+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/bedtools-2.30.0nb1/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/bedtools-2.30.0nb1/work.log => Bootstrap dependency digest>=20211023: found digest-20220214 ===> Building for bedtools-2.30.0nb1 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/python3.10] 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&, 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::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 src/sampleFile/sampleFile.cpp:112:1: fatal error: opening dependency file obj/sampleFile.Td: Disc quota exceeded 112 | } | ^ compilation terminated. gmake: *** [src/sampleFile/Makefile.frag:7: obj/sampleFile.o] 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