Mock Version: 1.2.17 Mock Version: 1.2.17 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/BEDTools.spec'], user='mockbuild'shell=Falseenv={'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'HOSTNAME': 'mock', 'TERM': 'vt100'}gid=425chrootPath='/var/lib/mock/f25-build-6000474-618627/root'logger=timeout=172800printOutput=Falseuid=1000) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/BEDTools.spec'] with env {'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'HOSTNAME': 'mock', 'TERM': 'vt100'} and shell False warning: Could not canonicalize hostname: arm04-builder13.arm.fedoraproject.org Building target platforms: armv7hl Building for target armv7hl Wrote: /builddir/build/SRPMS/BEDTools-2.26.0-1.fc25.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/BEDTools.spec'], user='mockbuild'shell=Falseenv={'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'HOSTNAME': 'mock', 'TERM': 'vt100'}gid=425chrootPath='/var/lib/mock/f25-build-6000474-618627/root'logger=timeout=172800printOutput=Falseuid=1000private_network=True) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/BEDTools.spec'] with env {'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'HOSTNAME': 'mock', 'TERM': 'vt100'} and shell False Building target platforms: armv7hl Building for target armv7hl Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.09IVj6 + 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 . + rm -rf src/utils/curl + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.b8cj3Y + umask 022 + cd /builddir/build/BUILD + cd bedtools2 + make -j4 '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 -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard' V=1 Building BEDTools: ========================================================= DETECTED_VERSION = v2.26.0 CURRENT_VERSION = Updating version file. * Creating BamTools API - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/FileReaders - Building in src/utils/FileRecordTools/Records - Building in src/utils/bedFile * compiling FileRecordMgr.cpp * compiling Record.cpp * compiling bedFile.cpp * compiling FileReader.cpp * compiling SingleLineDelimTextFileReader.cpp * compiling EmptyRecord.cpp * compiling FileRecordMergeMgr.cpp * compiling Bed3Interval.cpp * compiling BamFileReader.cpp * compiling FileRecordMgr.cpp * compiling Bed4Interval.cpp * compiling BufferedStreamMgr.cpp * compiling BedGraphInterval.cpp * compiling FileRecordMergeMgr.cpp * compiling InputStreamMgr.cpp * compiling Bed5Interval.cpp - Building in FileReaders make[2]: Nothing to be done for 'all'. - Building in Records * compiling Bed6Interval.cpp * compiling Bed6Interval.cpp - Building in src/utils/BinTree * compiling BinTree.cpp * compiling PlusFields.cpp * compiling PlusFields.cpp * compiling BedPlusInterval.cpp - Building in src/utils/version * compiling version.cpp - Building in src/utils/bedGraphFile - Building in src/utils/chromsweep * compiling bedGraphFile.cpp * compiling chromsweep.cpp * compiling BedPlusInterval.cpp * compiling Bed12Interval.cpp - Building in src/utils/Contexts * compiling ContextBase.cpp * compiling Bed12Interval.cpp * compiling BamRecord.cpp * compiling BamRecord.cpp * compiling GffRecord.cpp * compiling ContextIntersect.cpp * compiling GffRecord.cpp * compiling GffPlusRecord.cpp - Building in src/utils/general * compiling QuickString.cpp * compiling GffPlusRecord.cpp * compiling VcfRecord.cpp * compiling ContextFisher.cpp * compiling ParseTools.cpp * compiling VcfRecord.cpp * compiling NoPosPlusRecord.cpp * compiling PushBackStreamBuf.cpp * compiling ContextMap.cpp * compiling CompressionTools.cpp * compiling NoPosPlusRecord.cpp * compiling BlockMgr.cpp * compiling Tokenizer.cpp * compiling ContextSample.cpp * compiling BlockMgr.cpp * compiling CommonHelp.cpp * compiling StrandQueue.cpp * compiling ContextSpacing.cpp * compiling StrandQueue.cpp - Building in src/utils/gzstream 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 -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -c -o ../../../obj//gzstream.o gzstream.C -I. * compiling RecordMgr.cpp * compiling RecordList.cpp * compiling ContextMerge.cpp * compiling RecordMgr.cpp * compiling RecordKeyList.cpp * compiling RecordKeyVector.cpp * compiling ContextJaccard.cpp * compiling ContextClosest.cpp * compiling ContextSubtract.cpp - Building in src/utils/fileType * compiling fileType.cpp * compiling ContextCoverage.cpp * compiling ContextComplement.cpp * compiling FileRecordTypeChecker.cpp * compiling RecordKeyList.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++) { ~~^~~~~ * compiling ContextGroupBy.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp - Building in src/utils/KeyListOps * compiling KeyListOps.cpp - Building in src/utils/NewChromsweep * compiling NewChromsweep.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 KeyListOpsMethods.cpp - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp * compiling CloseSweep.cpp * compiling BamMultiReader.cpp * compiling BamReader.cpp - Building in src/utils/BlockedIntervals * compiling BlockedIntervals.cpp * compiling BamWriter.cpp * compiling BamAncillary.cpp - Building in src/utils/Fasta * compiling Fasta.cpp * compiling SamHeader.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 SamProgram.cpp * compiling SamProgramChain.cpp - Building in src/utils/VectorOps * compiling VectorOps.cpp - Building in src/utils/GenomeFile * compiling GenomeFile.cpp * compiling split.cpp * compiling SamReadGroup.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; ^~ * compiling SamReadGroupDictionary.cpp - Building in src/utils/RecordOutputMgr * compiling RecordOutputMgr.cpp * compiling NewGenomeFile.cpp * compiling SamSequence.cpp - Building in src/utils/ToolBase * compiling ToolBase.cpp * compiling SamSequenceDictionary.cpp - Building in src/utils/driver * compiling BedtoolsDriver.cpp - Building in src/annotateBed * compiling annotateMain.cpp - Building in src/bamToBed * compiling bamToBed.cpp * compiling BamHeader_p.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; ^~~~~~~~~~ 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 annotateBed.cpp * compiling BamMultiReader_p.cpp - Building in src/bamToFastq * compiling bamToFastqMain.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; ^~~~~~~~~~ * compiling bamToFastq.cpp - Building in src/bedToBam * compiling bedToBam.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; ^~~~~~~~~~~ - Building in src/bedpeToBam * compiling bedpeToBam.cpp - Building in src/bedToIgv * compiling bedToIgv.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; ^~~~~~~~~~~ * compiling BamRandomAccessController_p.cpp - Building in src/bed12ToBed6 * compiling bed12ToBed6.cpp * compiling BamReader_p.cpp - Building in src/closestFile * compiling closestHelp.cpp - Building in src/clusterBed * compiling clusterMain.cpp - Building in src/complementFile * compiling complementHelp.cpp * compiling closestFile.cpp 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 complementFile.cpp * compiling clusterBed.cpp * compiling BamWriter_p.cpp - Building in src/coverageFile * compiling coverageHelp.cpp - Building in src/expand * compiling expand.cpp * compiling coverageFile.cpp * compiling BamIndexFactory_p.cpp - Building in src/fastaFromBed * compiling fastaFromBedMain.cpp * compiling BamStandardIndex_p.cpp - Building in src/flankBed * compiling flankBedMain.cpp * compiling fastaFromBed.cpp - Building in src/genomeCoverageBed * compiling genomeCoverageMain.cpp * compiling flankBed.cpp - Building in src/getOverlap * compiling getOverlap.cpp * compiling genomeCoverageBed.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 BamToolsIndex_p.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 :( ~~~^~~~~~~~~~~~~~ - Building in src/groupBy * compiling groupBy.cpp - Building in src/intersectFile * compiling intersectHelp.cpp * compiling intersectFile.cpp * compiling groupByHelp.cpp * compiling BamDeviceFactory_p.cpp - Building in src/fisher * compiling fisherHelp.cpp - Building in src/jaccard * compiling jaccardHelp.cpp - Building in src/linksBed * compiling linksMain.cpp * compiling BamFile_p.cpp * compiling fisher.cpp * compiling jaccard.cpp * compiling BamFtp_p.cpp * compiling linksBed.cpp - Building in src/maskFastaFromBed * compiling maskFastaFromBedMain.cpp * compiling kfunc.cpp - Building in src/mapFile * compiling mapHelp.cpp * compiling BamHttp_p.cpp * compiling maskFastaFromBed.cpp - Building in src/mergeFile * compiling mergeHelp.cpp * compiling mapFile.cpp * compiling mergeFile.cpp * compiling BamPipe_p.cpp - Building in src/multiBamCov * compiling multiBamCovMain.cpp * compiling BgzfStream_p.cpp - Building in src/multiIntersectBed * compiling multiIntersectBedMain.cpp - Building in src/nucBed * compiling nucBedMain.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; ^~~~~~~~~~~~ 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 multiBamCov.cpp * compiling nucBed.cpp * compiling ByteArray_p.cpp * compiling multiIntersectBed.cpp * compiling HostAddress_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) | ^~ - Building in src/pairToBed * compiling pairToBedMain.cpp - Building in src/pairToPair * compiling pairToPairMain.cpp 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 HostInfo_p.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; ^~~~~~~~~~~~ * compiling pairToPair.cpp * compiling pairToBed.cpp - Building in src/randomBed * compiling randomBedMain.cpp * compiling HttpHeader_p.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; ^~~~~~ 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; ^~~~~~~~~~ * compiling randomBed.cpp - Building in src/regressTest compiling RegressTest.cpp * compiling ILocalIODevice_p.cpp * compiling RollingBuffer_p.cpp 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/reldist * compiling reldistMain.cpp * compiling TcpSocketEngine_p.cpp * compiling TcpSocketEngine_unix_p.cpp * compiling reldist.cpp * compiling TcpSocket_p.cpp - Building in src/sampleFile * compiling sampleHelp.cpp * compiling sampleFile.cpp compiling regressTestMain.cpp reldist.cpp: In member function 'void RelativeDistance::ReportDistanceSummary()': reldist.cpp:73:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'unsigned int' [-Wformat=] (float) freqItr->second / (float) _tot_queries); ^ reldist.cpp:73:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=] * compiling SamFormatParser_p.cpp - Building in src/shiftBed * compiling shiftBedMain.cpp - Building in src/shuffleBed * compiling shuffleBedMain.cpp - Building in src/slopBed * compiling slopBedMain.cpp * compiling shiftBed.cpp * compiling SamFormatPrinter_p.cpp * compiling shuffleBed.cpp * compiling slopBed.cpp - Building in src/sortBed * compiling sortMain.cpp slopBed.cpp: In member function 'void BedSlop::AddSlop(BED&)': slopBed.cpp:85:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ((int)bed.end + (long)_leftSlop) <= chromSize ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ slopBed.cpp:107:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ((int)bed.end + (long)_rightSlop) <= chromSize ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ - Building in src/spacingFile * compiling spacingHelp.cpp * compiling sortBed.cpp * compiling SamHeaderValidator_p.cpp * compiling spacingFile.cpp - Building in src/split * compiling splitBed.cpp - Building in src/subtractFile * compiling subtractHelp.cpp * compiling BamException_p.cpp * compiling subtractFile.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/tagBam * compiling tagBamMain.cpp - Building in src/unionBedGraphs * compiling unionBedGraphsMain.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 tagBam.cpp * compiling unionBedGraphs.cpp - Building in src/windowBed * compiling windowMain.cpp - Building in src/windowMaker * compiling windowMakerMain.cpp * compiling windowMaker.cpp * compiling splitBedMain.cpp * compiling windowBed.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... [ 21%] content/tips-and-tricks reading sources... [ 23%] content/tools/annotate reading sources... [ 25%] content/tools/bamtobed reading sources... [ 26%] content/tools/bamtofastq reading sources... [ 28%] content/tools/bed12tobed6 reading sources... [ 30%] content/tools/bedpetobam reading sources... [ 32%] content/tools/bedtobam reading sources... [ 34%] content/tools/closest reading sources... [ 36%] content/tools/cluster reading sources... [ 38%] content/tools/complement reading sources... [ 40%] content/tools/coverage reading sources... [ 42%] content/tools/expand reading sources... [ 44%] content/tools/fisher reading sources... [ 46%] content/tools/flank reading sources... [ 48%] content/tools/genomecov reading sources... [ 50%] content/tools/getfasta reading sources... [ 51%] content/tools/groupby reading sources... [ 53%] content/tools/igv reading sources... [ 55%] content/tools/intersect reading sources... [ 57%] content/tools/jaccard 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". /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. looking for now-outdated files... none found pickling environment... /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... WARNING: html_favicon is not an .ico file done writing output... [ 1%] content/advanced-usage writing output... [ 3%] content/bedtools-suite writing output... [ 5%] content/example-usage writing output... [ 7%] content/faq /builddir/build/BUILD/bedtools2/docs/content/faq.rst:18: WARNING: Could not lex literal_block as "bash". Highlighting skipped. /builddir/build/BUILD/bedtools2/docs/content/faq.rst:67: WARNING: Could not lex literal_block as "bash". Highlighting skipped. writing output... [ 9%] content/general-usage writing output... [ 11%] content/history writing output... [ 13%] content/installation writing output... [ 15%] content/overview writing output... [ 17%] content/quick-start writing output... [ 19%] content/related-tools writing output... [ 21%] content/tips-and-tricks writing output... [ 23%] content/tools/annotate writing output... [ 25%] content/tools/bamtobed writing output... [ 26%] content/tools/bamtofastq writing output... [ 28%] content/tools/bed12tobed6 writing output... [ 30%] content/tools/bedpetobam writing output... [ 32%] content/tools/bedtobam writing output... [ 34%] content/tools/closest writing output... [ 36%] content/tools/cluster writing output... [ 38%] content/tools/complement writing output... [ 40%] content/tools/coverage writing output... [ 42%] content/tools/expand writing output... [ 44%] content/tools/fisher writing output... [ 46%] content/tools/flank writing output... [ 48%] content/tools/genomecov writing output... [ 50%] content/tools/getfasta writing output... [ 51%] content/tools/groupby writing output... [ 53%] content/tools/igv writing output... [ 55%] content/tools/intersect writing output... [ 57%] content/tools/jaccard writing output... [ 59%] content/tools/links writing output... [ 61%] content/tools/makewindows writing output... [ 63%] content/tools/map writing output... [ 65%] content/tools/maskfasta writing output... [ 67%] content/tools/merge writing output... [ 69%] content/tools/multicov writing output... [ 71%] content/tools/multiinter writing output... [ 73%] content/tools/nuc writing output... [ 75%] content/tools/overlap writing output... [ 76%] content/tools/pairtobed writing output... [ 78%] content/tools/pairtopair writing output... [ 80%] content/tools/random writing output... [ 82%] content/tools/reldist writing output... [ 84%] content/tools/shift writing output... [ 86%] content/tools/shuffle writing output... [ 88%] content/tools/slop writing output... [ 90%] content/tools/sort writing output... [ 92%] content/tools/subtract writing output... [ 94%] content/tools/tag writing output... [ 96%] content/tools/unionbedg writing output... [ 98%] content/tools/window writing output... [100%] index generating indices.../builddir/build/BUILD/bedtools2/docs/content/related-tools.rst:79: WARNING: undefined label: bedtools:map (if the link has no caption the label must precede a section header) genindex writing additional pages... search copying images... [ 3%] content/tools/../images/tool-glyphs/merge-glyph.png copying images... [ 7%] content/tools/../images/tool-glyphs/map-glyph.png copying images... [ 11%] content/images/github-zip-button.png copying images... [ 15%] content/images/speed-comparo.png copying images... [ 19%] content/tools/../images/tool-glyphs/closest-glyph.png copying images... [ 23%] content/tools/../images/tool-glyphs/jaccard-glyph.png copying images... [ 26%] content/tools/../images/tool-glyphs/subtract-glyph.png copying images... [ 30%] content/images/bedtoolsMenu.png copying images... [ 34%] content/tools/../images/tool-glyphs/intersect-glyph.png copying images... [ 38%] content/tools/../images/tool-glyphs/complement-glyph.png copying images... 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The HTML pages are in _build/html. + cd .. + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.sy6QS8 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm '!=' / ']' + rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm ++ dirname /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm + cd bedtools2 + rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm + mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/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-2.26.0-1.fc25.arm/usr/bin + mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/BEDTools + cp -a genomes/ /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/BEDTools + cp -a data/ /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/BEDTools + find /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/BEDTools -type f -exec chmod 0644 '{}' ';' + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip /usr/bin/strip + /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump + /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-2.26.0-1.fc25.armv7hl Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.XKsWJ3 + umask 022 + cd /builddir/build/BUILD + cd bedtools2 + DOCDIR=/builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/doc/BEDTools + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/doc/BEDTools + cp -pr README.md /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/doc/BEDTools + cp -pr RELEASE_HISTORY /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/doc/BEDTools + cp -pr LICENSE /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/doc/BEDTools + cp -pr docs/ /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm/usr/share/doc/BEDTools + exit 0 Provides: BEDTools = 2.26.0-1.fc25 BEDTools(armv7hl-32) = 2.26.0-1.fc25 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/sh ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libc.so.6 libc.so.6(GLIBC_2.15) libc.so.6(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libm.so.6 libm.so.6(GLIBC_2.23) libm.so.6(GLIBC_2.4) libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.8) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(CXXABI_ARM_1.3.3) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.9) libz.so.1 rtld(GNU_HASH) Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm Wrote: /builddir/build/RPMS/BEDTools-2.26.0-1.fc25.armv7hl.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.ykXE8o + umask 022 + cd /builddir/build/BUILD + cd bedtools2 + rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-1.fc25.arm + exit 0 Child return code was: 0