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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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Compile error on MacOS X 10.7.4 #44

Closed megancamilla closed 11 years ago

megancamilla commented 11 years ago

I've received the following compile error from SGA downloaded 21.03.13. I also have the newest version of Xcode 4.6.1

rsb-33-059:src meganm$ sudo make Password: make all-recursive Making all in bin make[2]: Nothing to be done for all'. Making all in Thirdparty g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT gzstream.o -MD -MP -MF .deps/gzstream.Tpo -c -o gzstream.o gzstream.C mv -f .deps/gzstream.Tpo .deps/gzstream.Po gcc -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -O3 -MT stdaln.o -MD -MP -MF .deps/stdaln.Tpo -c -o stdaln.o stdaln.c mv -f .deps/stdaln.Tpo .deps/stdaln.Po g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT overlapper.o -MD -MP -MF .deps/overlapper.Tpo -c -o overlapper.o overlapper.cpp mv -f .deps/overlapper.Tpo .deps/overlapper.Po g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT multiple_alignment.o -MD -MP -MF .deps/multiple_alignment.Tpo -c -o multiple_alignment.o multiple_alignment.cpp mv -f .deps/multiple_alignment.Tpo .deps/multiple_alignment.Po gcc -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -O3 -MT bcr.o -MD -MP -MF .deps/bcr.Tpo -c -o bcr.o bcr.c mv -f .deps/bcr.Tpo .deps/bcr.Po g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT MurmurHash3.o -MD -MP -MF .deps/MurmurHash3.Tpo -c -o MurmurHash3.o MurmurHash3.cpp mv -f .deps/MurmurHash3.Tpo .deps/MurmurHash3.Po g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT count_min_sketch.o -MD -MP -MF .deps/count_min_sketch.Tpo -c -o count_min_sketch.o count_min_sketch.cpp mv -f .deps/count_min_sketch.Tpo .deps/count_min_sketch.Po rm -f libthirdparty.a ar cru libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o ranlib libthirdparty.a Making all in Util g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Util.o -MD -MP -MF .deps/libutil_a-Util.Tpo -c -o libutil_a-Util.otest -f 'Util.cpp' || echo './'Util.cpp mv -f .deps/libutil_a-Util.Tpo .deps/libutil_a-Util.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Alphabet.o -MD -MP -MF .deps/libutil_a-Alphabet.Tpo -c -o libutil_a-Alphabet.otest -f 'Alphabet.cpp' || echo './'Alphabet.cpp mv -f .deps/libutil_a-Alphabet.Tpo .deps/libutil_a-Alphabet.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Contig.o -MD -MP -MF .deps/libutil_a-Contig.Tpo -c -o libutil_a-Contig.otest -f 'Contig.cpp' || echo './'Contig.cpp mv -f .deps/libutil_a-Contig.Tpo .deps/libutil_a-Contig.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-ReadTable.o -MD -MP -MF .deps/libutil_a-ReadTable.Tpo -c -o libutil_a-ReadTable.otest -f 'ReadTable.cpp' || echo './'ReadTable.cpp mv -f .deps/libutil_a-ReadTable.Tpo .deps/libutil_a-ReadTable.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-ReadInfoTable.o -MD -MP -MF .deps/libutil_a-ReadInfoTable.Tpo -c -o libutil_a-ReadInfoTable.otest -f 'ReadInfoTable.cpp' || echo './'ReadInfoTable.cpp mv -f .deps/libutil_a-ReadInfoTable.Tpo .deps/libutil_a-ReadInfoTable.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-SeqReader.o -MD -MP -MF .deps/libutil_a-SeqReader.Tpo -c -o libutil_a-SeqReader.otest -f 'SeqReader.cpp' || echo './'SeqReader.cpp mv -f .deps/libutil_a-SeqReader.Tpo .deps/libutil_a-SeqReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-DNAString.o -MD -MP -MF .deps/libutil_a-DNAString.Tpo -c -o libutil_a-DNAString.otest -f 'DNAString.cpp' || echo './'DNAString.cpp mv -f .deps/libutil_a-DNAString.Tpo .deps/libutil_a-DNAString.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Match.o -MD -MP -MF .deps/libutil_a-Match.Tpo -c -o libutil_a-Match.otest -f 'Match.cpp' || echo './'Match.cpp mv -f .deps/libutil_a-Match.Tpo .deps/libutil_a-Match.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Pileup.o -MD -MP -MF .deps/libutil_a-Pileup.Tpo -c -o libutil_a-Pileup.otest -f 'Pileup.cpp' || echo './'Pileup.cpp mv -f .deps/libutil_a-Pileup.Tpo .deps/libutil_a-Pileup.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-BitChar.o -MD -MP -MF .deps/libutil_a-BitChar.Tpo -c -o libutil_a-BitChar.otest -f 'BitChar.cpp' || echo './'BitChar.cpp mv -f .deps/libutil_a-BitChar.Tpo .deps/libutil_a-BitChar.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Interval.o -MD -MP -MF .deps/libutil_a-Interval.Tpo -c -o libutil_a-Interval.otest -f 'Interval.cpp' || echo './'Interval.cpp mv -f .deps/libutil_a-Interval.Tpo .deps/libutil_a-Interval.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-SeqCoord.o -MD -MP -MF .deps/libutil_a-SeqCoord.Tpo -c -o libutil_a-SeqCoord.otest -f 'SeqCoord.cpp' || echo './'SeqCoord.cpp mv -f .deps/libutil_a-SeqCoord.Tpo .deps/libutil_a-SeqCoord.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-MultiOverlap.o -MD -MP -MF .deps/libutil_a-MultiOverlap.Tpo -c -o libutil_a-MultiOverlap.otest -f 'MultiOverlap.cpp' || echo './'MultiOverlap.cpp mv -f .deps/libutil_a-MultiOverlap.Tpo .deps/libutil_a-MultiOverlap.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-QualityVector.o -MD -MP -MF .deps/libutil_a-QualityVector.Tpo -c -o libutil_a-QualityVector.otest -f 'QualityVector.cpp' || echo './'QualityVector.cpp mv -f .deps/libutil_a-QualityVector.Tpo .deps/libutil_a-QualityVector.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Stats.o -MD -MP -MF .deps/libutil_a-Stats.Tpo -c -o libutil_a-Stats.otest -f 'Stats.cpp' || echo './'Stats.cpp mv -f .deps/libutil_a-Stats.Tpo .deps/libutil_a-Stats.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Quality.o -MD -MP -MF .deps/libutil_a-Quality.Tpo -c -o libutil_a-Quality.otest -f 'Quality.cpp' || echo './'Quality.cpp mv -f .deps/libutil_a-Quality.Tpo .deps/libutil_a-Quality.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-PrimerScreen.o -MD -MP -MF .deps/libutil_a-PrimerScreen.Tpo -c -o libutil_a-PrimerScreen.otest -f 'PrimerScreen.cpp' || echo './'PrimerScreen.cpp mv -f .deps/libutil_a-PrimerScreen.Tpo .deps/libutil_a-PrimerScreen.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-BitVector.o -MD -MP -MF .deps/libutil_a-BitVector.Tpo -c -o libutil_a-BitVector.otest -f 'BitVector.cpp' || echo './'BitVector.cpp mv -f .deps/libutil_a-BitVector.Tpo .deps/libutil_a-BitVector.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-CorrectionThresholds.o -MD -MP -MF .deps/libutil_a-CorrectionThresholds.Tpo -c -o libutil_a-CorrectionThresholds.otest -f 'CorrectionThresholds.cpp' || echo './'CorrectionThresholds.cpp mv -f .deps/libutil_a-CorrectionThresholds.Tpo .deps/libutil_a-CorrectionThresholds.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-KmerDistribution.o -MD -MP -MF .deps/libutil_a-KmerDistribution.Tpo -c -o libutil_a-KmerDistribution.otest -f 'KmerDistribution.cpp' || echo './'KmerDistribution.cpp mv -f .deps/libutil_a-KmerDistribution.Tpo .deps/libutil_a-KmerDistribution.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-ClusterReader.o -MD -MP -MF .deps/libutil_a-ClusterReader.Tpo -c -o libutil_a-ClusterReader.otest -f 'ClusterReader.cpp' || echo './'ClusterReader.cpp mv -f .deps/libutil_a-ClusterReader.Tpo .deps/libutil_a-ClusterReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-MultiAlignment.o -MD -MP -MF .deps/libutil_a-MultiAlignment.Tpo -c -o libutil_a-MultiAlignment.otest -f 'MultiAlignment.cpp' || echo './'MultiAlignment.cpp mv -f .deps/libutil_a-MultiAlignment.Tpo .deps/libutil_a-MultiAlignment.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-StdAlnTools.o -MD -MP -MF .deps/libutil_a-StdAlnTools.Tpo -c -o libutil_a-StdAlnTools.otest -f 'StdAlnTools.cpp' || echo './'StdAlnTools.cpp mv -f .deps/libutil_a-StdAlnTools.Tpo .deps/libutil_a-StdAlnTools.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-VCFUtil.o -MD -MP -MF .deps/libutil_a-VCFUtil.Tpo -c -o libutil_a-VCFUtil.otest -f 'VCFUtil.cpp' || echo './'VCFUtil.cpp mv -f .deps/libutil_a-VCFUtil.Tpo .deps/libutil_a-VCFUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-QualityTable.o -MD -MP -MF .deps/libutil_a-QualityTable.Tpo -c -o libutil_a-QualityTable.otest -f 'QualityTable.cpp' || echo './'QualityTable.cpp mv -f .deps/libutil_a-QualityTable.Tpo .deps/libutil_a-QualityTable.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-BloomFilter.o -MD -MP -MF .deps/libutil_a-BloomFilter.Tpo -c -o libutil_a-BloomFilter.otest -f 'BloomFilter.cpp' || echo './'BloomFilter.cpp mv -f .deps/libutil_a-BloomFilter.Tpo .deps/libutil_a-BloomFilter.Po rm -f libutil.a ar cru libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-Stats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o ranlib libutil.a Making all in SQG g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsqg_a-SQG.o -MD -MP -MF .deps/libsqg_a-SQG.Tpo -c -o libsqg_a-SQG.otest -f 'SQG.cpp' || echo './'SQG.cpp mv -f .deps/libsqg_a-SQG.Tpo .deps/libsqg_a-SQG.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsqg_a-ASQG.o -MD -MP -MF .deps/libsqg_a-ASQG.Tpo -c -o libsqg_a-ASQG.otest -f 'ASQG.cpp' || echo './'ASQG.cpp mv -f .deps/libsqg_a-ASQG.Tpo .deps/libsqg_a-ASQG.Po rm -f libsqg.a ar cru libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o ranlib libsqg.a Making all in Bigraph g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libbigraph_a-Bigraph.o -MD -MP -MF .deps/libbigraph_a-Bigraph.Tpo -c -o libbigraph_a-Bigraph.otest -f 'Bigraph.cpp' || echo './'Bigraph.cpp mv -f .deps/libbigraph_a-Bigraph.Tpo .deps/libbigraph_a-Bigraph.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libbigraph_a-Vertex.o -MD -MP -MF .deps/libbigraph_a-Vertex.Tpo -c -o libbigraph_a-Vertex.otest -f 'Vertex.cpp' || echo './'Vertex.cpp mv -f .deps/libbigraph_a-Vertex.Tpo .deps/libbigraph_a-Vertex.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libbigraph_a-Edge.o -MD -MP -MF .deps/libbigraph_a-Edge.Tpo -c -o libbigraph_a-Edge.otest -f 'Edge.cpp' || echo './'Edge.cpp mv -f .deps/libbigraph_a-Edge.Tpo .deps/libbigraph_a-Edge.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libbigraph_a-EdgeDesc.o -MD -MP -MF .deps/libbigraph_a-EdgeDesc.Tpo -c -o libbigraph_a-EdgeDesc.otest -f 'EdgeDesc.cpp' || echo './'EdgeDesc.cpp mv -f .deps/libbigraph_a-EdgeDesc.Tpo .deps/libbigraph_a-EdgeDesc.Po rm -f libbigraph.a ar cru libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o ranlib libbigraph.a Making all in Algorithm g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-OverlapAlgorithm.o -MD -MP -MF .deps/libalgorithm_a-OverlapAlgorithm.Tpo -c -o libalgorithm_a-OverlapAlgorithm.otest -f 'OverlapAlgorithm.cpp' || echo './'OverlapAlgorithm.cpp mv -f .deps/libalgorithm_a-OverlapAlgorithm.Tpo .deps/libalgorithm_a-OverlapAlgorithm.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-SearchSeed.o -MD -MP -MF .deps/libalgorithm_a-SearchSeed.Tpo -c -o libalgorithm_a-SearchSeed.otest -f 'SearchSeed.cpp' || echo './'SearchSeed.cpp mv -f .deps/libalgorithm_a-SearchSeed.Tpo .deps/libalgorithm_a-SearchSeed.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-OverlapBlock.o -MD -MP -MF .deps/libalgorithm_a-OverlapBlock.Tpo -c -o libalgorithm_a-OverlapBlock.otest -f 'OverlapBlock.cpp' || echo './'OverlapBlock.cpp mv -f .deps/libalgorithm_a-OverlapBlock.Tpo .deps/libalgorithm_a-OverlapBlock.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-SearchHistory.o -MD -MP -MF .deps/libalgorithm_a-SearchHistory.Tpo -c -o libalgorithm_a-SearchHistory.otest -f 'SearchHistory.cpp' || echo './'SearchHistory.cpp mv -f .deps/libalgorithm_a-SearchHistory.Tpo .deps/libalgorithm_a-SearchHistory.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ErrorCorrectProcess.o -MD -MP -MF .deps/libalgorithm_a-ErrorCorrectProcess.Tpo -c -o libalgorithm_a-ErrorCorrectProcess.otest -f 'ErrorCorrectProcess.cpp' || echo './'ErrorCorrectProcess.cpp mv -f .deps/libalgorithm_a-ErrorCorrectProcess.Tpo .deps/libalgorithm_a-ErrorCorrectProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-QCProcess.o -MD -MP -MF .deps/libalgorithm_a-QCProcess.Tpo -c -o libalgorithm_a-QCProcess.otest -f 'QCProcess.cpp' || echo './'QCProcess.cpp mv -f .deps/libalgorithm_a-QCProcess.Tpo .deps/libalgorithm_a-QCProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-OverlapTools.o -MD -MP -MF .deps/libalgorithm_a-OverlapTools.Tpo -c -o libalgorithm_a-OverlapTools.otest -f 'OverlapTools.cpp' || echo './'OverlapTools.cpp mv -f .deps/libalgorithm_a-OverlapTools.Tpo .deps/libalgorithm_a-OverlapTools.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-DPAlignment.o -MD -MP -MF .deps/libalgorithm_a-DPAlignment.Tpo -c -o libalgorithm_a-DPAlignment.otest -f 'DPAlignment.cpp' || echo './'DPAlignment.cpp mv -f .deps/libalgorithm_a-DPAlignment.Tpo .deps/libalgorithm_a-DPAlignment.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ConnectProcess.o -MD -MP -MF .deps/libalgorithm_a-ConnectProcess.Tpo -c -o libalgorithm_a-ConnectProcess.otest -f 'ConnectProcess.cpp' || echo './'ConnectProcess.cpp mv -f .deps/libalgorithm_a-ConnectProcess.Tpo .deps/libalgorithm_a-ConnectProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-StringGraphGenerator.o -MD -MP -MF .deps/libalgorithm_a-StringGraphGenerator.Tpo -c -o libalgorithm_a-StringGraphGenerator.otest -f 'StringGraphGenerator.cpp' || echo './'StringGraphGenerator.cpp mv -f .deps/libalgorithm_a-StringGraphGenerator.Tpo .deps/libalgorithm_a-StringGraphGenerator.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-FMMergeProcess.o -MD -MP -MF .deps/libalgorithm_a-FMMergeProcess.Tpo -c -o libalgorithm_a-FMMergeProcess.otest -f 'FMMergeProcess.cpp' || echo './'FMMergeProcess.cpp mv -f .deps/libalgorithm_a-FMMergeProcess.Tpo .deps/libalgorithm_a-FMMergeProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-StatsProcess.o -MD -MP -MF .deps/libalgorithm_a-StatsProcess.Tpo -c -o libalgorithm_a-StatsProcess.otest -f 'StatsProcess.cpp' || echo './'StatsProcess.cpp mv -f .deps/libalgorithm_a-StatsProcess.Tpo .deps/libalgorithm_a-StatsProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ClusterProcess.o -MD -MP -MF .deps/libalgorithm_a-ClusterProcess.Tpo -c -o libalgorithm_a-ClusterProcess.otest -f 'ClusterProcess.cpp' || echo './'ClusterProcess.cpp mv -f .deps/libalgorithm_a-ClusterProcess.Tpo .deps/libalgorithm_a-ClusterProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ReadCluster.o -MD -MP -MF .deps/libalgorithm_a-ReadCluster.Tpo -c -o libalgorithm_a-ReadCluster.otest -f 'ReadCluster.cpp' || echo './'ReadCluster.cpp mv -f .deps/libalgorithm_a-ReadCluster.Tpo .deps/libalgorithm_a-ReadCluster.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-LRAlignment.o -MD -MP -MF .deps/libalgorithm_a-LRAlignment.Tpo -c -o libalgorithm_a-LRAlignment.otest -f 'LRAlignment.cpp' || echo './'LRAlignment.cpp mv -f .deps/libalgorithm_a-LRAlignment.Tpo .deps/libalgorithm_a-LRAlignment.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-StringThreader.o -MD -MP -MF .deps/libalgorithm_a-StringThreader.Tpo -c -o libalgorithm_a-StringThreader.otest -f 'StringThreader.cpp' || echo './'StringThreader.cpp mv -f .deps/libalgorithm_a-StringThreader.Tpo .deps/libalgorithm_a-StringThreader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ExtensionDP.o -MD -MP -MF .deps/libalgorithm_a-ExtensionDP.Tpo -c -o libalgorithm_a-ExtensionDP.otest -f 'ExtensionDP.cpp' || echo './'ExtensionDP.cpp mv -f .deps/libalgorithm_a-ExtensionDP.Tpo .deps/libalgorithm_a-ExtensionDP.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-HaplotypeBuilder.o -MD -MP -MF .deps/libalgorithm_a-HaplotypeBuilder.Tpo -c -o libalgorithm_a-HaplotypeBuilder.otest -f 'HaplotypeBuilder.cpp' || echo './'HaplotypeBuilder.cpp mv -f .deps/libalgorithm_a-HaplotypeBuilder.Tpo .deps/libalgorithm_a-HaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-GapFillProcess.o -MD -MP -MF .deps/libalgorithm_a-GapFillProcess.Tpo -c -o libalgorithm_a-GapFillProcess.otest -f 'GapFillProcess.cpp' || echo './'GapFillProcess.cpp mv -f .deps/libalgorithm_a-GapFillProcess.Tpo .deps/libalgorithm_a-GapFillProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-VariationBuilderCommon.o -MD -MP -MF .deps/libalgorithm_a-VariationBuilderCommon.Tpo -c -o libalgorithm_a-VariationBuilderCommon.otest -f 'VariationBuilderCommon.cpp' || echo './'VariationBuilderCommon.cpp mv -f .deps/libalgorithm_a-VariationBuilderCommon.Tpo .deps/libalgorithm_a-VariationBuilderCommon.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-KmerOverlaps.o -MD -MP -MF .deps/libalgorithm_a-KmerOverlaps.Tpo -c -o libalgorithm_a-KmerOverlaps.otest -f 'KmerOverlaps.cpp' || echo './'KmerOverlaps.cpp mv -f .deps/libalgorithm_a-KmerOverlaps.Tpo .deps/libalgorithm_a-KmerOverlaps.Po rm -f libalgorithm.a ar cru libalgorithm.a libalgorithm_a-OverlapAlgorithm.o libalgorithm_a-SearchSeed.o libalgorithm_a-OverlapBlock.o libalgorithm_a-SearchHistory.o libalgorithm_a-ErrorCorrectProcess.o libalgorithm_a-QCProcess.o libalgorithm_a-OverlapTools.o libalgorithm_a-DPAlignment.o libalgorithm_a-ConnectProcess.o libalgorithm_a-StringGraphGenerator.o libalgorithm_a-FMMergeProcess.o libalgorithm_a-StatsProcess.o libalgorithm_a-ClusterProcess.o libalgorithm_a-ReadCluster.o libalgorithm_a-LRAlignment.o libalgorithm_a-StringThreader.o libalgorithm_a-ExtensionDP.o libalgorithm_a-HaplotypeBuilder.o libalgorithm_a-GapFillProcess.o libalgorithm_a-VariationBuilderCommon.o libalgorithm_a-KmerOverlaps.o ranlib libalgorithm.a Making all in StringGraph g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGUtil.o -MD -MP -MF .deps/libstringgraph_a-SGUtil.Tpo -c -o libstringgraph_a-SGUtil.otest -f 'SGUtil.cpp' || echo './'SGUtil.cpp mv -f .deps/libstringgraph_a-SGUtil.Tpo .deps/libstringgraph_a-SGUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGAlgorithms.o -MD -MP -MF .deps/libstringgraph_a-SGAlgorithms.Tpo -c -o libstringgraph_a-SGAlgorithms.otest -f 'SGAlgorithms.cpp' || echo './'SGAlgorithms.cpp mv -f .deps/libstringgraph_a-SGAlgorithms.Tpo .deps/libstringgraph_a-SGAlgorithms.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGVisitors.o -MD -MP -MF .deps/libstringgraph_a-SGVisitors.Tpo -c -o libstringgraph_a-SGVisitors.otest -f 'SGVisitors.cpp' || echo './'SGVisitors.cpp mv -f .deps/libstringgraph_a-SGVisitors.Tpo .deps/libstringgraph_a-SGVisitors.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-CompleteOverlapSet.o -MD -MP -MF .deps/libstringgraph_a-CompleteOverlapSet.Tpo -c -o libstringgraph_a-CompleteOverlapSet.otest -f 'CompleteOverlapSet.cpp' || echo './'CompleteOverlapSet.cpp mv -f .deps/libstringgraph_a-CompleteOverlapSet.Tpo .deps/libstringgraph_a-CompleteOverlapSet.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-RemovalAlgorithm.o -MD -MP -MF .deps/libstringgraph_a-RemovalAlgorithm.Tpo -c -o libstringgraph_a-RemovalAlgorithm.otest -f 'RemovalAlgorithm.cpp' || echo './'RemovalAlgorithm.cpp mv -f .deps/libstringgraph_a-RemovalAlgorithm.Tpo .deps/libstringgraph_a-RemovalAlgorithm.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGSearch.o -MD -MP -MF .deps/libstringgraph_a-SGSearch.Tpo -c -o libstringgraph_a-SGSearch.otest -f 'SGSearch.cpp' || echo './'SGSearch.cpp mv -f .deps/libstringgraph_a-SGSearch.Tpo .deps/libstringgraph_a-SGSearch.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGWalk.o -MD -MP -MF .deps/libstringgraph_a-SGWalk.Tpo -c -o libstringgraph_a-SGWalk.otest -f 'SGWalk.cpp' || echo './'SGWalk.cpp mv -f .deps/libstringgraph_a-SGWalk.Tpo .deps/libstringgraph_a-SGWalk.Po rm -f libstringgraph.a ar cru libstringgraph.a libstringgraph_a-SGUtil.o libstringgraph_a-SGAlgorithms.o libstringgraph_a-SGVisitors.o libstringgraph_a-CompleteOverlapSet.o libstringgraph_a-RemovalAlgorithm.o libstringgraph_a-SGSearch.o libstringgraph_a-SGWalk.o ranlib libstringgraph.a Making all in Concurrency g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libconcurrency_a-OverlapProcess.o -MD -MP -MF .deps/libconcurrency_a-OverlapProcess.Tpo -c -o libconcurrency_a-OverlapProcess.otest -f 'OverlapProcess.cpp' || echo './'OverlapProcess.cpp mv -f .deps/libconcurrency_a-OverlapProcess.Tpo .deps/libconcurrency_a-OverlapProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libconcurrency_a-RmdupProcess.o -MD -MP -MF .deps/libconcurrency_a-RmdupProcess.Tpo -c -o libconcurrency_a-RmdupProcess.otest -f 'RmdupProcess.cpp' || echo './'RmdupProcess.cpp mv -f .deps/libconcurrency_a-RmdupProcess.Tpo .deps/libconcurrency_a-RmdupProcess.Po rm -f libconcurrency.a ar cru libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o ranlib libconcurrency.a Making all in SuffixTools g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-STCommon.o -MD -MP -MF .deps/libsuffixtools_a-STCommon.Tpo -c -o libsuffixtools_a-STCommon.otest -f 'STCommon.cpp' || echo './'STCommon.cpp mv -f .deps/libsuffixtools_a-STCommon.Tpo .deps/libsuffixtools_a-STCommon.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-Occurrence.o -MD -MP -MF .deps/libsuffixtools_a-Occurrence.Tpo -c -o libsuffixtools_a-Occurrence.otest -f 'Occurrence.cpp' || echo './'Occurrence.cpp mv -f .deps/libsuffixtools_a-Occurrence.Tpo .deps/libsuffixtools_a-Occurrence.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SuffixArray.o -MD -MP -MF .deps/libsuffixtools_a-SuffixArray.Tpo -c -o libsuffixtools_a-SuffixArray.otest -f 'SuffixArray.cpp' || echo './'SuffixArray.cpp mv -f .deps/libsuffixtools_a-SuffixArray.Tpo .deps/libsuffixtools_a-SuffixArray.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SuffixCompare.o -MD -MP -MF .deps/libsuffixtools_a-SuffixCompare.Tpo -c -o libsuffixtools_a-SuffixCompare.otest -f 'SuffixCompare.cpp' || echo './'SuffixCompare.cpp mv -f .deps/libsuffixtools_a-SuffixCompare.Tpo .deps/libsuffixtools_a-SuffixCompare.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-InverseSuffixArray.o -MD -MP -MF .deps/libsuffixtools_a-InverseSuffixArray.Tpo -c -o libsuffixtools_a-InverseSuffixArray.otest -f 'InverseSuffixArray.cpp' || echo './'InverseSuffixArray.cpp mv -f .deps/libsuffixtools_a-InverseSuffixArray.Tpo .deps/libsuffixtools_a-InverseSuffixArray.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SACAInducedCopying.o -MD -MP -MF .deps/libsuffixtools_a-SACAInducedCopying.Tpo -c -o libsuffixtools_a-SACAInducedCopying.otest -f 'SACAInducedCopying.cpp' || echo './'SACAInducedCopying.cpp mv -f .deps/libsuffixtools_a-SACAInducedCopying.Tpo .deps/libsuffixtools_a-SACAInducedCopying.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTAlgorithms.o -MD -MP -MF .deps/libsuffixtools_a-BWTAlgorithms.Tpo -c -o libsuffixtools_a-BWTAlgorithms.otest -f 'BWTAlgorithms.cpp' || echo './'BWTAlgorithms.cpp mv -f .deps/libsuffixtools_a-BWTAlgorithms.Tpo .deps/libsuffixtools_a-BWTAlgorithms.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTDiskConstruction.o -MD -MP -MF .deps/libsuffixtools_a-BWTDiskConstruction.Tpo -c -o libsuffixtools_a-BWTDiskConstruction.otest -f 'BWTDiskConstruction.cpp' || echo './'BWTDiskConstruction.cpp mv -f .deps/libsuffixtools_a-BWTDiskConstruction.Tpo .deps/libsuffixtools_a-BWTDiskConstruction.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTReader.o -MD -MP -MF .deps/libsuffixtools_a-BWTReader.Tpo -c -o libsuffixtools_a-BWTReader.otest -f 'BWTReader.cpp' || echo './'BWTReader.cpp mv -f .deps/libsuffixtools_a-BWTReader.Tpo .deps/libsuffixtools_a-BWTReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTWriter.o -MD -MP -MF .deps/libsuffixtools_a-BWTWriter.Tpo -c -o libsuffixtools_a-BWTWriter.otest -f 'BWTWriter.cpp' || echo './'BWTWriter.cpp mv -f .deps/libsuffixtools_a-BWTWriter.Tpo .deps/libsuffixtools_a-BWTWriter.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SAReader.o -MD -MP -MF .deps/libsuffixtools_a-SAReader.Tpo -c -o libsuffixtools_a-SAReader.otest -f 'SAReader.cpp' || echo './'SAReader.cpp mv -f .deps/libsuffixtools_a-SAReader.Tpo .deps/libsuffixtools_a-SAReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SAWriter.o -MD -MP -MF .deps/libsuffixtools_a-SAWriter.Tpo -c -o libsuffixtools_a-SAWriter.otest -f 'SAWriter.cpp' || echo './'SAWriter.cpp mv -f .deps/libsuffixtools_a-SAWriter.Tpo .deps/libsuffixtools_a-SAWriter.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-GapArray.o -MD -MP -MF .deps/libsuffixtools_a-GapArray.Tpo -c -o libsuffixtools_a-GapArray.otest -f 'GapArray.cpp' || echo './'GapArray.cpp mv -f .deps/libsuffixtools_a-GapArray.Tpo .deps/libsuffixtools_a-GapArray.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-RankProcess.o -MD -MP -MF .deps/libsuffixtools_a-RankProcess.Tpo -c -o libsuffixtools_a-RankProcess.otest -f 'RankProcess.cpp' || echo './'RankProcess.cpp mv -f .deps/libsuffixtools_a-RankProcess.Tpo .deps/libsuffixtools_a-RankProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SBWT.o -MD -MP -MF .deps/libsuffixtools_a-SBWT.Tpo -c -o libsuffixtools_a-SBWT.otest -f 'SBWT.cpp' || echo './'SBWT.cpp mv -f .deps/libsuffixtools_a-SBWT.Tpo .deps/libsuffixtools_a-SBWT.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-RLBWT.o -MD -MP -MF .deps/libsuffixtools_a-RLBWT.Tpo -c -o libsuffixtools_a-RLBWT.otest -f 'RLBWT.cpp' || echo './'RLBWT.cpp mv -f .deps/libsuffixtools_a-RLBWT.Tpo .deps/libsuffixtools_a-RLBWT.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTWriterBinary.o -MD -MP -MF .deps/libsuffixtools_a-BWTWriterBinary.Tpo -c -o libsuffixtools_a-BWTWriterBinary.otest -f 'BWTWriterBinary.cpp' || echo './'BWTWriterBinary.cpp mv -f .deps/libsuffixtools_a-BWTWriterBinary.Tpo .deps/libsuffixtools_a-BWTWriterBinary.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTReaderBinary.o -MD -MP -MF .deps/libsuffixtools_a-BWTReaderBinary.Tpo -c -o libsuffixtools_a-BWTReaderBinary.otest -f 'BWTReaderBinary.cpp' || echo './'BWTReaderBinary.cpp mv -f .deps/libsuffixtools_a-BWTReaderBinary.Tpo .deps/libsuffixtools_a-BWTReaderBinary.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTWriterAscii.o -MD -MP -MF .deps/libsuffixtools_a-BWTWriterAscii.Tpo -c -o libsuffixtools_a-BWTWriterAscii.otest -f 'BWTWriterAscii.cpp' || echo './'BWTWriterAscii.cpp mv -f .deps/libsuffixtools_a-BWTWriterAscii.Tpo .deps/libsuffixtools_a-BWTWriterAscii.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTReaderAscii.o -MD -MP -MF .deps/libsuffixtools_a-BWTReaderAscii.Tpo -c -o libsuffixtools_a-BWTReaderAscii.otest -f 'BWTReaderAscii.cpp' || echo './'BWTReaderAscii.cpp mv -f .deps/libsuffixtools_a-BWTReaderAscii.Tpo .deps/libsuffixtools_a-BWTReaderAscii.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTIntervalCache.o -MD -MP -MF .deps/libsuffixtools_a-BWTIntervalCache.Tpo -c -o libsuffixtools_a-BWTIntervalCache.otest -f 'BWTIntervalCache.cpp' || echo './'BWTIntervalCache.cpp mv -f .deps/libsuffixtools_a-BWTIntervalCache.Tpo .deps/libsuffixtools_a-BWTIntervalCache.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-QuickBWT.o -MD -MP -MF .deps/libsuffixtools_a-QuickBWT.Tpo -c -o libsuffixtools_a-QuickBWT.otest -f 'QuickBWT.cpp' || echo './'QuickBWT.cpp mv -f .deps/libsuffixtools_a-QuickBWT.Tpo .deps/libsuffixtools_a-QuickBWT.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SampledSuffixArray.o -MD -MP -MF .deps/libsuffixtools_a-SampledSuffixArray.Tpo -c -o libsuffixtools_a-SampledSuffixArray.otest -f 'SampledSuffixArray.cpp' || echo './'SampledSuffixArray.cpp mv -f .deps/libsuffixtools_a-SampledSuffixArray.Tpo .deps/libsuffixtools_a-SampledSuffixArray.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTCABauerCoxRosone.o -MD -MP -MF .deps/libsuffixtools_a-BWTCABauerCoxRosone.Tpo -c -o libsuffixtools_a-BWTCABauerCoxRosone.otest -f 'BWTCABauerCoxRosone.cpp' || echo './'BWTCABauerCoxRosone.cpp mv -f .deps/libsuffixtools_a-BWTCABauerCoxRosone.Tpo .deps/libsuffixtools_a-BWTCABauerCoxRosone.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTCARopebwt.o -MD -MP -MF .deps/libsuffixtools_a-BWTCARopebwt.Tpo -c -o libsuffixtools_a-BWTCARopebwt.otest -f 'BWTCARopebwt.cpp' || echo './'BWTCARopebwt.cpp mv -f .deps/libsuffixtools_a-BWTCARopebwt.Tpo .deps/libsuffixtools_a-BWTCARopebwt.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-PopulationIndex.o -MD -MP -MF .deps/libsuffixtools_a-PopulationIndex.Tpo -c -o libsuffixtools_a-PopulationIndex.otest -f 'PopulationIndex.cpp' || echo './'PopulationIndex.cpp mv -f .deps/libsuffixtools_a-PopulationIndex.Tpo .deps/libsuffixtools_a-PopulationIndex.Po rm -f libsuffixtools.a ar cru libsuffixtools.a libsuffixtools_a-STCommon.o libsuffixtools_a-Occurrence.o libsuffixtools_a-SuffixArray.o libsuffixtools_a-SuffixCompare.o libsuffixtools_a-InverseSuffixArray.o libsuffixtools_a-SACAInducedCopying.o libsuffixtools_a-BWTAlgorithms.o libsuffixtools_a-BWTDiskConstruction.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-SAReader.o libsuffixtools_a-SAWriter.o libsuffixtools_a-GapArray.o libsuffixtools_a-RankProcess.o libsuffixtools_a-SBWT.o libsuffixtools_a-RLBWT.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-BWTWriterBinary.o libsuffixtools_a-BWTReaderBinary.o libsuffixtools_a-BWTWriterAscii.o libsuffixtools_a-BWTReaderAscii.o libsuffixtools_a-BWTIntervalCache.o libsuffixtools_a-QuickBWT.o libsuffixtools_a-SampledSuffixArray.o libsuffixtools_a-BWTCABauerCoxRosone.o libsuffixtools_a-BWTCARopebwt.o libsuffixtools_a-PopulationIndex.o ranlib libsuffixtools.a Making all in Scaffold g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldVertex.o -MD -MP -MF .deps/libscaffold_a-ScaffoldVertex.Tpo -c -o libscaffold_a-ScaffoldVertex.otest -f 'ScaffoldVertex.cpp' || echo './'ScaffoldVertex.cpp mv -f .deps/libscaffold_a-ScaffoldVertex.Tpo .deps/libscaffold_a-ScaffoldVertex.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldEdge.o -MD -MP -MF .deps/libscaffold_a-ScaffoldEdge.Tpo -c -o libscaffold_a-ScaffoldEdge.otest -f 'ScaffoldEdge.cpp' || echo './'ScaffoldEdge.cpp mv -f .deps/libscaffold_a-ScaffoldEdge.Tpo .deps/libscaffold_a-ScaffoldEdge.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldGraph.o -MD -MP -MF .deps/libscaffold_a-ScaffoldGraph.Tpo -c -o libscaffold_a-ScaffoldGraph.otest -f 'ScaffoldGraph.cpp' || echo './'ScaffoldGraph.cpp mv -f .deps/libscaffold_a-ScaffoldGraph.Tpo .deps/libscaffold_a-ScaffoldGraph.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldVisitors.o -MD -MP -MF .deps/libscaffold_a-ScaffoldVisitors.Tpo -c -o libscaffold_a-ScaffoldVisitors.otest -f 'ScaffoldVisitors.cpp' || echo './'ScaffoldVisitors.cpp mv -f .deps/libscaffold_a-ScaffoldVisitors.Tpo .deps/libscaffold_a-ScaffoldVisitors.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldLink.o -MD -MP -MF .deps/libscaffold_a-ScaffoldLink.Tpo -c -o libscaffold_a-ScaffoldLink.otest -f 'ScaffoldLink.cpp' || echo './'ScaffoldLink.cpp mv -f .deps/libscaffold_a-ScaffoldLink.Tpo .deps/libscaffold_a-ScaffoldLink.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldRecord.o -MD -MP -MF .deps/libscaffold_a-ScaffoldRecord.Tpo -c -o libscaffold_a-ScaffoldRecord.otest -f 'ScaffoldRecord.cpp' || echo './'ScaffoldRecord.cpp mv -f .deps/libscaffold_a-ScaffoldRecord.Tpo .deps/libscaffold_a-ScaffoldRecord.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldGroup.o -MD -MP -MF .deps/libscaffold_a-ScaffoldGroup.Tpo -c -o libscaffold_a-ScaffoldGroup.otest -f 'ScaffoldGroup.cpp' || echo './'ScaffoldGroup.cpp mv -f .deps/libscaffold_a-ScaffoldGroup.Tpo .deps/libscaffold_a-ScaffoldGroup.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldSearch.o -MD -MP -MF .deps/libscaffold_a-ScaffoldSearch.Tpo -c -o libscaffold_a-ScaffoldSearch.otest -f 'ScaffoldSearch.cpp' || echo './'ScaffoldSearch.cpp mv -f .deps/libscaffold_a-ScaffoldSearch.Tpo .deps/libscaffold_a-ScaffoldSearch.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldWalk.o -MD -MP -MF .deps/libscaffold_a-ScaffoldWalk.Tpo -c -o libscaffold_a-ScaffoldWalk.otest -f 'ScaffoldWalk.cpp' || echo './'ScaffoldWalk.cpp mv -f .deps/libscaffold_a-ScaffoldWalk.Tpo .deps/libscaffold_a-ScaffoldWalk.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldAlgorithms.o -MD -MP -MF .deps/libscaffold_a-ScaffoldAlgorithms.Tpo -c -o libscaffold_a-ScaffoldAlgorithms.otest -f 'ScaffoldAlgorithms.cpp' || echo './'ScaffoldAlgorithms.cpp mv -f .deps/libscaffold_a-ScaffoldAlgorithms.Tpo .deps/libscaffold_a-ScaffoldAlgorithms.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldSequenceCollection.o -MD -MP -MF .deps/libscaffold_a-ScaffoldSequenceCollection.Tpo -c -o libscaffold_a-ScaffoldSequenceCollection.otest -f 'ScaffoldSequenceCollection.cpp' || echo './'ScaffoldSequenceCollection.cpp mv -f .deps/libscaffold_a-ScaffoldSequenceCollection.Tpo .deps/libscaffold_a-ScaffoldSequenceCollection.Po rm -f libscaffold.a ar cru libscaffold.a libscaffold_a-ScaffoldVertex.o libscaffold_a-ScaffoldEdge.o libscaffold_a-ScaffoldGraph.o libscaffold_a-ScaffoldVisitors.o libscaffold_a-ScaffoldLink.o libscaffold_a-ScaffoldRecord.o libscaffold_a-ScaffoldGroup.o libscaffold_a-ScaffoldSearch.o libscaffold_a-ScaffoldWalk.o libscaffold_a-ScaffoldAlgorithms.o libscaffold_a-ScaffoldSequenceCollection.o ranlib libscaffold.a Making all in GraphDiff g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelUtil.o -MD -MP -MF .deps/libgraphdiff_a-DindelUtil.Tpo -c -o libgraphdiff_a-DindelUtil.otest -f 'DindelUtil.cpp' || echo './'DindelUtil.cpp mv -f .deps/libgraphdiff_a-DindelUtil.Tpo .deps/libgraphdiff_a-DindelUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelRealignWindow.o -MD -MP -MF .deps/libgraphdiff_a-DindelRealignWindow.Tpo -c -o libgraphdiff_a-DindelRealignWindow.otest -f 'DindelRealignWindow.cpp' || echo './'DindelRealignWindow.cpp mv -f .deps/libgraphdiff_a-DindelRealignWindow.Tpo .deps/libgraphdiff_a-DindelRealignWindow.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelHMM.o -MD -MP -MF .deps/libgraphdiff_a-DindelHMM.Tpo -c -o libgraphdiff_a-DindelHMM.otest -f 'DindelHMM.cpp' || echo './'DindelHMM.cpp mv -f .deps/libgraphdiff_a-DindelHMM.Tpo .deps/libgraphdiff_a-DindelHMM.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-OverlapHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Tpo -c -o libgraphdiff_a-OverlapHaplotypeBuilder.otest -f 'OverlapHaplotypeBuilder.cpp' || echo './'OverlapHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Tpo .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-StringHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-StringHaplotypeBuilder.Tpo -c -o libgraphdiff_a-StringHaplotypeBuilder.otest -f 'StringHaplotypeBuilder.cpp' || echo './'StringHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-StringHaplotypeBuilder.Tpo .deps/libgraphdiff_a-StringHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DeBruijnHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Tpo -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.otest -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'DeBruijnHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Tpo .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-HapgenUtil.o -MD -MP -MF .deps/libgraphdiff_a-HapgenUtil.Tpo -c -o libgraphdiff_a-HapgenUtil.otest -f 'HapgenUtil.cpp' || echo './'HapgenUtil.cpp mv -f .deps/libgraphdiff_a-HapgenUtil.Tpo .deps/libgraphdiff_a-HapgenUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-VCFTester.o -MD -MP -MF .deps/libgraphdiff_a-VCFTester.Tpo -c -o libgraphdiff_a-VCFTester.otest -f 'VCFTester.cpp' || echo './'VCFTester.cpp mv -f .deps/libgraphdiff_a-VCFTester.Tpo .deps/libgraphdiff_a-VCFTester.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-GraphCompare.o -MD -MP -MF .deps/libgraphdiff_a-GraphCompare.Tpo -c -o libgraphdiff_a-GraphCompare.otest -f 'GraphCompare.cpp' || echo './'GraphCompare.cpp mv -f .deps/libgraphdiff_a-GraphCompare.Tpo .deps/libgraphdiff_a-GraphCompare.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-OverlapExtractorWithCorrection.o -MD -MP -MF .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo -c -o libgraphdiff_a-OverlapExtractorWithCorrection.otest -f 'OverlapExtractorWithCorrection.cpp' || echo './'OverlapExtractorWithCorrection.cpp mv -f .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Po rm -f libgraphdiff.a ar cru libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o ranlib libgraphdiff.a Making all in SGA g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-sga.o -MD -MP -MF .deps/sga-sga.Tpo -c -o sga-sga.otest -f 'sga.cpp' || echo './'sga.cpp mv -f .deps/sga-sga.Tpo .deps/sga-sga.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-index.o -MD -MP -MF .deps/sga-index.Tpo -c -o sga-index.otest -f 'index.cpp' || echo './'index.cpp mv -f .deps/sga-index.Tpo .deps/sga-index.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-overlap.o -MD -MP -MF .deps/sga-overlap.Tpo -c -o sga-overlap.otest -f 'overlap.cpp' || echo './'overlap.cpp mv -f .deps/sga-overlap.Tpo .deps/sga-overlap.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-assemble.o -MD -MP -MF .deps/sga-assemble.Tpo -c -o sga-assemble.otest -f 'assemble.cpp' || echo './'assemble.cpp mv -f .deps/sga-assemble.Tpo .deps/sga-assemble.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-correct.o -MD -MP -MF .deps/sga-correct.Tpo -c -o sga-correct.otest -f 'correct.cpp' || echo './'correct.cpp mv -f .deps/sga-correct.Tpo .deps/sga-correct.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-oview.o -MD -MP -MF .deps/sga-oview.Tpo -c -o sga-oview.otest -f 'oview.cpp' || echo './'oview.cpp mv -f .deps/sga-oview.Tpo .deps/sga-oview.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-preprocess.o -MD -MP -MF .deps/sga-preprocess.Tpo -c -o sga-preprocess.otest -f 'preprocess.cpp' || echo './'preprocess.cpp mv -f .deps/sga-preprocess.Tpo .deps/sga-preprocess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-rmdup.o -MD -MP -MF .deps/sga-rmdup.Tpo -c -o sga-rmdup.otest -f 'rmdup.cpp' || echo './'rmdup.cpp mv -f .deps/sga-rmdup.Tpo .deps/sga-rmdup.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-merge.o -MD -MP -MF .deps/sga-merge.Tpo -c -o sga-merge.otest -f 'merge.cpp' || echo './'merge.cpp mv -f .deps/sga-merge.Tpo .deps/sga-merge.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-subgraph.o -MD -MP -MF .deps/sga-subgraph.Tpo -c -o sga-subgraph.otest -f 'subgraph.cpp' || echo './'subgraph.cpp mv -f .deps/sga-subgraph.Tpo .deps/sga-subgraph.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-scaffold.o -MD -MP -MF .deps/sga-scaffold.Tpo -c -o sga-scaffold.otest -f 'scaffold.cpp' || echo './'scaffold.cpp mv -f .deps/sga-scaffold.Tpo .deps/sga-scaffold.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-scaffold2fasta.o -MD -MP -MF .deps/sga-scaffold2fasta.Tpo -c -o sga-scaffold2fasta.otest -f 'scaffold2fasta.cpp' || echo './'scaffold2fasta.cpp mv -f .deps/sga-scaffold2fasta.Tpo .deps/sga-scaffold2fasta.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-connect.o -MD -MP -MF .deps/sga-connect.Tpo -c -o sga-connect.otest -f 'connect.cpp' || echo './'connect.cpp mv -f .deps/sga-connect.Tpo .deps/sga-connect.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-walk.o -MD -MP -MF .deps/sga-walk.Tpo -c -o sga-walk.otest -f 'walk.cpp' || echo './'walk.cpp mv -f .deps/sga-walk.Tpo .deps/sga-walk.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-filter.o -MD -MP -MF .deps/sga-filter.Tpo -c -o sga-filter.otest -f 'filter.cpp' || echo './'filter.cpp mv -f .deps/sga-filter.Tpo .deps/sga-filter.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-stats.o -MD -MP -MF .deps/sga-stats.Tpo -c -o sga-stats.otest -f 'stats.cpp' || echo './'`stats.cpp mv -f .deps/sga-stats.Tpo .deps/sga-stats.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-fm-merge.o -MD -MP -MF .deps/sga-fm-merge.Tpo -c -o s

megancamilla commented 11 years ago

Sorry that didn't post properly... here's the error message

g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-variant-detectability.o -MD -MP -MF .deps/sga-variant-detectability.Tpo -c -o sga-variant-detectability.o test -f 'variant-detectability.cpp' || echo './'variant-detectability.cpp mv -f .deps/sga-variant-detectability.Tpo .deps/sga-variant-detectability.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-rewrite-evidence-bam.o -MD -MP -MF .deps/sga-rewrite-evidence-bam.Tpo -c -o sga-rewrite-evidence-bam.o test -f 'rewrite-evidence-bam.cpp' || echo './'rewrite-evidence-bam.cpp mv -f .deps/sga-rewrite-evidence-bam.Tpo .deps/sga-rewrite-evidence-bam.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-haplotype-filter.o -MD -MP -MF .deps/sga-haplotype-filter.Tpo -c -o sga-haplotype-filter.o test -f 'haplotype-filter.cpp' || echo './'haplotype-filter.cpp haplotype-filter.cpp: In function ‘double _haploidNonUniform(const std::vector<double, std::allocator >&, const std::vector<long unsigned int, std::allocator >&, double)’: haplotype-filter.cpp:494: error: ‘Stats’ has not been declared haplotype-filter.cpp:495: error: ‘Stats’ has not been declared haplotype-filter.cpp: In function ‘double LMDiploid(double, const std::vector<long unsigned int, std::allocator >&)’: haplotype-filter.cpp:546: error: ‘Stats’ has not been declared haplotype-filter.cpp:548: error: ‘Stats’ has not been declared haplotype-filter.cpp: In function ‘double _diploidNonUniform(const std::vector<double, std::allocator >&, const std::vector<long unsigned int, std::allocator >&, double)’: haplotype-filter.cpp:673: error: ‘Stats’ has not been declared haplotype-filter.cpp:675: error: ‘Stats’ has not been declared make[2]: * [sga-haplotype-filter.o] Error 1 make[1]: * [all-recursive] Error 1 make: *\ [all] Error 2

jts commented 11 years ago

Hi,

Thanks for the bug report. This was a subtle problem where the filename 'Stats.h' clashed with an OSX file so the wrong header was loaded. It is fixed in 930671f5a2c.