Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'], chrootPath='/var/lib/mock/rhel+epel-8-x86_64-1672348713.251555/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f0307638550>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k31r3a0p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k31r3a0p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '3facc2e26585460a9e8750656a0d798d', '-D', '/var/lib/mock/rhel+epel-8-x86_64-1672348713.251555/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k31r3a0p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', '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': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/BEDTools-2.30.0-3.el8.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/BEDTools.spec'], chrootPath='/var/lib/mock/rhel+epel-8-x86_64-1672348713.251555/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f0307638550>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k31r3a0p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k31r3a0p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'fe3b7b288c214e7e91107b66d0520d81', '-D', '/var/lib/mock/rhel+epel-8-x86_64-1672348713.251555/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k31r3a0p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', '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': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.nBOtnE
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bedtools2-2.30.0
+ /usr/bin/gzip -dc /builddir/build/SOURCES/bedtools2-2.30.0.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bedtools2-2.30.0
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #1 (BEDTools-python3.patch):
+ echo 'Patch #1 (BEDTools-python3.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .BEDTools.python3 --fuzz=0
patching file Makefile
patching file scripts/makeBashScripts.py
patching file test/fisher/cmp.sh
+ rm -rf src/utils/curl
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.bfoBK2
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2-2.30.0
+ make -j2 '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 -fcf-protection' V=1
Building BEDTools:
DETECTED_VERSION = v2.30.0
CURRENT_VERSION  = 
Updating version file.
=========================================================
CXXFLAGS is [-g -Wall -O2 -std=c++11 -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 -fcf-protection]
cd src/utils/htslib && make config.h
make[1]: Entering directory '/builddir/build/BUILD/bedtools2-2.30.0/src/utils/htslib'
  * compiling src/htsutil.cpp
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#ifndef __APPLE__' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
make[1]: Leaving directory '/builddir/build/BUILD/bedtools2-2.30.0/src/utils/htslib'
  * compiling src/bedtools.cpp
  * compiling src/annotateBed/annotateMain.cpp
  * compiling src/annotateBed/annotateBed.cpp
  * compiling src/bamToBed/bamToBed.cpp
src/bamToBed/bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
src/bamToBed/bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
     bool useAlignmentScore = false;
          ^~~~~~~~~~~~~~~~~
In file included from src/utils/BamTools/include/api/BamReader.h:1,
                 from src/bamToBed/bamToBed.cpp:12:
src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)':
src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   sam_hdr_write(fp, hdr);
   ~~~~~~~~~~~~~^~~~~~~~~
  * compiling src/bamToFastq/bamToFastqMain.cpp
src/bamToFastq/bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
     bool haveFastq2    = false;
          ^~~~~~~~~~
  * compiling src/bamToFastq/bamToFastq.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1,
                 from src/bamToFastq/bamToFastq.h:15,
                 from src/bamToFastq/bamToFastq.cpp:15:
src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)':
src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   sam_hdr_write(fp, hdr);
   ~~~~~~~~~~~~~^~~~~~~~~
  * compiling src/bedToBam/bedToBam.cpp
src/bedToBam/bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
src/bedToBam/bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
     bool haveMapQual     = false;
          ^~~~~~~~~~~
  * compiling src/bedpeToBam/bedpeToBam.cpp
src/bedpeToBam/bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
     bool haveMapQual     = false;
          ^~~~~~~~~~~
  * compiling src/bedToIgv/bedToIgv.cpp
  * compiling src/bed12ToBed6/bed12ToBed6.cpp
  * compiling src/closestFile/closestHelp.cpp
  * compiling src/closestFile/closestFile.cpp
  * compiling src/clusterBed/clusterMain.cpp
src/clusterBed/clusterMain.cpp: In function 'int cluster_main(int, char**)':
src/clusterBed/clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
     bool haveMaxDistance = false;
          ^~~~~~~~~~~~~~~
  * compiling src/clusterBed/clusterBed.cpp
  * compiling src/complementFile/complementHelp.cpp
  * compiling src/complementFile/complementFile.cpp
  * compiling src/coverageFile/coverageHelp.cpp
  * compiling src/coverageFile/coverageFile.cpp
  * compiling src/expand/expand.cpp
src/coverageFile/coverageFile.cpp: In member function 'virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)':
src/coverageFile/coverageFile.cpp:100:11: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   asprintf(&depthPctString, "%0.7f", depthPct);
   ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)':
src/coverageFile/coverageFile.cpp:181:10: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
  asprintf(&meanString, "%0.7f", mean);
  ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)':
src/coverageFile/coverageFile.cpp:210:11: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   asprintf(&coveredFractionString, "%0.7f", coveredFraction);
   ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)':
src/coverageFile/coverageFile.cpp:230:10: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
  asprintf(&coveredFractionString, "%0.7f", coveredFraction);
  ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  * compiling src/fastaFromBed/fastaFromBedMain.cpp
  * compiling src/fastaFromBed/fastaFromBed.cpp
  * compiling src/flankBed/flankBedMain.cpp
  * compiling src/flankBed/flankBed.cpp
  * compiling src/genomeCoverageBed/genomeCoverageMain.cpp
  * compiling src/genomeCoverageBed/genomeCoverageBed.cpp
  * compiling src/getOverlap/getOverlap.cpp
src/getOverlap/getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
src/getOverlap/getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
     bool haveColumns = false;
          ^~~~~~~~~~~
In file included from src/utils/BamTools/include/api/BamReader.h:1,
                 from src/utils/GenomeFile/NewGenomeFile.h:20,
                 from src/genomeCoverageBed/genomeCoverageBed.h:13,
                 from src/genomeCoverageBed/genomeCoverageBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)':
src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   sam_hdr_write(fp, hdr);
   ~~~~~~~~~~~~~^~~~~~~~~
  * compiling src/groupBy/groupByHelp.cpp
  * compiling src/groupBy/groupBy.cpp
  * compiling src/intersectFile/intersectHelp.cpp
  * compiling src/intersectFile/intersectFile.cpp
  * compiling src/fisher/fisherHelp.cpp
  * compiling src/fisher/fisher.cpp
  * compiling src/fisher/kfunc.cpp
  * compiling src/jaccard/jaccardHelp.cpp
  * compiling src/jaccard/jaccard.cpp
  * compiling src/linksBed/linksMain.cpp
  * compiling src/linksBed/linksBed.cpp
  * compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp
  * compiling src/maskFastaFromBed/maskFastaFromBed.cpp
  * compiling src/mapFile/mapHelp.cpp
  * compiling src/mapFile/mapFile.cpp
  * compiling src/mergeFile/mergeHelp.cpp
  * compiling src/mergeFile/mergeFile.cpp
  * compiling src/multiBamCov/multiBamCovMain.cpp
  * compiling src/multiBamCov/multiBamCov.cpp
src/multiBamCov/multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
     bool haveBed           = false;
          ^~~~~~~
src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
     bool haveBams          = false;
          ^~~~~~~~
src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
     bool haveFraction       = false;
          ^~~~~~~~~~~~
In file included from src/utils/BamTools/include/BamReader.hpp:4,
                 from src/utils/BamTools/include/api/BamMultiReader.h:4,
                 from src/multiBamCov/multiBamCov.h:16,
                 from src/multiBamCov/multiBamCov.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)':
src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   sam_hdr_write(fp, hdr);
   ~~~~~~~~~~~~~^~~~~~~~~
  * compiling src/multiIntersectBed/multiIntersectBedMain.cpp
src/multiIntersectBed/multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
     bool haveFiles         = false;
          ^~~~~~~~~
src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
     bool haveGenome        = false;
          ^~~~~~~~~~
src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
     bool haveFiller        = true;
          ^~~~~~~~~~
  * compiling src/multiIntersectBed/multiIntersectBed.cpp
  * compiling src/nucBed/nucBedMain.cpp
  * compiling src/nucBed/nucBed.cpp
  * compiling src/pairToBed/pairToBedMain.cpp
  * compiling src/pairToBed/pairToBed.cpp
src/pairToBed/pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
src/pairToBed/pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
     bool haveFraction       = false;
          ^~~~~~~~~~~~
src/pairToBed/pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
src/pairToBed/pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
     CHRPOS spanLength = 0;
            ^~~~~~~~~~
src/pairToBed/pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
src/pairToBed/pairToBed.cpp:310:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
     CHRPOS spanLength = 0;
            ^~~~~~~~~~
In file included from src/utils/BamTools/include/api/BamReader.h:1,
                 from src/pairToBed/pairToBed.h:15,
                 from src/pairToBed/pairToBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)':
src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   sam_hdr_write(fp, hdr);
   ~~~~~~~~~~~~~^~~~~~~~~
  * compiling src/pairToPair/pairToPairMain.cpp
src/pairToPair/pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
src/pairToPair/pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
     bool haveFraction = false;
          ^~~~~~~~~~~~
  * compiling src/pairToPair/pairToPair.cpp
src/pairToPair/pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
src/pairToPair/pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
         bool found1 = false;
              ^~~~~~
src/pairToPair/pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
         bool found2 = false;
              ^~~~~~
  * compiling src/randomBed/randomBedMain.cpp
  * compiling src/randomBed/randomBed.cpp
  * compiling src/regressTest/regressTestMain.cpp
  * compiling src/regressTest/RegressTest.cpp
  * compiling src/reldist/reldistMain.cpp
src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
src/regressTest/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());
  ~~~~~~^~~~~~~~~~~~~~~~~
src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
src/regressTest/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);
  ~~~~~^~~~~~~~~~~~~~~~~
src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
src/regressTest/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 src/reldist/reldist.cpp
src/reldist/reldist.cpp: In member function 'void RelativeDistance::CalculateRelativeDistance()':
src/reldist/reldist.cpp:129:25: warning: comparison of integer expressions of different signedness: 'CHRPOS' {aka 'long int'} and 'std::vector<long int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
             if (low_idx != chrom_mids->size() - 1)
                 ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
  * compiling src/sampleFile/sampleHelp.cpp
  * compiling src/sampleFile/sampleFile.cpp
  * compiling src/shiftBed/shiftBedMain.cpp
  * compiling src/shiftBed/shiftBed.cpp
  * compiling src/shuffleBed/shuffleBedMain.cpp
  * compiling src/shuffleBed/shuffleBed.cpp
  * compiling src/slopBed/slopBedMain.cpp
  * compiling src/slopBed/slopBed.cpp
  * compiling src/sortBed/sortMain.cpp
  * compiling src/sortBed/sortBed.cpp
  * compiling src/spacingFile/spacingHelp.cpp
  * compiling src/spacingFile/spacingFile.cpp
  * compiling src/split/splitBedMain.cpp
  * compiling src/split/splitBed.cpp
  * compiling src/subtractFile/subtractHelp.cpp
  * compiling src/subtractFile/subtractFile.cpp
  * compiling src/summaryFile/summaryHelp.cpp
  * compiling src/summaryFile/summaryFile.cpp
  * compiling src/tagBam/tagBamMain.cpp
  * compiling src/tagBam/tagBam.cpp
  * compiling src/unionBedGraphs/unionBedGraphsMain.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1,
                 from src/tagBam/tagBam.h:17,
                 from src/tagBam/tagBam.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)':
src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   sam_hdr_write(fp, hdr);
   ~~~~~~~~~~~~~^~~~~~~~~
src/unionBedGraphs/unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
     bool haveFiles         = false;
          ^~~~~~~~~
src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
     bool haveGenome        = false;
          ^~~~~~~~~~
src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
     bool haveFiller        = true;
          ^~~~~~~~~~
  * compiling src/unionBedGraphs/unionBedGraphs.cpp
  * compiling src/windowBed/windowMain.cpp
  * compiling src/windowBed/windowBed.cpp
  * compiling src/windowMaker/windowMakerMain.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1,
                 from src/windowBed/windowBed.h:15,
                 from src/windowBed/windowBed.cpp:13:
src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)':
src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   sam_hdr_write(fp, hdr);
   ~~~~~~~~~~~~~^~~~~~~~~
  * compiling src/windowMaker/windowMaker.cpp
  * compiling src/utils/FileRecordTools/FileRecordMgr.cpp
  * compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp
  * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp
  * compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
  * compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
  * compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function 'bool BufferedStreamMgr::readFileChunk()':
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   if (_mainBufCurrLen < _useBufSize) {
       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
  * compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
  * compiling src/utils/FileRecordTools/Records/Record.cpp
In file included from src/utils/BamTools/include/api/BamReader.h:1,
                 from src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:14,
                 from src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:8:
src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)':
src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   sam_hdr_write(fp, hdr);
   ~~~~~~~~~~~~~^~~~~~~~~
  * compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp
  * compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp
  * compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp
  * compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp
  * compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp
  * compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp
  * compiling src/utils/FileRecordTools/Records/PlusFields.cpp
  * compiling src/utils/FileRecordTools/Records/GffRecord.cpp
  * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp
  * compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp
  * compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp
  * compiling src/utils/FileRecordTools/Records/Bed12Interval.cpp
  * compiling src/utils/FileRecordTools/Records/BamRecord.cpp
  * compiling src/utils/FileRecordTools/Records/VcfRecord.cpp
  * compiling src/utils/FileRecordTools/Records/BlockMgr.cpp
src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function 'int BlockMgr::getNonRedundantOverlap()':
src/utils/FileRecordTools/Records/BlockMgr.cpp:194:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   for (int i = 1; i < _overlapStarts.size(); ++i)
                   ~~^~~~~~~~~~~~~~~~~~~~~~~
  * compiling src/utils/FileRecordTools/Records/StrandQueue.cpp
  * compiling src/utils/FileRecordTools/Records/RecordMgr.cpp
  * compiling src/utils/FileRecordTools/Records/RecordList.cpp
  * compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp
  * compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp
  * compiling src/utils/bedFile/bedFile.cpp
  * compiling src/utils/BinTree/BinTree.cpp
  * compiling src/utils/version/version.cpp
  * compiling src/utils/bedGraphFile/bedGraphFile.cpp
  * compiling src/utils/chromsweep/chromsweep.cpp
  * compiling src/utils/Contexts/ContextBase.cpp
  * compiling src/utils/Contexts/ContextIntersect.cpp
  * compiling src/utils/Contexts/ContextFisher.cpp
  * compiling src/utils/Contexts/ContextMap.cpp
  * compiling src/utils/Contexts/ContextSample.cpp
  * compiling src/utils/Contexts/ContextSpacing.cpp
  * compiling src/utils/Contexts/ContextMerge.cpp
  * compiling src/utils/Contexts/ContextJaccard.cpp
  * compiling src/utils/Contexts/ContextClosest.cpp
  * compiling src/utils/Contexts/ContextSubtract.cpp
  * compiling src/utils/Contexts/ContextCoverage.cpp
  * compiling src/utils/Contexts/ContextComplement.cpp
  * compiling src/utils/Contexts/ContextGroupBy.cpp
  * compiling src/utils/Contexts/ContextSummary.cpp
  * compiling src/utils/general/ParseTools.cpp
  * compiling src/utils/general/PushBackStreamBuf.cpp
  * compiling src/utils/general/CompressionTools.cpp
  * compiling src/utils/general/Tokenizer.cpp
  * compiling src/utils/general/CommonHelp.cpp
  * compiling src/utils/general/ErrorMsg.cpp
  * compiling src/utils/general/Random.cpp
g++ -g -Wall -O2 -std=c++11 -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 -fcf-protection -Isrc/utils/gzstream  -c -o obj/gzstream.o src/utils/gzstream/gzstream.C
  * compiling src/utils/fileType/fileType.cpp
  * compiling src/utils/fileType/FileRecordTypeChecker.cpp
  * compiling src/utils/bedFilePE/bedFilePE.cpp
src/utils/fileType/FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)':
src/utils/fileType/FileRecordTypeChecker.cpp:366:19: 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 src/utils/KeyListOps/KeyListOps.cpp
  * compiling src/utils/KeyListOps/KeyListOpsMethods.cpp
  * compiling src/utils/NewChromsweep/NewChromsweep.cpp
  * compiling src/utils/NewChromsweep/CloseSweep.cpp
  * compiling src/utils/sequenceUtilities/sequenceUtils.cpp
  * compiling src/utils/tabFile/tabFile.cpp
  * compiling src/utils/BamTools-Ancillary/BamAncillary.cpp
  * compiling src/utils/BlockedIntervals/BlockedIntervals.cpp
  * compiling src/utils/Fasta/Fasta.cpp
  * compiling src/utils/Fasta/split.cpp
src/utils/Fasta/Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)':
src/utils/Fasta/Fasta.cpp:292:14: 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);
         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/utils/Fasta/Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, CHRPOS, CHRPOS)':
src/utils/Fasta/Fasta.cpp:334:14: 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 src/utils/VectorOps/VectorOps.cpp
  * compiling src/utils/GenomeFile/NewGenomeFile.cpp
  * compiling src/utils/GenomeFile/GenomeFile.cpp
  * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp
src/utils/GenomeFile/GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
                     long c2;
                          ^~
src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector<long int>*)':
src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:42: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   if (context->getNumClosestHitsWanted() > keyList.size())
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)':
src/utils/RecordOutputMgr/RecordOutputMgr.cpp:455:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   for (size_t i = 1; i < _context->getNumInputFiles(); i++)
                      ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  * compiling src/utils/ToolBase/ToolBase.cpp
  * compiling src/utils/driver/BedtoolsDriver.cpp
cd src/utils/htslib && make lib-static
make[1]: Entering directory '/builddir/build/BUILD/bedtools2-2.30.0/src/utils/htslib'
gcc -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
- Creating executables for old CLI.
done.
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9"' > version.h
gcc -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -I.  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:2095:9: warning: 'strncpy' specified bound 4096 equals destination size [-Wstringop-truncation]
         strncpy(path, path2, PATH_MAX);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
In function 'full_path',
    inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3823:17:
cram/cram_io.c:3748:13: warning: 'strncpy' specified bound 4096 equals destination size [-Wstringop-truncation]
             strncpy(out, in, PATH_MAX);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:3740:9: warning: 'strncpy' specified bound 4096 equals destination size [-Wstringop-truncation]
         strncpy(out, in, PATH_MAX);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -I.  -c -o hts.o hts.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
make[1]: Leaving directory '/builddir/build/BUILD/bedtools2-2.30.0/src/utils/htslib'
- Building main bedtools binary.
done.
+ cd docs
+ make clean html
rm -rf _build/*
sphinx-build -b html -d _build/doctrees   . _build/html
Running Sphinx v1.7.6
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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/bedtools2-2.30.0/docs/content/faq.rst:18: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/builddir/build/BUILD/bedtools2-2.30.0/docs/content/faq.rst:74: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/builddir/build/BUILD/bedtools2-2.30.0/docs/content/overview.rst:74: WARNING: unknown document: tools/sample
/builddir/build/BUILD/bedtools2-2.30.0/docs/content/overview.rst:79: WARNING: unknown document: tools/spacing
/builddir/build/BUILD/bedtools2-2.30.0/docs/content/overview.rst:80: WARNING: unknown document: tools/split
/builddir/build/BUILD/bedtools2-2.30.0/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/images/github-zip-button.png
copying images... [  7%] content/images/bedtoolsMenu.png
copying images... [ 11%] content/images/galaxy-bedtools.png
copying images... [ 15%] content/tools/../images/tool-glyphs/closest-glyph.png
copying images... [ 19%] content/tools/../images/tool-glyphs/cluster-glyph.png
copying images... [ 23%] content/tools/../images/tool-glyphs/complement-glyph.png
copying images... [ 26%] content/tools/../images/fisher/res-genes.png
copying images... [ 30%] content/tools/../images/tool-glyphs/flank-glyph.png
copying images... [ 34%] content/tools/../images/tool-glyphs/genomecov-glyph.png
copying images... [ 38%] content/tools/../images/tool-glyphs/barski_binding_site.png
copying images... [ 42%] content/tools/../images/tool-glyphs/getfasta-glyph.png
copying images... [ 46%] content/tools/../images/tool-glyphs/intersect-glyph.png
copying images... [ 50%] content/tools/../images/tool-glyphs/jaccard-glyph.png
copying images... [ 53%] content/tools/../images/tool-glyphs/map-glyph.png
copying images... [ 57%] content/tools/../images/tool-glyphs/map-speed-comparo.png
copying images... [ 61%] content/tools/../images/tool-glyphs/maskfasta-glyph.png
copying images... [ 65%] content/tools/../images/tool-glyphs/merge-glyph.png
copying images... [ 69%] content/tools/../images/tool-glyphs/random-glyph.png
copying images... [ 73%] content/tools/../images/tool-glyphs/reldist-glyph.png
copying images... [ 76%] content/tools/../images/tool-glyphs/reldist-plot.png
copying images... [ 80%] content/tools/../images/tool-glyphs/shuffle-glyph.png
copying images... [ 84%] content/tools/../images/tool-glyphs/slop-glyph.png
copying images... [ 88%] content/tools/../images/tool-glyphs/subtract-glyph.png
copying images... [ 92%] content/tools/../images/tool-glyphs/window-glyph.png
copying images... [ 96%] content/images/speed-comparo.png
copying images... [100%] content/images/memory-comparo.png
copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 35 warnings.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
+ cd ..
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.lj1dtp
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64
++ dirname /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64
+ cd bedtools2-2.30.0
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64
+ mkdir -p /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.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-2.30.0-3.el8.x86_64/usr/bin
+ mkdir -p /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/BEDTools
+ cp -a genomes/ /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/BEDTools
+ cp -a data/ /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/BEDTools
+ find /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/BEDTools -type f -exec chmod 0644 '{}' ';'
+ /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 2.30.0-3.el8 --unique-debug-suffix -2.30.0-3.el8.x86_64 --unique-debug-src-base BEDTools-2.30.0-3.el8.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bedtools2-2.30.0
extracting debug info from /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/bin/bedtools
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
4941 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 '' 1
+ /usr/lib/rpm/brp-python-hardlink
+ PYTHON3=/usr/bin/python3.6
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
*** WARNING: ./usr/src/debug/BEDTools-2.30.0-3.el8.x86_64/src/utils/BamTools/include/BamAlignment.hpp is executable but has no shebang, removing executable bit
Processing files: BEDTools-2.30.0-3.el8.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.OZ73Lm
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2-2.30.0
+ DOCDIR=/builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/doc/BEDTools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/doc/BEDTools
+ cp -pr README.md /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/doc/BEDTools
+ cp -pr LICENSE /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/doc/BEDTools
+ cp -pr docs/ /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64/usr/share/doc/BEDTools
+ exit 0
Provides: BEDTools = 2.30.0-3.el8 BEDTools(x86-64) = 2.30.0-3.el8
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /bin/sh libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_2.8)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpthread.so.0(GLIBC_2.3.2)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(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) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH)
Processing files: BEDTools-debugsource-2.30.0-3.el8.x86_64
Provides: BEDTools-debugsource = 2.30.0-3.el8 BEDTools-debugsource(x86-64) = 2.30.0-3.el8
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: BEDTools-debuginfo-2.30.0-3.el8.x86_64
Provides: BEDTools-debuginfo = 2.30.0-3.el8 BEDTools-debuginfo(x86-64) = 2.30.0-3.el8 debuginfo(build-id) = cc5e48c0acf479c0fc8dfe11b2be58b6928b55f6
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: BEDTools-debugsource(x86-64) = 2.30.0-3.el8
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64
Wrote: /builddir/build/RPMS/BEDTools-2.30.0-3.el8.x86_64.rpm
Wrote: /builddir/build/RPMS/BEDTools-debugsource-2.30.0-3.el8.x86_64.rpm
Wrote: /builddir/build/RPMS/BEDTools-debuginfo-2.30.0-3.el8.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.L2i5Gu
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2-2.30.0
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.30.0-3.el8.x86_64
+ exit 0
Child return code was: 0