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-9-x86_64-1674273252.657801/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 0x7f8c60edbb90>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.93r_c088:/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.93r_c088:/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', '00adc1eeb4854f6c882a56ac85051ba7', '-D', '/var/lib/mock/rhel+epel-9-x86_64-1674273252.657801/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.93r_c088:/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
setting SOURCE_DATE_EPOCH=1674172800
Wrote: /builddir/build/SRPMS/BEDTools-2.30.0-5.el9.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-9-x86_64-1674273252.657801/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 0x7f8c60edbb90>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.93r_c088:/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.93r_c088:/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', '41ebdc97294146dab8b468292bd50dc3', '-D', '/var/lib/mock/rhel+epel-9-x86_64-1674273252.657801/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.93r_c088:/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
setting SOURCE_DATE_EPOCH=1674172800
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jgqxTh
+ 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
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.yOvZeA
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2-2.30.0
+ make -j2 'CXXFLAGS=-I. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -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]
   88 |     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:32:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   32 |                 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]
   38 |     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:32:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   32 |                 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]
   60 |     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]
   61 |     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]
   38 |     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:100:25: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
  100 |                 asprintf(&depthPctString, "%0.7f", depthPct);
      |                 ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)':
src/coverageFile/coverageFile.cpp:181:17: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
  181 |         asprintf(&meanString, "%0.7f", mean);
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)':
src/coverageFile/coverageFile.cpp:210:25: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
  210 |                 asprintf(&coveredFractionString, "%0.7f", coveredFraction);
      |                 ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)':
src/coverageFile/coverageFile.cpp:230:17: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
  230 |         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
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:32:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   32 |                 sam_hdr_write(fp, hdr);
      |                 ~~~~~~~~~~~~~^~~~~~~~~
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]
   44 |     bool haveColumns = false;
      |          ^~~~~~~~~~~
  * 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]
   38 |     bool haveBed           = false;
      |          ^~~~~~~
src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
   39 |     bool haveBams          = false;
      |          ^~~~~~~~
src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
   47 |     bool haveFraction       = false;
      |          ^~~~~~~~~~~~
  * compiling src/multiIntersectBed/multiIntersectBedMain.cpp
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:32:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   32 |                 sam_hdr_write(fp, hdr);
      |                 ~~~~~~~~~~~~~^~~~~~~~~
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]
   45 |     bool haveFiles         = false;
      |          ^~~~~~~~~
src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
   47 |     bool haveGenome        = false;
      |          ^~~~~~~~~~
src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
   48 |     bool haveFiller        = true;
      |          ^~~~~~~~~~
  * compiling src/multiIntersectBed/multiIntersectBed.cpp
  * compiling src/nucBed/nucBedMain.cpp
  * compiling src/nucBed/nucBed.cpp
  * compiling src/pairToBed/pairToBedMain.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]
   43 |     bool haveFraction       = false;
      |          ^~~~~~~~~~~~
  * compiling src/pairToBed/pairToBed.cpp
  * compiling src/pairToPair/pairToPairMain.cpp
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]
  257 |     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]
  310 |     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:32:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   32 |                 sam_hdr_write(fp, hdr);
      |                 ~~~~~~~~~~~~~^~~~~~~~~
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]
   44 |     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]
  112 |         bool found1 = false;
      |              ^~~~~~
src/pairToPair/pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
  113 |         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:431:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  431 |         system(diffCmd.c_str());
      |         ~~~~~~^~~~~~~~~~~~~~~~~
src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
src/regressTest/RegressTest.cpp:573:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  573 |         fgets(sLine, 4192, fp);
      |         ~~~~~^~~~~~~~~~~~~~~~~
src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
src/regressTest/RegressTest.cpp:622:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  622 |                 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]
  129 |             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:32:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   32 |                 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]
   46 |     bool haveFiles         = false;
      |          ^~~~~~~~~
src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
   48 |     bool haveGenome        = false;
      |          ^~~~~~~~~~
src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
   49 |     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:32:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   32 |                 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
  * compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function 'bool BufferedStreamMgr::readFileChunk()':
src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  148 |                 if (_mainBufCurrLen < _useBufSize) {
      |                     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
  * 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:32:30: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   32 |                 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
  * compiling src/utils/FileRecordTools/Records/StrandQueue.cpp
src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function 'int BlockMgr::getNonRedundantOverlap()':
src/utils/FileRecordTools/Records/BlockMgr.cpp:194:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  194 |                 for (int i = 1; i < _overlapStarts.size(); ++i)
      |                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
  * 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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64-v2 -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:366:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  366 |                 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::string FastaReference::getSequence(std::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]
  292 |         fread(seq, sizeof(char), seqlen, file);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/utils/Fasta/Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::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]
  334 |         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
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]
   60 |                     long c2;
      |                          ^~
  * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp
src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector<long int>*)':
src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:56: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  170 |                 if (context->getNumClosestHitsWanted() > keyList.size())
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)':
src/utils/RecordOutputMgr/RecordOutputMgr.cpp:455:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  455 |                 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
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
- Creating executables for old CLI.
done.
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]
 2095 |         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]
 3748 |             strncpy(out, in, PATH_MAX);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c: In function 'cram_dopen':
cram/cram_io.c:4126:9: warning: 'strncpy' specified bound 20 equals destination size [-Wstringop-truncation]
 4126 |         strncpy(def->file_id, filename, 20);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
In function 'string_ndup',
    inlined from 'string_dup' at cram/string_alloc.c:143:12:
cram/string_alloc.c:151:5: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  151 |     strncpy(str, instr, len);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
cram/string_alloc.c: In function 'string_dup':
cram/string_alloc.c:143:12: note: length computed here
  143 |     return string_ndup(a_str, instr, strlen(instr));
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -Wall -O2 -I.  -c -o hts.o hts.c
hts.c: In function 'hts_idx_init':
hts.c:1397:59: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int' changes value from 'idx->z.last_bin = 4294967295' to '-1' [-Woverflow]
 1397 |     idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
      |                                                           ^~~
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 v3.4.3
WARNING: while setting up extension matplotlib.sphinxext.plot_directive: extension 'matplotlib.sphinxext.plot_directive' returned an unsupported object from its setup() function; it should return None or a metadata dictionary
making output directory... done
loading intersphinx inventory from http://bedtools.readthedocs.org/en/latest/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
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 0x7f57111d5dc0>: 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: [new config] 52 added, 0 changed, 0 removed
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/builddir/build/BUILD/bedtools2-2.30.0/docs/content/tools/merge.rst:244: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2-2.30.0/docs/content/tools/merge.rst:250: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2-2.30.0/docs/content/tools/pairtopair.rst:31: WARNING: Block quote ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2-2.30.0/docs/content/tools/random.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2-2.30.0/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
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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
generating indices... genindex done
writing additional pages... search done
copying images... [  3%] content/images/github-zip-button.png
copying images... [  7%] content/images/bedtoolsMenu.png
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copying static files... done
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dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 34 warnings.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
+ cd ..
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.T94JpI
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64
++ dirname /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64
+ cd bedtools2-2.30.0
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64
+ mkdir -p /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.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-2.30.0-5.el9.x86_64/usr/bin
+ mkdir -p /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/share/BEDTools
+ cp -a genomes/ /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/share/BEDTools
+ cp -a data/ /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/share/BEDTools
+ find /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.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 2.30.0-5.el9 --unique-debug-suffix -2.30.0-5.el9.x86_64 --unique-debug-src-base BEDTools-2.30.0-5.el9.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/bedtools2-2.30.0
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/bin/bedtools
extracting debug info from /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/bin/bedtools
original debug info size: 30652kB, size after compression: 23316kB
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
4941 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
*** WARNING: ./usr/src/debug/BEDTools-2.30.0-5.el9.x86_64/src/utils/BamTools/include/BamAlignment.hpp is executable but has no shebang, removing executable bit
mangling shebang in /usr/bin/windowMaker from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/windowBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/unionBedGraphs from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/tagBam from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/subtractBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/sortBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/slopBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/shuffleBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/shiftBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/randomBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/pairToPair from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/pairToBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/nucBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/multiIntersectBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/multiBamCov from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/mergeBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/maskFastaFromBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/mapBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/linksBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/intersectBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/groupBy from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/getOverlap from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/genomeCoverageBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/flankBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/fastaFromBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/expandCols from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/coverageBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/complementBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/clusterBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/closestBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/bedpeToBam from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/bedToIgv from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/bedToBam from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/bed12ToBed6 from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/bamToFastq from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/bamToBed from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/annotateBed from /bin/sh to #!/usr/bin/sh
Processing files: BEDTools-2.30.0-5.el9.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.iEL9C9
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2-2.30.0
+ DOCDIR=/builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/share/doc/BEDTools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/share/doc/BEDTools
+ cp -pr README.md /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/share/doc/BEDTools
+ cp -pr LICENSE /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/share/doc/BEDTools
+ cp -pr docs/ /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64/usr/share/doc/BEDTools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: BEDTools = 2.30.0-5.el9 BEDTools(x86-64) = 2.30.0-5.el9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/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_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(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) libgcc_s.so.1(GCC_3.3.1)(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) libm.so.6(GLIBC_2.29)(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_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(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-2.30.0-5.el9.x86_64
Provides: BEDTools-debugsource = 2.30.0-5.el9 BEDTools-debugsource(x86-64) = 2.30.0-5.el9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: BEDTools-debuginfo-2.30.0-5.el9.x86_64
Provides: BEDTools-debuginfo = 2.30.0-5.el9 BEDTools-debuginfo(x86-64) = 2.30.0-5.el9 debuginfo(build-id) = b1b76ad11c35a4cd32cb4156b46e0b5041f79539
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: BEDTools-debugsource(x86-64) = 2.30.0-5.el9
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64
Wrote: /builddir/build/RPMS/BEDTools-2.30.0-5.el9.x86_64.rpm
Wrote: /builddir/build/RPMS/BEDTools-debugsource-2.30.0-5.el9.x86_64.rpm
Wrote: /builddir/build/RPMS/BEDTools-debuginfo-2.30.0-5.el9.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.0Zr5lI
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2-2.30.0
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.30.0-5.el9.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0