Mock Version: 1.3.4
Mock Version: 1.3.4
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'], chrootPath='/var/lib/mock/f28-build-11735371-873015/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f400d190e48>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/BEDTools-2.26.0-7.fc28.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/f28-build-11735371-873015/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f400d190e48>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', '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.hfFwlp
+ 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 .
+ /usr/bin/cat /builddir/build/SOURCES/BEDTools-double-parenthesis.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch
+ /usr/bin/cat /builddir/build/SOURCES/0001-Ditch-bizarre-inclusion-then-mock-out-of-matplotlib-.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch
+ rm -rf src/utils/curl
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.loNqUA
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2
+ make -j6 'CXXFLAGS=-I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -mcet -fcf-protection' 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/Records
- Building in src/utils/BinTree
- Building in src/utils/bedFile
- Building in src/utils/version
- Building in src/utils/FileRecordTools/FileReaders
  * compiling FileRecordMgr.cpp
  * compiling Record.cpp
  * compiling bedFile.cpp
  * compiling BinTree.cpp
  * compiling version.cpp
  * compiling FileReader.cpp
- Building in src/utils/bedGraphFile
  * compiling bedGraphFile.cpp
  * compiling EmptyRecord.cpp
  * compiling SingleLineDelimTextFileReader.cpp
- Building in src/utils/chromsweep
  * compiling chromsweep.cpp
  * compiling FileRecordMergeMgr.cpp
  * compiling FileRecordMgr.cpp
  * compiling Bed3Interval.cpp
  * compiling BamFileReader.cpp
- Building in FileReaders
  * compiling BufferedStreamMgr.cpp
  * compiling Bed4Interval.cpp
  * compiling FileRecordMergeMgr.cpp
  * compiling InputStreamMgr.cpp
  * compiling BedGraphInterval.cpp
  * compiling BufferedStreamMgr.cpp
- Building in Records
  * compiling Bed5Interval.cpp
- Building in src/utils/Contexts
- Building in src/utils/general
  * compiling ContextBase.cpp
  * compiling QuickString.cpp
  * compiling ParseTools.cpp
  * compiling ContextIntersect.cpp
  * compiling Bed5Interval.cpp
  * compiling PushBackStreamBuf.cpp
  * compiling CompressionTools.cpp
  * compiling Bed6Interval.cpp
  * compiling Tokenizer.cpp
  * compiling CommonHelp.cpp
  * compiling ContextFisher.cpp
  * compiling PlusFields.cpp
  * compiling BedPlusInterval.cpp
- Building in src/utils/gzstream
  * compiling ContextMap.cpp
  * compiling ContextSample.cpp
  * compiling Bed6Interval.cpp
  * compiling Bed12Interval.cpp
  * compiling ContextSpacing.cpp
  * compiling ContextMerge.cpp
- Building in src/utils/fileType
g++ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -mcet -fcf-protection  -c -o ../../../obj//gzstream.o gzstream.C -I.
  * compiling fileType.cpp
  * compiling ContextJaccard.cpp
  * compiling ContextClosest.cpp
  * compiling ContextSubtract.cpp
  * compiling FileRecordTypeChecker.cpp
- Building in src/utils/KeyListOps
- Building in src/utils/bedFilePE
  * compiling bedFilePE.cpp
  * compiling KeyListOps.cpp
  * compiling ContextCoverage.cpp
FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)':
FileRecordTypeChecker.cpp:355:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   for (int j=0; j < len; j++) {
                 ~~^~~~~
  * compiling ContextComplement.cpp
  * compiling ContextGroupBy.cpp
- Building in src/utils/NewChromsweep
  * compiling NewChromsweep.cpp
  * compiling KeyListOpsMethods.cpp
  * compiling CloseSweep.cpp
  * compiling Bed12Interval.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 BamRecord.cpp
 * compiling BamMultiReader.cpp
- Building in src/utils/BamTools-Ancillary
  * compiling BamAncillary.cpp
  * compiling GffRecord.cpp
 * compiling BamReader.cpp
- Building in src/utils/BlockedIntervals
  * compiling BlockedIntervals.cpp
- Building in src/utils/Fasta
  * compiling Fasta.cpp
Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)':
Fasta.cpp:290:14: 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:332:14: 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 BamAncillary.cpp
- Building in src/utils/VectorOps
  * compiling VectorOps.cpp
  * compiling split.cpp
- Building in src/utils/GenomeFile
  * compiling GenomeFile.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;
                          ^~
  * compiling NewGenomeFile.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 BamRecord.cpp
 * compiling BamWriter.cpp
  * compiling annotateBed.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 SamHeader.cpp
 * compiling SamProgram.cpp
- Building in src/bamToBed
  * compiling bamToBed.cpp
 * compiling SamProgramChain.cpp
 * compiling SamReadGroup.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 SamReadGroupDictionary.cpp
 * compiling SamSequence.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
- Building in src/bedpeToBam
  * compiling bedpeToBam.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;
          ^~~~~~~~~~~
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 GffPlusRecord.cpp
- Building in src/bedToIgv
  * compiling bedToIgv.cpp
  * compiling VcfRecord.cpp
  * compiling NoPosPlusRecord.cpp
  * compiling BlockMgr.cpp
  * compiling GffPlusRecord.cpp
- Building in src/bed12ToBed6
  * compiling bed12ToBed6.cpp
  * compiling StrandQueue.cpp
- Building in src/closestFile
  * compiling closestHelp.cpp
  * compiling closestFile.cpp
- Building in src/clusterBed
  * compiling clusterMain.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 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
  * compiling RecordMgr.cpp
- Building in src/genomeCoverageBed
  * compiling genomeCoverageMain.cpp
  * compiling genomeCoverageBed.cpp
genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::CoverageBam(std::__cxx11::string)':
genomeCoverageBed.cpp:322:23: warning: comparison of integer expressions of different signedness: 'CHRPOS' {aka 'unsigned int'} and 'int' [-Wsign-compare]
                 if(end<_fragmentSize) { //sometimes fragmentSize is bigger :(
                    ~~~^~~~~~~~~~~~~~
- Building in src/getOverlap
  * compiling getOverlap.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;
          ^~~~~~~~~~~
- 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
  * compiling RecordList.cpp
  * compiling RecordKeyList.cpp
- Building in src/maskFastaFromBed
  * compiling maskFastaFromBedMain.cpp
  * compiling maskFastaFromBed.cpp
  * compiling RecordKeyVector.cpp
- Building in src/mapFile
  * compiling mapHelp.cpp
 * compiling SamSequenceDictionary.cpp
 * compiling BamHeader_p.cpp
- Building in src/mergeFile
  * compiling mergeHelp.cpp
  * compiling mapFile.cpp
  * compiling mergeFile.cpp
 * compiling BamMultiReader_p.cpp
 * compiling BamRandomAccessController_p.cpp
- Building in src/multiBamCov
  * compiling multiBamCovMain.cpp
- Building in src/multiIntersectBed
  * compiling multiIntersectBedMain.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;
          ^~~~~~~~~~~~
 * compiling BamReader_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 multiIntersectBed.cpp
  * compiling StrandQueue.cpp
 * compiling BamWriter_p.cpp
  * compiling multiBamCov.cpp
- Building in src/nucBed
  * compiling nucBedMain.cpp
 * compiling BamIndexFactory_p.cpp
- Building in src/pairToBed
  * compiling pairToBedMain.cpp
  * compiling nucBed.cpp
  * compiling pairToBed.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;
          ^~~~~~~~~~~~
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, 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 BamStandardIndex_p.cpp
 * compiling BamToolsIndex_p.cpp
- Building in src/pairToPair
- Building in src/randomBed
- Building in src/regressTest
  * compiling pairToPairMain.cpp
compiling RegressTest.cpp
  * compiling randomBedMain.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 of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare]
     if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
          ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
          ^~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
RegressTest.cpp:431:8: 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:573:7: 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:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(sLine, 4192, fp);
   ~~~~~^~~~~~~~~~~~~~~~~
  * compiling randomBed.cpp
  * compiling pairToPair.cpp
- Building in src/reldist
  * compiling reldistMain.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;
              ^~~~~~
- Building in src/sampleFile
  * compiling sampleHelp.cpp
compiling regressTestMain.cpp
  * compiling sampleFile.cpp
  * compiling reldist.cpp
 * compiling BamDeviceFactory_p.cpp
 * compiling BamFile_p.cpp
- Building in src/shiftBed
  * compiling shiftBedMain.cpp
  * compiling shiftBed.cpp
- Building in src/shuffleBed
  * compiling shuffleBedMain.cpp
 * compiling BamFtp_p.cpp
- Building in src/slopBed
  * compiling slopBedMain.cpp
  * compiling shuffleBed.cpp
 * compiling BamHttp_p.cpp
 * compiling BamPipe_p.cpp
  * compiling slopBed.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 of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare]
     return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize );
              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
 * compiling BgzfStream_p.cpp
 * compiling ByteArray_p.cpp
- Building in src/sortBed
  * compiling sortMain.cpp
 * compiling HostAddress_p.cpp
- Building in src/spacingFile
- Building in src/split
  * compiling spacingHelp.cpp
  * compiling splitBed.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 'void BamTools::Internal::HostAddress::Clear()':
src/api/internal/io/HostAddress_p.cpp:283:49: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct BamTools::Internal::IPv6Address'; use assignment or value-initialization instead [-Wclass-memaccess]
     memset(&m_ip6Address, 0, sizeof(IPv6Address));
                                                 ^
In file included from src/api/internal/io/HostAddress_p.cpp:10:
src/api/internal/io/HostAddress_p.h:30:8: note: 'struct BamTools::Internal::IPv6Address' declared here
 struct IPv6Address {
        ^~~~~~~~~~~
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 were guarded by the 'if'
                 ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
                 ^~
  * compiling spacingFile.cpp
  * compiling splitBedMain.cpp
- Building in src/subtractFile
  * compiling subtractHelp.cpp
  * compiling subtractFile.cpp
  * compiling sortBed.cpp
 * compiling HostInfo_p.cpp
- Building in src/tagBam
  * compiling tagBamMain.cpp
- Building in src/unionBedGraphs
  * compiling unionBedGraphsMain.cpp
 * compiling HttpHeader_p.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 ILocalIODevice_p.cpp
 * compiling RollingBuffer_p.cpp
  * compiling unionBedGraphs.cpp
 * compiling TcpSocketEngine_p.cpp
  * compiling tagBam.cpp
- Building in src/windowBed
  * compiling windowMain.cpp
 * compiling TcpSocketEngine_unix_p.cpp
- Building in src/windowMaker
  * compiling windowMakerMain.cpp
 * compiling SamFormatParser_p.cpp
 * compiling TcpSocket_p.cpp
  * compiling windowBed.cpp
  * compiling windowMaker.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 main bedtools binary.
done.
- Creating executables for old CLI.
DEPRECATION WARNING: python2 invoked with /usr/bin/python.
    Use /usr/bin/python3 or /usr/bin/python2
    /usr/bin/python will be removed or switched to Python 3 in the future.
    If you cannot make the switch now, please follow instructions at https://fedoraproject.org/wiki/Changes/Avoid_usr_bin_python_in_RPM_Build#Quick_Opt-Out
done.
+ cd docs
+ make clean html
rm -rf _build/*
sphinx-build -b html -d _build/doctrees   . _build/html
Running Sphinx v1.6.6
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 <class 'requests.exceptions.ConnectionError'>: HTTPConnectionPool(host='bedtools.readthedocs.org', port=80): Max retries exceeded with url: /en/latest/objects.inv (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fe6f03b9a50>: Failed to establish a new connection: [Errno -2] Name or service not known',))
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... [ 59%] content/tools/links
reading sources... [ 61%] content/tools/makewindows
reading sources... [ 63%] content/tools/map
reading sources... [ 65%] content/tools/maskfasta
reading sources... [ 67%] content/tools/merge
reading sources... [ 69%] content/tools/multicov
reading sources... [ 71%] content/tools/multiinter
reading sources... [ 73%] content/tools/nuc
reading sources... [ 75%] content/tools/overlap
reading sources... [ 76%] content/tools/pairtobed
reading sources... [ 78%] content/tools/pairtopair
reading sources... [ 80%] content/tools/random
reading sources... [ 82%] content/tools/reldist
reading sources... [ 84%] content/tools/shift
reading sources... [ 86%] content/tools/shuffle
reading sources... [ 88%] content/tools/slop
reading sources... [ 90%] content/tools/sort
reading sources... [ 92%] content/tools/subtract
reading sources... [ 94%] content/tools/tag
reading sources... [ 96%] content/tools/unionbedg
reading sources... [ 98%] content/tools/window
reading sources... [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: WARNING: 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:: WARNING: image file not readable: content/tools/../images/tool-glyphs/shift-glyph.png
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  1%] content/advanced-usage
writing output... [  3%] content/bedtools-suite
writing output... [  5%] content/example-usage
writing output... [  7%] content/faq
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
/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.
/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)
generating indices... 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... [ 42%] content/tools/../images/tool-glyphs/random-glyph.png
copying images... [ 46%] content/tools/../images/tool-glyphs/barski_binding_site.png
copying images... [ 50%] content/tools/../images/tool-glyphs/reldist-glyph.png
copying images... [ 53%] content/tools/../images/tool-glyphs/cluster-glyph.png
copying images... [ 57%] content/tools/../images/tool-glyphs/map-speed-comparo.png
copying images... [ 61%] content/tools/../images/tool-glyphs/slop-glyph.png
copying images... [ 65%] content/images/galaxy-bedtools.png
copying images... [ 69%] content/tools/../images/tool-glyphs/genomecov-glyph.png
copying images... [ 73%] content/tools/../images/tool-glyphs/flank-glyph.png
copying images... [ 76%] content/tools/../images/tool-glyphs/shuffle-glyph.png
copying images... [ 80%] content/images/memory-comparo.png
copying images... [ 84%] content/tools/../images/tool-glyphs/window-glyph.png
copying images... [ 88%] content/tools/../images/tool-glyphs/getfasta-glyph.png
copying images... [ 92%] content/tools/../images/tool-glyphs/reldist-plot.png
copying images... [ 96%] content/tools/../images/fisher/res-genes.png
copying images... [100%] content/tools/../images/tool-glyphs/maskfasta-glyph.png
copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 20 warnings.
Build finished. The HTML pages are in _build/html.
+ cd ..
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.WzkxGb
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64
++ dirname /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64
+ cd bedtools2
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64
+ mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.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-2.26.0-7.fc28.x86_64/usr/bin
+ mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/BEDTools
+ cp -a genomes/ /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/BEDTools
+ cp -a data/ /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/BEDTools
+ find /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/BEDTools -type f -exec chmod 0644 '{}' ';'
+ /usr/lib/rpm/find-debuginfo.sh -j6 --strict-build-id -m -i --build-id-seed 2.26.0-7.fc28 --unique-debug-suffix -2.26.0-7.fc28.x86_64 --unique-debug-src-base BEDTools-2.26.0-7.fc28.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bedtools2
extracting debug info from /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/bin/bedtools
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
3641 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
/sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
+ /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-mangle-shebangs '' ''
Processing files: BEDTools-2.26.0-7.fc28.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.jxAJH1
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2
+ DOCDIR=/builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/doc/BEDTools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/doc/BEDTools
+ cp -pr README.md /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/doc/BEDTools
+ cp -pr RELEASE_HISTORY /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/doc/BEDTools
+ cp -pr LICENSE /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/doc/BEDTools
+ cp -pr docs/_build/html/ /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64/usr/share/doc/BEDTools
+ exit 0
Provides: BEDTools = 2.26.0-7.fc28 BEDTools(x86-64) = 2.26.0-7.fc28
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-debugsource-2.26.0-7.fc28.x86_64
Provides: BEDTools-debugsource = 2.26.0-7.fc28 BEDTools-debugsource(x86-64) = 2.26.0-7.fc28
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: BEDTools-debuginfo-2.26.0-7.fc28.x86_64
Provides: BEDTools-debuginfo = 2.26.0-7.fc28 BEDTools-debuginfo(x86-64) = 2.26.0-7.fc28 debuginfo(build-id) = 5f3601d91c56baa9f1c0416ae9373ca9b004f009
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: BEDTools-debugsource(x86-64) = 2.26.0-7.fc28
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64
Wrote: /builddir/build/RPMS/BEDTools-2.26.0-7.fc28.x86_64.rpm
Wrote: /builddir/build/RPMS/BEDTools-debugsource-2.26.0-7.fc28.x86_64.rpm
Wrote: /builddir/build/RPMS/BEDTools-debuginfo-2.26.0-7.fc28.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Y4iph6
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.x86_64
+ exit 0
Child return code was: 0