Mock Version: 1.2.18 Mock Version: 1.2.18 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'], chrootPath='/var/lib/mock/f25-build-6175287-625614/root'env={'TERM': 'vt100', 'PS1': ' \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8'}printOutput=Falseuid=1000timeout=172800user='mockbuild'gid=425logger=shell=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'] with env {'TERM': 'vt100', 'PS1': ' \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8'} and shell False warning: Could not canonicalize hostname: buildhw-12.phx2.fedoraproject.org Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/BEDTools-2.26.0-2.fc25.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'], chrootPath='/var/lib/mock/f25-build-6175287-625614/root'env={'TERM': 'vt100', 'PS1': ' \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8'}printOutput=Falseuid=1000private_network=Trueuser='mockbuild'gid=425timeout=172800logger=shell=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'] with env {'TERM': 'vt100', 'PS1': ' \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.wQogMY + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bedtools2 + /usr/bin/gzip -dc /builddir/build/SOURCES/bedtools-2.26.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd bedtools2 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (BEDTools-double-parenthesis.patch): + echo 'Patch #0 (BEDTools-double-parenthesis.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .BEDTools.double-parenthesis --fuzz=0 patching file src/annotateBed/Makefile patching file src/bamToBed/Makefile patching file src/bamToFastq/Makefile patching file src/bed12ToBed6/Makefile patching file src/bedpeToBam/Makefile patching file src/bedToBam/Makefile patching file src/bedToIgv/Makefile patching file src/closestFile/Makefile patching file src/clusterBed/Makefile patching file src/complementFile/Makefile patching file src/coverageFile/Makefile patching file src/expand/Makefile patching file src/fastaFromBed/Makefile patching file src/fisher/Makefile patching file src/flankBed/Makefile patching file src/genomeCoverageBed/Makefile patching file src/getOverlap/Makefile patching file src/groupBy/Makefile patching file src/intersectFile/Makefile patching file src/jaccard/Makefile patching file src/linksBed/Makefile patching file src/mapFile/Makefile patching file src/maskFastaFromBed/Makefile patching file src/mergeFile/Makefile patching file src/multiBamCov/Makefile patching file src/multiIntersectBed/Makefile patching file src/nekSandbox1/Makefile patching file src/nucBed/Makefile patching file src/pairToBed/Makefile patching file src/pairToPair/Makefile patching file src/randomBed/Makefile patching file src/regressTest/Makefile patching file src/reldist/Makefile patching file src/sampleFile/Makefile patching file src/shiftBed/Makefile patching file src/shuffleBed/Makefile patching file src/slopBed/Makefile patching file src/sortBed/Makefile patching file src/spacingFile/Makefile patching file src/split/Makefile patching file src/subtractFile/Makefile patching file src/tagBam/Makefile patching file src/unionBedGraphs/Makefile patching file src/utils/BamTools-Ancillary/Makefile patching file src/utils/bedFile/Makefile patching file src/utils/bedFilePE/Makefile patching file src/utils/bedGraphFile/Makefile patching file src/utils/BinTree/Makefile patching file src/utils/BlockedIntervals/Makefile patching file src/utils/chromsweep/Makefile patching file src/utils/Contexts/Makefile patching file src/utils/driver/Makefile patching file src/utils/Fasta/Makefile patching file src/utils/FileRecordTools/FileReaders/Makefile patching file src/utils/FileRecordTools/Makefile patching file src/utils/FileRecordTools/Records/Makefile patching file src/utils/fileType/Makefile patching file src/utils/general/Makefile patching file src/utils/GenomeFile/Makefile patching file src/utils/gzstream/Makefile patching file src/utils/KeyListOps/Makefile patching file src/utils/NewChromsweep/Makefile patching file src/utils/RecordOutputMgr/Makefile patching file src/utils/sequenceUtilities/Makefile patching file src/utils/tabFile/Makefile patching file src/utils/ToolBase/Makefile patching file src/utils/VectorOps/Makefile patching file src/utils/version/Makefile patching file src/windowBed/Makefile patching file src/windowMaker/Makefile + rm -rf src/utils/curl + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.6RP0Z7 + umask 022 + cd /builddir/build/BUILD + cd bedtools2 + make -j16 'CXXFLAGS=-I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic' V=1 Building BEDTools: ========================================================= * Creating BamTools API DETECTED_VERSION = v2.26.0 CURRENT_VERSION = Updating version file. - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/FileReaders - Building in src/utils/FileRecordTools/Records - Building in src/utils/bedFile - Building in src/utils/BinTree - Building in src/utils/version - Building in src/utils/bedGraphFile - Building in src/utils/general - Building in src/utils/chromsweep * compiling FileReader.cpp - Building in src/utils/KeyListOps - Building in src/utils/Contexts - Building in src/utils/gzstream * compiling FileRecordMgr.cpp * compiling SingleLineDelimTextFileReader.cpp * compiling bedFile.cpp - Building in src/utils/NewChromsweep - Building in src/utils/bedFilePE * compiling Record.cpp * compiling bedGraphFile.cpp - Building in src/utils/fileType * compiling version.cpp * compiling BinTree.cpp g++ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -c -o ../../../obj//gzstream.o gzstream.C -I. * compiling bedFilePE.cpp * compiling ContextBase.cpp * compiling QuickString.cpp * compiling KeyListOps.cpp * compiling NewChromsweep.cpp * compiling chromsweep.cpp * compiling fileType.cpp * compiling ContextIntersect.cpp * compiling FileRecordTypeChecker.cpp * compiling ContextFisher.cpp - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp * compiling ParseTools.cpp * compiling EmptyRecord.cpp * compiling PushBackStreamBuf.cpp FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)': FileRecordTypeChecker.cpp:355:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; j < len; j++) { ~~^~~~~ - Building in src/utils/tabFile * compiling FileRecordMergeMgr.cpp * compiling tabFile.cpp * compiling BamFileReader.cpp * compiling CompressionTools.cpp * compiling Tokenizer.cpp - Building in src/utils/BamTools * compiling BamAlignment.cpp * compiling ContextMap.cpp * compiling ContextSample.cpp * compiling Bed3Interval.cpp * compiling CommonHelp.cpp - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp * compiling CloseSweep.cpp * compiling BamAncillary.cpp * compiling FileRecordMgr.cpp * compiling BufferedStreamMgr.cpp * compiling KeyListOpsMethods.cpp * compiling BamMultiReader.cpp - Building in src/utils/BlockedIntervals * compiling BlockedIntervals.cpp - Building in src/utils/Fasta * compiling Fasta.cpp * compiling Bed4Interval.cpp * compiling ContextSpacing.cpp * compiling ContextMerge.cpp * compiling ContextJaccard.cpp - Building in src/utils/VectorOps * compiling VectorOps.cpp * compiling InputStreamMgr.cpp Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)': Fasta.cpp:290:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), seqlen, file); ^ Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)': Fasta.cpp:332:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), (off_t) seqlen, file); ^ * compiling FileRecordMergeMgr.cpp * compiling BamReader.cpp * compiling BedGraphInterval.cpp - Building in src/utils/GenomeFile * compiling GenomeFile.cpp * compiling ContextClosest.cpp * compiling ContextSubtract.cpp * compiling ContextCoverage.cpp * compiling ContextComplement.cpp - Building in src/utils/RecordOutputMgr * compiling RecordOutputMgr.cpp GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()': GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable] long c2; ^~ - Building in src/utils/ToolBase * compiling BamWriter.cpp - Building in src/utils/driver * compiling ToolBase.cpp * compiling BedtoolsDriver.cpp - Building in src/annotateBed * compiling annotateMain.cpp * compiling Bed5Interval.cpp - Building in FileReaders make[2]: Nothing to be done for 'all'. - Building in Records * compiling Bed6Interval.cpp * compiling split.cpp * compiling SamHeader.cpp * compiling PlusFields.cpp * compiling ContextGroupBy.cpp annotateMain.cpp: In function 'int annotate_main(int, char**)': annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable] bool haveTitles = false; ^~~~~~~~~~ * compiling BedPlusInterval.cpp * compiling NewGenomeFile.cpp * compiling Bed12Interval.cpp * compiling annotateBed.cpp - Building in src/bamToBed * compiling bamToBed.cpp * compiling Bed6Interval.cpp * compiling BamRecord.cpp * compiling BamRecord.cpp - Building in src/bamToFastq * compiling bamToFastqMain.cpp * compiling bamToFastq.cpp - Building in src/bedToBam * compiling bedToBam.cpp * compiling SamProgram.cpp - Building in src/bedpeToBam * compiling bedpeToBam.cpp - Building in src/bedToIgv * compiling bedToIgv.cpp bamToBed.cpp: In function 'int bamtobed_main(int, char**)': bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable] bool useAlignmentScore = false; ^~~~~~~~~~~~~~~~~ * compiling GffRecord.cpp * compiling GffPlusRecord.cpp bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)': bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable] bool haveFastq2 = false; ^~~~~~~~~~ - Building in src/bed12ToBed6 * compiling SamProgramChain.cpp * compiling bed12ToBed6.cpp * compiling VcfRecord.cpp * compiling GffRecord.cpp - Building in src/closestFile * compiling closestHelp.cpp bedToBam.cpp: In function 'int bedtobam_main(int, char**)': bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ * compiling closestFile.cpp bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)': bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ - Building in src/clusterBed * compiling clusterMain.cpp * compiling VcfRecord.cpp * compiling NoPosPlusRecord.cpp * compiling BlockMgr.cpp * compiling SamReadGroup.cpp * compiling StrandQueue.cpp * compiling RecordMgr.cpp - Building in src/complementFile * compiling complementHelp.cpp * compiling NoPosPlusRecord.cpp * compiling RecordList.cpp - Building in src/coverageFile clusterMain.cpp: In function 'int cluster_main(int, char**)': clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] bool haveMaxDistance = false; ^~~~~~~~~~~~~~~ * compiling coverageHelp.cpp * compiling SamReadGroupDictionary.cpp * compiling complementFile.cpp * compiling clusterBed.cpp - Building in src/expand * compiling expand.cpp * compiling RecordKeyList.cpp * compiling coverageFile.cpp * compiling RecordList.cpp * compiling SamSequence.cpp * compiling RecordKeyVector.cpp * compiling RecordKeyVector.cpp * compiling SamSequenceDictionary.cpp - Building in src/fastaFromBed * compiling fastaFromBedMain.cpp * compiling fastaFromBed.cpp * compiling BamHeader_p.cpp - Building in src/flankBed * compiling flankBedMain.cpp * compiling flankBed.cpp * compiling BamMultiReader_p.cpp * compiling BamRandomAccessController_p.cpp * compiling BamReader_p.cpp - Building in src/genomeCoverageBed * compiling genomeCoverageMain.cpp - Building in src/getOverlap * compiling BamWriter_p.cpp * compiling getOverlap.cpp * compiling BamIndexFactory_p.cpp * compiling BamStandardIndex_p.cpp - Building in src/groupBy - Building in src/intersectFile * compiling groupBy.cpp * compiling intersectHelp.cpp * compiling BamToolsIndex_p.cpp * compiling BamDeviceFactory_p.cpp getOverlap.cpp: In function 'int getoverlap_main(int, char**)': getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable] bool haveColumns = false; ^~~~~~~~~~~ * compiling intersectFile.cpp - Building in src/fisher * compiling fisherHelp.cpp * compiling BamFile_p.cpp * compiling BamFtp_p.cpp - Building in src/jaccard * compiling jaccardHelp.cpp src/api/internal/index/BamStandardIndex_p.cpp: In member function 'void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)': src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) ) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling BamHttp_p.cpp * compiling BamPipe_p.cpp - Building in src/linksBed * compiling linksMain.cpp * compiling fisher.cpp * compiling jaccard.cpp - Building in src/maskFastaFromBed * compiling maskFastaFromBedMain.cpp * compiling BgzfStream_p.cpp * compiling ByteArray_p.cpp * compiling genomeCoverageBed.cpp src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendRequest(size_t)': src/api/internal/io/BamHttp_p.cpp:396:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize ); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ * compiling HostAddress_p.cpp * compiling groupByHelp.cpp - Building in src/mapFile * compiling mapHelp.cpp - Building in src/mergeFile * compiling mergeHelp.cpp * compiling HostInfo_p.cpp * compiling HttpHeader_p.cpp src/api/internal/io/HostAddress_p.cpp: In member function 'bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const': src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] return m_ip4Address < m_ip4Address; ~~~~~~~~~~~~~^~~~~~~~~~~~~~ src/api/internal/io/HostAddress_p.cpp: In member function 'std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const': src/api/internal/io/HostAddress_p.cpp:325:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if ( i != 0 ) ^~ src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if' ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | ^~ * compiling ILocalIODevice_p.cpp * compiling linksBed.cpp - Building in src/multiBamCov * compiling multiBamCovMain.cpp genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::CoverageBam(std::__cxx11::string)': genomeCoverageBed.cpp:322:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(end<_fragmentSize) { //sometimes fragmentSize is bigger :( ~~~^~~~~~~~~~~~~~ * compiling maskFastaFromBed.cpp * compiling RollingBuffer_p.cpp * compiling TcpSocketEngine_p.cpp - Building in src/multiIntersectBed * compiling multiIntersectBedMain.cpp * compiling TcpSocketEngine_unix_p.cpp * compiling mapFile.cpp * compiling TcpSocket_p.cpp * compiling SamFormatParser_p.cpp * compiling mergeFile.cpp * compiling kfunc.cpp * compiling SamFormatPrinter_p.cpp * compiling SamHeaderValidator_p.cpp multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)': multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable] bool haveBed = false; ^~~~~~~ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable] bool haveBams = false; ^~~~~~~~ multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ - Building in src/nucBed * compiling nucBedMain.cpp * compiling multiBamCov.cpp * compiling BamException_p.cpp multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)': multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ * compiling nucBed.cpp * compiling multiIntersectBed.cpp - Building in src/pairToBed - Building in src/pairToPair * compiling pairToBedMain.cpp * compiling pairToPairMain.cpp * compiling pairToPair.cpp * compiling pairToBed.cpp - Building in src/randomBed * compiling randomBedMain.cpp - Building in src/regressTest compiling RegressTest.cpp - Building in src/reldist * compiling reldistMain.cpp - Building in src/sampleFile * compiling sampleHelp.cpp * compiling sampleFile.cpp - Building in src/shiftBed * compiling shiftBedMain.cpp - Building in src/shuffleBed * compiling shuffleBedMain.cpp pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)': pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)': pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ * compiling shuffleBed.cpp pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)': pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable] bool found1 = false; ^~~~~~ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] bool found2 = false; ^~~~~~ * compiling reldist.cpp pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)': pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] CHRPOS spanLength = 0; ^~~~~~~~~~ pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)': pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] int spanLength = 0; ^~~~~~~~~~ - Building in src/slopBed - Building in src/sortBed * compiling slopBedMain.cpp * compiling sortMain.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 * compiling randomBed.cpp ranlib lib/libbamtools.a RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)': RegressTest.cpp:431:25: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ^ RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)': RegressTest.cpp:573:24: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ^ RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()': RegressTest.cpp:622:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ^ - Building in src/spacingFile * compiling spacingHelp.cpp * compiling spacingFile.cpp - Building in src/split * compiling splitBed.cpp * compiling splitBedMain.cpp * compiling sortBed.cpp * compiling shiftBed.cpp - Building in src/subtractFile * compiling subtractHelp.cpp - Building in src/tagBam - Building in src/unionBedGraphs * compiling tagBamMain.cpp * compiling unionBedGraphsMain.cpp - Building in src/windowBed * compiling windowMain.cpp * compiling windowBed.cpp * compiling subtractFile.cpp * compiling slopBed.cpp * compiling unionBedGraphs.cpp - Building in src/windowMaker * compiling windowMakerMain.cpp unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)': unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ * compiling windowMaker.cpp * compiling tagBam.cpp compiling regressTestMain.cpp - Building main bedtools binary. done. - Creating executables for old CLI. done. + cd docs + make clean html rm -rf _build/* sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v1.4.4 making output directory... WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead. loading pickled environment... not yet created loading intersphinx inventory from http://bedtools.readthedocs.org/en/latest/objects.inv... WARNING: intersphinx inventory 'http://bedtools.readthedocs.org/en/latest/objects.inv' not fetchable due to : building [mo]: targets for 0 po files that are out of date building [html]: targets for 52 source files that are out of date updating environment: 52 added, 0 changed, 0 removed reading sources... [ 1%] content/advanced-usage reading sources... [ 3%] content/bedtools-suite reading sources... [ 5%] content/example-usage reading sources... [ 7%] content/faq reading sources... [ 9%] content/general-usage reading sources... [ 11%] content/history reading sources... [ 13%] content/installation reading sources... [ 15%] content/overview reading sources... [ 17%] content/quick-start reading sources... [ 19%] content/related-tools reading sources... 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[100%] index /builddir/build/BUILD/bedtools2/docs/content/history.rst:107: WARNING: Enumerated list ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/history.rst:110: WARNING: Block quote ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/history.rst:112: WARNING: Enumerated list ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/history.rst:115: WARNING: Block quote ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/related-tools.rst:3: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... /builddir/build/BUILD/bedtools2/docs/content/tools/closest.rst:355: ERROR: Content block expected for the "note" directive; none found. /builddir/build/BUILD/bedtools2/docs/content/tools/cluster.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/tools/intersect.rst:67: WARNING: Block quote ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/tools/merge.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/tools/merge.rst:238: WARNING: Explicit markup ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/tools/merge.rst:244: WARNING: Explicit markup ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/tools/merge.rst:250: WARNING: Explicit markup ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/tools/pairtopair.rst:30: WARNING: Block quote ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/tools/random.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent. /builddir/build/BUILD/bedtools2/docs/content/tools/shift.rst:None: WARNING: image file not readable: content/tools/../images/tool-glyphs/shift-glyph.png done checking consistency... done preparing documents... 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The HTML pages are in _build/html. + cd .. + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.uPWWlY + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64 ++ dirname /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64 + cd bedtools2 + rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64 + mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/bin + install -m 0755 bin/annotateBed bin/bamToBed bin/bamToFastq bin/bed12ToBed6 bin/bedToBam bin/bedToIgv bin/bedpeToBam bin/bedtools bin/closestBed bin/clusterBed bin/complementBed bin/coverageBed bin/expandCols bin/fastaFromBed bin/flankBed bin/genomeCoverageBed bin/getOverlap bin/groupBy bin/intersectBed bin/linksBed bin/mapBed bin/maskFastaFromBed bin/mergeBed bin/multiBamCov bin/multiIntersectBed bin/nucBed bin/pairToBed bin/pairToPair bin/randomBed bin/shiftBed bin/shuffleBed bin/slopBed bin/sortBed bin/subtractBed bin/tagBam bin/unionBedGraphs bin/windowBed bin/windowMaker /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/bin + mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/BEDTools + cp -a genomes/ /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/BEDTools + cp -a data/ /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/BEDTools + find /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/BEDTools -type f -exec chmod 0644 '{}' ';' + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/bedtools2 extracting debug info from /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/bin/bedtools dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 3641 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Processing files: BEDTools-2.26.0-2.fc25.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.BF15G9 + umask 022 + cd /builddir/build/BUILD + cd bedtools2 + DOCDIR=/builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/doc/BEDTools + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/doc/BEDTools + cp -pr README.md /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/doc/BEDTools + cp -pr RELEASE_HISTORY /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/doc/BEDTools + cp -pr LICENSE /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/doc/BEDTools + cp -pr docs/ /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64/usr/share/doc/BEDTools + exit 0 Provides: BEDTools = 2.26.0-2.fc25 BEDTools(x86-64) = 2.26.0-2.fc25 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/sh libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: BEDTools-debuginfo-2.26.0-2.fc25.x86_64 Provides: BEDTools-debuginfo = 2.26.0-2.fc25 BEDTools-debuginfo(x86-64) = 2.26.0-2.fc25 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64 Wrote: /builddir/build/RPMS/BEDTools-2.26.0-2.fc25.x86_64.rpm Wrote: /builddir/build/RPMS/BEDTools-debuginfo-2.26.0-2.fc25.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.xQRaEI + umask 022 + cd /builddir/build/BUILD + cd bedtools2 + rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-2.fc25.x86_64 + exit 0 Child return code was: 0