+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=39 WRKLOG=/tmp/bulklog/bedtools-2.30.0/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=39 WRKLOG=/tmp/bulklog/bedtools-2.30.0/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for bedtools-2.30.0
Building BEDTools:
=========================================================
CXXFLAGS is [-g -Wall -O2 -std=c++11 -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9]
DETECTED_VERSION = v2.30.0
CURRENT_VERSION =
Updating version file.
* 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;
| ^~~~~~~~~~~~~~~~~
* 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
* 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
* 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]
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
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/multiBamCov/multiBamCov.cpp
* 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]
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
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;
| ^~~~~~~~~~
* 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]
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
* 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
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
* 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]
148 | if (_mainBufCurrLen < _useBufSize) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
* compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
* compiling src/utils/FileRecordTools/Records/Record.cpp
* 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]
194 | 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 -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -Isrc/utils/gzstream -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -c -o obj/gzstream.o src/utils/gzstream/gzstream.C
* compiling src/utils/fileType/fileType.cpp
* compiling src/utils/fileType/FileRecordTypeChecker.cpp
src/utils/fileType/FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, std::size_t)':
src/utils/fileType/FileRecordTypeChecker.cpp:366:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare]
366 | for (int j=0; j < len; j++) {
| ~~^~~~~
* compiling src/utils/bedFilePE/bedFilePE.cpp
* 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
* 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:170:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::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:455:24: warning: comparison of integer expressions of different signedness: 'std::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 && /opt/pkg/bin/gmake config.h
gmake[1]: Entering directory '/home/pbulk/build/biology/bedtools/work/bedtools2-2.30.0/src/utils/htslib'
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
gmake[1]: Leaving directory '/home/pbulk/build/biology/bedtools/work/bedtools2-2.30.0/src/utils/htslib'
cd src/utils/htslib && /opt/pkg/bin/gmake lib-static
gmake[1]: Entering directory '/home/pbulk/build/biology/bedtools/work/bedtools2-2.30.0/src/utils/htslib'
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o kfunc.o kfunc.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o knetfile.o knetfile.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o kstring.o kstring.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o bgzf.o bgzf.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o errmod.o errmod.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o faidx.o faidx.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o hfile.o hfile.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9"' > version.h
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -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;
| ^~~
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o hts_os.o hts_os.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o md5.o md5.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o multipart.o multipart.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o probaln.o probaln.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o realn.o realn.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o regidx.o regidx.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o sam.o sam.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o tbx.o tbx.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o textutils.o textutils.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o thread_pool.o thread_pool.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o vcf.o vcf.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o vcfutils.o vcfutils.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/files.o cram/files.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/sam_header.o cram/sam_header.c
gcc -pipe -fno-aggressive-loop-optimizations -pipe -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.9 -I. -c -o cram/string_alloc.o cram/string_alloc.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
gmake[1]: Leaving directory '/home/pbulk/build/biology/bedtools/work/bedtools2-2.30.0/src/utils/htslib'
- Building main bedtools binary.
Undefined first referenced
symbol in file
recv src/utils/htslib/libhts.a(hfile.o)
send src/utils/htslib/libhts.a(hfile.o)
socket src/utils/htslib/libhts.a(knetfile.o)
setsockopt src/utils/htslib/libhts.a(knetfile.o)
connect src/utils/htslib/libhts.a(knetfile.o)
getaddrinfo src/utils/htslib/libhts.a(knetfile.o)
freeaddrinfo src/utils/htslib/libhts.a(knetfile.o)
gai_strerror src/utils/htslib/libhts.a(knetfile.o)
ld: fatal: symbol referencing errors. No output written to bin/bedtools
collect2: error: ld returned 1 exit status
gmake: *** [Makefile:179: bin/bedtools] Error 1
*** Error code 2
Stop.
bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools
*** Error code 1
Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools