[package - 114amd64-quarterly][biology/abyss] Failed for abyss-2.3.1 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 27 Jul 2021 01:41:16 GMT
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:     yuri_at_FreeBSD.org
Log URL:        http://beefy3.nyi.freebsd.org/data/114amd64-quarterly/861e2a11357f/logs/abyss-2.3.1.log
Build URL:      http://beefy3.nyi.freebsd.org/build.html?mastername=114amd64-quarterly&build=861e2a11357f
Log:

=>> Building biology/abyss
build started at Tue Jul 27 01:34:01 UTC 2021
port directory: /usr/ports/biology/abyss
package name: abyss-2.3.1
building for: FreeBSD 114amd64-quarterly-job-09 11.4-RELEASE-p12 FreeBSD 11.4-RELEASE-p12 amd64
maintained by: yuri_at_FreeBSD.org
Makefile ident: 
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Host OSVERSION: 1400008
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Job Id: 09

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===> The following configuration options are available for abyss-2.3.1:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
yuri_at_FreeBSD.org
--End MAINTAINER--

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--PLIST_SUB--
PORTDOCS="" OSREL=11.4 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--

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=======================<phase: check-sanity   >============================
===>  License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   abyss-2.3.1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.16.3.txz
[114amd64-quarterly-job-09] Installing pkg-1.16.3...
[114amd64-quarterly-job-09] Extracting pkg-1.16.3: .......... done
===>   abyss-2.3.1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of abyss-2.3.1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.1 for building
=> SHA256 Checksum OK for bcgsc-abyss-2.3.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by abyss-2.3.1 for building
===>  Extracting for abyss-2.3.1
=> SHA256 Checksum OK for bcgsc-abyss-2.3.1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for abyss-2.3.1
===>  Applying FreeBSD patches for abyss-2.3.1 from /usr/ports/biology/abyss/files
===========================================================================
=======================<phase: build-depends  >============================
===>   abyss-2.3.1 depends on file: /usr/local/include/boost/version.hpp - not found
===>   Installing existing package /packages/All/boost-libs-1.72.0_5.txz
[114amd64-quarterly-job-09] Installing boost-libs-1.72.0_5...
[114amd64-quarterly-job-09] `-- Installing icu-69.1,1...
[114amd64-quarterly-job-09] `-- Extracting icu-69.1,1: .......... done
[114amd64-quarterly-job-09] Extracting boost-libs-1.72.0_5: .......... done
=====
Message from boost-libs-1.72.0_5:

--
You have built the Boost library with thread support.

Don't forget to add -pthread to your linker options when
linking your code.
===>   abyss-2.3.1 depends on file: /usr/local/include/boost/version.hpp - found
===>   Returning to build of abyss-2.3.1
<snip>
mv -f .deps/konnector-konnector.Tpo .deps/konnector-konnector.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Konnector'
Making all in Consensus
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Consensus'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT Consensus-Consensus.o -MD -MP -MF .deps/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
mv -f .deps/Consensus-Consensus.Tpo .deps/Consensus-Consensus.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 Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Consensus'
Making all in DAssembler
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/DAssembler'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT DAssembler-DAssembler.o -MD -MP -MF .deps/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp
mv -f .deps/DAssembler-DAssembler.Tpo .deps/DAssembler-DAssembler.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT DAssembler-RotatedRead.o -MD -MP -MF .deps/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
mv -f .deps/DAssembler-RotatedRead.Tpo .deps/DAssembler-RotatedRead.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 DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/DAssembler'
Making all in DistanceEst
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/DistanceEst'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT DistanceEst-DistanceEst.o -MD -MP -MF .deps/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
mv -f .deps/DistanceEst-DistanceEst.Tpo .deps/DistanceEst-DistanceEst.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT DistanceEst-MLE.o -MD -MP -MF .deps/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
mv -f .deps/DistanceEst-MLE.Tpo .deps/DistanceEst-MLE.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT DistanceEst_ssq-DistanceEst.o -MD -MP -MF .deps/DistanceEst_ssq-DistanceEst.Tpo -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
mv -f .deps/DistanceEst_ssq-DistanceEst.Tpo .deps/DistanceEst_ssq-DistanceEst.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT DistanceEst_ssq-MLE.o -MD -MP -MF .deps/DistanceEst_ssq-MLE.Tpo -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
mv -f .deps/DistanceEst_ssq-MLE.Tpo .deps/DistanceEst_ssq-MLE.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/DistanceEst'
Making all in KAligner
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/KAligner'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT KAligner-KAligner.o -MD -MP -MF .deps/KAligner-KAligner.Tpo -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp
mv -f .deps/KAligner-KAligner.Tpo .deps/KAligner-KAligner.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT KAligner-Aligner.o -MD -MP -MF .deps/KAligner-Aligner.Tpo -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
mv -f .deps/KAligner-Aligner.Tpo .deps/KAligner-Aligner.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 KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/KAligner'
Making all in Layout
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Layout'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/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_layout-layout.o -MD -MP -MF .deps/abyss_layout-layout.Tpo -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc
mv -f .deps/abyss_layout-layout.Tpo .deps/abyss_layout-layout.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-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Layout'
Making all in LogKmerCount
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/LogKmerCount'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT logcounter-logcounter.o -MD -MP -MF .deps/logcounter-logcounter.Tpo -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc
mv -f .deps/logcounter-logcounter.Tpo .deps/logcounter-logcounter.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/LogKmerCount'
Making all in Map
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Map'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/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_index-index.o -MD -MP -MF .deps/abyss_index-index.Tpo -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc
mv -f .deps/abyss_index-index.Tpo .deps/abyss_index-index.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-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_map-map.o -MD -MP -MF .deps/abyss_map-map.Tpo -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc
mv -f .deps/abyss_map-map.Tpo .deps/abyss_map-map.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_map_ssq-map.o -MD -MP -MF .deps/abyss_map_ssq-map.Tpo -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc
mv -f .deps/abyss_map_ssq-map.Tpo .deps/abyss_map_ssq-map.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_overlap-overlap.o -MD -MP -MF .deps/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc
mv -f .deps/abyss_overlap-overlap.Tpo .deps/abyss_overlap-overlap.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Map'
Making all in MergePaths
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/MergePaths'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT MergePaths-MergePaths.o -MD -MP -MF .deps/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp
mv -f .deps/MergePaths-MergePaths.Tpo .deps/MergePaths-MergePaths.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT MergeContigs-MergeContigs.o -MD -MP -MF .deps/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
mv -f .deps/MergeContigs-MergeContigs.Tpo .deps/MergeContigs-MergeContigs.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 MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT PathConsensus-PathConsensus.o -MD -MP -MF .deps/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp
mv -f .deps/PathConsensus-PathConsensus.Tpo .deps/PathConsensus-PathConsensus.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 PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/MergePaths'
Making all in Overlap
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Overlap'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT Overlap-Overlap.o -MD -MP -MF .deps/Overlap-Overlap.Tpo -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp
mv -f .deps/Overlap-Overlap.Tpo .deps/Overlap-Overlap.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 Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Overlap'
Making all in PairedDBG
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PairedDBG'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -DPAIRED_DBG -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/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_paired_dbg-abyss-paired-dbg.o -MD -MP -MF .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc
mv -f .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo .deps/abyss_paired_dbg-abyss-paired-dbg.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -DPAIRED_DBG -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/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_paired_dbg-KmerPair.o -MD -MP -MF .deps/abyss_paired_dbg-KmerPair.Tpo -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc
mv -f .deps/abyss_paired_dbg-KmerPair.Tpo .deps/abyss_paired_dbg-KmerPair.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-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -ldl -lm 
depbase=`echo KmerPair.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT KmerPair.o -MD -MP -MF $depbase.Tpo -c -o KmerPair.o KmerPair.cc &&\
mv -f $depbase.Tpo $depbase.Po
rm -f libpaireddbg.a
ar cru libpaireddbg.a KmerPair.o 
ranlib libpaireddbg.a
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PairedDBG'
Making all in ParseAligns
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/ParseAligns'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/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_fixmate-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
mv -f .deps/abyss_fixmate-abyss-fixmate.Tpo .deps/abyss_fixmate-abyss-fixmate.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-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -ldl -lm 
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/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_fixmate_ssq-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
mv -f .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo .deps/abyss_fixmate_ssq-abyss-fixmate.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-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../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-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT ParseAligns-ParseAligns.o -MD -MP -MF .deps/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
mv -f .deps/ParseAligns-ParseAligns.Tpo .deps/ParseAligns-ParseAligns.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 ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/ParseAligns'
Making all in PathOverlap
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PathOverlap'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT PathOverlap-PathOverlap.o -MD -MP -MF .deps/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp
mv -f .deps/PathOverlap-PathOverlap.Tpo .deps/PathOverlap-PathOverlap.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 PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PathOverlap'
Making all in PopBubbles
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PopBubbles'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT PopBubbles-PopBubbles.o -MD -MP -MF .deps/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp
mv -f .deps/PopBubbles-PopBubbles.Tpo .deps/PopBubbles-PopBubbles.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PopBubbles'
Making all in Scaffold
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Scaffold'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_scaffold-scaffold.o -MD -MP -MF .deps/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc
mv -f .deps/abyss_scaffold-scaffold.Tpo .deps/abyss_scaffold-scaffold.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../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-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_junction-junction.o -MD -MP -MF .deps/abyss_junction-junction.Tpo -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc
mv -f .deps/abyss_junction-junction.Tpo .deps/abyss_junction-junction.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-junction abyss_junction-junction.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-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_longseqdist-longseqdist.o -MD -MP -MF .deps/abyss_longseqdist-longseqdist.Tpo -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp
mv -f .deps/abyss_longseqdist-longseqdist.Tpo .deps/abyss_longseqdist-longseqdist.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-longseqdist abyss_longseqdist-longseqdist.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-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/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_drawgraph-drawgraph.o -MD -MP -MF .deps/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc
mv -f .deps/abyss_drawgraph-drawgraph.Tpo .deps/abyss_drawgraph-drawgraph.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-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Scaffold'
Making all in SimpleGraph
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/SimpleGraph'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT SimpleGraph-SimpleGraph.o -MD -MP -MF .deps/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp
mv -f .deps/SimpleGraph-SimpleGraph.Tpo .deps/SimpleGraph-SimpleGraph.Po
c++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include   -fstack-protector-strong -L/usr/local/lib  -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Common/libcommon.a -lpthread -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/SimpleGraph'
Making all in kmerprint
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/kmerprint'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Assembly -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT kmerprint-kmerprint.o -MD -MP -MF .deps/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc
mv -f .deps/kmerprint-kmerprint.Tpo .deps/kmerprint-kmerprint.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 kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/kmerprint'
Making all in FilterGraph
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/FilterGraph'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_filtergraph-FilterGraph.o -MD -MP -MF .deps/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc
mv -f .deps/abyss_filtergraph-FilterGraph.Tpo .deps/abyss_filtergraph-FilterGraph.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/FilterGraph'
Making all in GapFiller
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/GapFiller'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_gapfill-gapfill.o -MD -MP -MF .deps/abyss_gapfill-gapfill.Tpo -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp
mv -f .deps/abyss_gapfill-gapfill.Tpo .deps/abyss_gapfill-gapfill.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/GapFiller'
Making all in Sealer
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Sealer'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_sealer-sealer.o -MD -MP -MF .deps/abyss_sealer-sealer.Tpo -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc
mv -f .deps/abyss_sealer-sealer.Tpo .deps/abyss_sealer-sealer.Po
c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -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-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
pandoc -s -o abyss-sealer.1 README.md
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Sealer'
Making all in RResolver
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/RResolver'
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_rresolver_short-RResolverShort.o -MD -MP -MF .deps/abyss_rresolver_short-RResolverShort.Tpo -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp
mv -f .deps/abyss_rresolver_short-RResolverShort.Tpo .deps/abyss_rresolver_short-RResolverShort.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT abyss_rresolver_short-Contigs.o -MD -MP -MF .deps/abyss_rresolver_short-Contigs.Tpo -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp
mv -f .deps/abyss_rresolver_short-Contigs.Tpo .deps/abyss_rresolver_short-Contigs.Po
c++ -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1     -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -MT libralgorithmsshort_a-RAlgorithmsShort.o -MD -MP -MF .deps/libralgorithmsshort_a-RAlgorithmsShort.Tpo -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp
In file included from RAlgorithmsShort.cpp:5:
./btllib/include/btllib/seq_reader.hpp:650:14: error: use of undeclared identifier 'getline'; did you mean 'std::getline'?
  s.s_size = getline(&(s.s), &(s.s_cap), source);
             ^~~~~~~
             std::getline
/usr/include/c++/v1/istream:1507:1: note: 'std::getline' declared here
getline(basic_istream<_CharT, _Traits>& __is,
^
In file included from RAlgorithmsShort.cpp:5:
./btllib/include/btllib/seq_reader.hpp:650:14: error: no matching function for call to 'getline'
  s.s_size = getline(&(s.s), &(s.s_cap), source);
             ^~~~~~~
/usr/include/c++/v1/istream:1507:1: note: candidate template ignored: could not match 'basic_istream<type-parameter-0-0, type-parameter-0-1>' against 'char **'
getline(basic_istream<_CharT, _Traits>& __is,
^
2 errors generated.
gmake[3]: *** [Makefile:485: libralgorithmsshort_a-RAlgorithmsShort.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/RResolver'
gmake[2]: *** [Makefile:490: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1'
gmake[1]: *** [Makefile:410: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/abyss
Received on Tue Jul 27 2021 - 01:41:16 UTC

Original text of this message