make: Entering directory '/Users/distiller/project/miniconda/conda-bld/quast_1634305262562/work/quast_libs/bedtools'
$CXXFLAGS is [-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem /Users/distiller/project/miniconda/conda-bld/quast_1634305262562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include -fdebug-prefix-map=/Users/distiller/project/miniconda/conda-bld/quast_1634305262562/work=/usr/local/src/conda/quast-5.0.2 -fdebug-prefix-map=/Users/distiller/project/miniconda/conda-bld/quast_1634305262562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla=/usr/local/src/conda-prefix -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver  -std=c++11]
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.27.1
CURRENT_VERSION  = 
Updating version file.
 * Creating BamTools API
- Building in src/utils/FileRecordTools
  * compiling FileRecordMgr.cpp
  * compiling FileRecordMergeMgr.cpp
- Building in FileReaders
  * compiling FileReader.cpp
  * compiling SingleLineDelimTextFileReader.cpp
  * compiling BamFileReader.cpp
  * compiling BufferedStreamMgr.cpp
  * compiling InputStreamMgr.cpp
- Building in Records
  * compiling Record.cpp
  * compiling EmptyRecord.cpp
  * compiling Bed3Interval.cpp
  * compiling Bed4Interval.cpp
  * compiling BedGraphInterval.cpp
  * compiling Bed5Interval.cpp
  * compiling Bed6Interval.cpp
  * compiling PlusFields.cpp
  * compiling BedPlusInterval.cpp
  * compiling Bed12Interval.cpp
  * compiling BamRecord.cpp
  * compiling GffRecord.cpp
  * compiling GffPlusRecord.cpp
  * compiling VcfRecord.cpp
  * compiling NoPosPlusRecord.cpp
  * compiling BlockMgr.cpp
  * compiling StrandQueue.cpp
  * compiling RecordMgr.cpp
  * compiling RecordList.cpp
  * compiling RecordKeyList.cpp
  * compiling RecordKeyVector.cpp
- Building in src/utils/FileRecordTools/FileReaders
make[1]: Nothing to be done for 'all'.
- Building in src/utils/FileRecordTools/Records
make[1]: Nothing to be done for 'all'.
- Building in src/utils/bedFile
  * compiling bedFile.cpp
- Building in src/utils/BinTree
  * compiling BinTree.cpp
- Building in src/utils/version
  * compiling version.cpp
- Building in src/utils/bedGraphFile
  * compiling bedGraphFile.cpp
- Building in src/utils/chromsweep
  * compiling chromsweep.cpp
- Building in src/utils/Contexts
  * compiling ContextBase.cpp
  * compiling ContextIntersect.cpp
  * compiling ContextFisher.cpp
  * compiling ContextMap.cpp
  * compiling ContextSample.cpp
  * compiling ContextSpacing.cpp
  * compiling ContextMerge.cpp
  * compiling ContextJaccard.cpp
  * compiling ContextClosest.cpp
  * compiling ContextSubtract.cpp
  * compiling ContextCoverage.cpp
  * compiling ContextComplement.cpp
  * compiling ContextGroupBy.cpp
- Building in src/utils/general
  * compiling ParseTools.cpp
  * compiling PushBackStreamBuf.cpp
  * compiling CompressionTools.cpp
  * compiling Tokenizer.cpp
  * compiling CommonHelp.cpp
- Building in src/utils/gzstream
g++ -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem /Users/distiller/project/miniconda/conda-bld/quast_1634305262562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include -fdebug-prefix-map=/Users/distiller/project/miniconda/conda-bld/quast_1634305262562/work=/usr/local/src/conda/quast-5.0.2 -fdebug-prefix-map=/Users/distiller/project/miniconda/conda-bld/quast_1634305262562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla=/usr/local/src/conda-prefix -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver  -std=c++11 -D_FORTIFY_SOURCE=2 -isystem /Users/distiller/project/miniconda/conda-bld/quast_1634305262562/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include -mmacosx-version-min=10.9 -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
  * compiling fileType.cpp
  * compiling FileRecordTypeChecker.cpp
- Building in src/utils/bedFilePE
  * compiling bedFilePE.cpp
- Building in src/utils/KeyListOps
  * compiling KeyListOps.cpp
  * compiling KeyListOpsMethods.cpp
- Building in src/utils/NewChromsweep
  * compiling NewChromsweep.cpp
  * compiling CloseSweep.cpp
- Building in src/utils/sequenceUtilities
  * compiling sequenceUtils.cpp
- Building in src/utils/tabFile
  * compiling tabFile.cpp
- Building in src/utils/BamTools
 * compiling BamAlignment.cpp
 * compiling BamMultiReader.cpp
 * compiling BamReader.cpp
 * compiling BamWriter.cpp
 * compiling SamHeader.cpp
 * compiling SamProgram.cpp
 * compiling SamProgramChain.cpp
 * compiling SamReadGroup.cpp
 * compiling SamReadGroupDictionary.cpp
 * compiling SamSequence.cpp
 * compiling SamSequenceDictionary.cpp
 * compiling BamHeader_p.cpp
 * compiling BamMultiReader_p.cpp
 * compiling BamRandomAccessController_p.cpp
 * compiling BamReader_p.cpp
 * compiling BamWriter_p.cpp
 * compiling BamIndexFactory_p.cpp
 * compiling BamStandardIndex_p.cpp
 * compiling BamToolsIndex_p.cpp
 * compiling BamDeviceFactory_p.cpp
 * compiling BamFile_p.cpp
 * compiling BamFtp_p.cpp
 * compiling BamHttp_p.cpp
 * compiling BamPipe_p.cpp
 * compiling BgzfStream_p.cpp
 * compiling ByteArray_p.cpp
 * compiling HostAddress_p.cpp
 * compiling HostInfo_p.cpp
 * compiling HttpHeader_p.cpp
 * compiling ILocalIODevice_p.cpp
 * compiling RollingBuffer_p.cpp
 * compiling TcpSocketEngine_p.cpp
 * compiling TcpSocketEngine_unix_p.cpp
 * compiling TcpSocket_p.cpp
 * compiling SamFormatParser_p.cpp
 * compiling SamFormatPrinter_p.cpp
 * compiling SamHeaderValidator_p.cpp
 * compiling BamException_p.cpp
 * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
ranlib lib/libbamtools.a
- Building in src/utils/BamTools-Ancillary
  * compiling BamAncillary.cpp
  * compiling BamAncillary.cpp
- Building in src/utils/BlockedIntervals
  * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
  * compiling Fasta.cpp
  * compiling split.cpp
- Building in src/utils/VectorOps
  * compiling VectorOps.cpp
- Building in src/utils/GenomeFile
  * compiling GenomeFile.cpp
  * compiling NewGenomeFile.cpp
- Building in src/utils/RecordOutputMgr
  * compiling RecordOutputMgr.cpp
- Building in src/utils/ToolBase
  * compiling ToolBase.cpp
- Building in src/utils/driver
  * compiling BedtoolsDriver.cpp
- Building in src/annotateBed
  * compiling annotateMain.cpp
  * compiling annotateBed.cpp
- Building in src/bamToBed
  * compiling bamToBed.cpp
- Building in src/bamToFastq
  * compiling bamToFastqMain.cpp
  * compiling bamToFastq.cpp
- Building in src/bedToBam
  * compiling bedToBam.cpp
- Building in src/bedpeToBam
  * compiling bedpeToBam.cpp
- Building in src/bedToIgv
  * compiling bedToIgv.cpp
- Building in src/bed12ToBed6
  * compiling bed12ToBed6.cpp
- Building in src/closestFile
  * compiling closestHelp.cpp
  * compiling closestFile.cpp
- Building in src/clusterBed
  * compiling clusterMain.cpp
  * compiling clusterBed.cpp
- Building in src/complementFile
  * compiling complementHelp.cpp
  * compiling complementFile.cpp
- Building in src/coverageFile
  * compiling coverageHelp.cpp
  * compiling coverageFile.cpp
- Building in src/expand
  * compiling expand.cpp
- Building in src/fastaFromBed
  * compiling fastaFromBedMain.cpp
  * compiling fastaFromBed.cpp
- Building in src/flankBed
  * compiling flankBedMain.cpp
  * compiling flankBed.cpp
- Building in src/genomeCoverageBed
  * compiling genomeCoverageMain.cpp
  * compiling genomeCoverageBed.cpp
- Building in src/getOverlap
  * compiling getOverlap.cpp
- Building in src/groupBy
  * compiling groupBy.cpp
  * compiling groupByHelp.cpp
- Building in src/intersectFile
  * compiling intersectHelp.cpp
  * compiling intersectFile.cpp
- Building in src/fisher
  * compiling fisherHelp.cpp
  * compiling fisher.cpp
  * compiling kfunc.cpp
- Building in src/jaccard
  * compiling jaccardHelp.cpp
  * compiling jaccard.cpp
- Building in src/linksBed
  * compiling linksMain.cpp
  * compiling linksBed.cpp
- Building in src/maskFastaFromBed
  * compiling maskFastaFromBedMain.cpp
  * compiling maskFastaFromBed.cpp
- Building in src/mapFile
  * compiling mapHelp.cpp
  * compiling mapFile.cpp
- Building in src/mergeFile
  * compiling mergeHelp.cpp
  * compiling mergeFile.cpp
- Building in src/multiBamCov
  * compiling multiBamCovMain.cpp
  * compiling multiBamCov.cpp
- Building in src/multiIntersectBed
  * compiling multiIntersectBedMain.cpp
  * compiling multiIntersectBed.cpp
- Building in src/nucBed
  * compiling nucBedMain.cpp
  * compiling nucBed.cpp
- Building in src/pairToBed
  * compiling pairToBedMain.cpp
  * compiling pairToBed.cpp
- Building in src/pairToPair
  * compiling pairToPairMain.cpp
  * compiling pairToPair.cpp
- Building in src/randomBed
  * compiling randomBedMain.cpp
  * compiling randomBed.cpp
- Building in src/regressTest
compiling RegressTest.cpp
compiling regressTestMain.cpp
- Building in src/reldist
  * compiling reldistMain.cpp
  * compiling reldist.cpp
- Building in src/sampleFile
  * compiling sampleHelp.cpp
  * compiling sampleFile.cpp
- Building in src/shiftBed
  * compiling shiftBedMain.cpp
  * compiling shiftBed.cpp
- Building in src/shuffleBed
  * compiling shuffleBedMain.cpp
  * compiling shuffleBed.cpp
- Building in src/slopBed
  * compiling slopBedMain.cpp
  * compiling slopBed.cpp
- Building in src/sortBed
  * compiling sortMain.cpp
  * compiling sortBed.cpp
- Building in src/spacingFile
  * compiling spacingHelp.cpp
  * compiling spacingFile.cpp
- Building in src/split
  * compiling splitBed.cpp
  * compiling splitBedMain.cpp
- Building in src/subtractFile
  * compiling subtractHelp.cpp
  * compiling subtractFile.cpp
- Building in src/tagBam
  * compiling tagBamMain.cpp
  * compiling tagBam.cpp
- Building in src/unionBedGraphs
  * compiling unionBedGraphsMain.cpp
  * compiling unionBedGraphs.cpp
- Building in src/windowBed
  * compiling windowMain.cpp
  * compiling windowBed.cpp
- Building in src/windowMaker
  * compiling windowMakerMain.cpp
  * compiling windowMaker.cpp
- Building main bedtools binary.
done.
- Creating executables for old CLI.
done.
make: Leaving directory '/Users/distiller/project/miniconda/conda-bld/quast_1634305262562/work/quast_libs/bedtools'
