
ContigNode>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/usr/include/c++/v1/__config:945:39: note: expanded from macro 
'_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/usr/include/c++/v1/__config:934:48: note: expanded from macro 
'_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 errors generated.
gmake[3]: *** [Makefile:460: abyss_todot-todot.o] Error 1
gmake[3]: *** Waiting for unfinished jobs....
mv -f .deps/abyss_gc-gc.Tpo .deps/abyss_gc-gc.Po
gmake[3]: Leaving directory 
'/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Graph'
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'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1

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