+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/rna-star-2.7.10b/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/rna-star-2.7.10b/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for rna-star-2.7.10b
echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c
BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c
'rm' -f ./Depend.list
g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:38:38+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list
g++: warning: parametersDefault.xxd: linker input file unused because linking not done
'rm' -f STAR.o Parameters.o
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include systemFunctions.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_collapseUMI_Graph.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_collapseUMIall.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ParametersClip_initialize.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ClipMate_clip.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ClipCR4.cpp
cd opal && \
g++ -c -I./ -std=c++11 -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -mavx2 opal.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ClipMate_clipChunk.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ClipMate_initialize.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_loadRawMatrix.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_emptyDrops_CR.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include soloInputFeatureUMI.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_countSmartSeq.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_redistributeReadsByCB.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_quantTranscript.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_sumThreads.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_countVelocyto.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_countCBgeneUMI.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include Transcriptome_classifyAlign.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_cellFiltering.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_statsOutput.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include bamSortByCoordinate.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloBarcode.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ParametersSolo.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloRead.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloRead_record.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloReadBarcode.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloReadBarcode_getCBandUMI.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloBarcode_extractBarcode.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloReadFeature.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloReadFeature_record.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloReadFeature_inputRecords.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include Solo.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_outputResults.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_processRecords.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SoloFeature_addBAMtags.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ReadAlign_transformGenome.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include Genome_transformGenome.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include Transcript_convertGenomeCigar.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include twoPassRunPass1.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include samHeaders.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include Genome_genomeLoad.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include Genome_genomeOutLoad.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include Transcript_transformGenome.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ReadAlign_outputSpliceGraphSAM.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ReadAlign_mapOneReadSpliceGraph.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SpliceGraph.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SpliceGraph_swScoreSpliced.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SpliceGraph_swTraceBack.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SpliceGraph_findSuperTr.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include sjAlignSplit.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include GTF.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include GTF_transcriptGeneSJ.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include GTF_superTranscript.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SuperTranscriptome.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ReadAlign_outputAlignments.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include ReadAlign.cpp
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include STAR.cpp
STAR.cpp: In function 'int main(int, char**)':
STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result]
190 | bgzf_flush(P.inOut->outBAMfileUnsorted);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result]
194 | bgzf_flush(P.inOut->outQuantBAMfile);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -I/opt/pkg/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-02-18T08:39:10+0000 :/home/pbulk/build/biology/rna-star/work/STAR-2.7.10b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include SharedMemory.cpp
SharedMemory.cpp: In member function 'void SharedMemory::CreateAndInitSharedObject(size_t)':
SharedMemory.cpp:109:59: error: 'SHM_NORESERVE' was not declared in this scope; did you mean 'MAP_NORESERVE'?
109 | _shmID=shmget(_key, toReserve, IPC_CREAT | IPC_EXCL | SHM_NORESERVE | 0666); // _shmID = shmget(shmKey, shmSize, IPC_CREAT | SHM_NORESERVE | SHM_HUGETLB | 0666);
| ^~~~~~~~~~~~~
| MAP_NORESERVE
SharedMemory.cpp: In member function 'void SharedMemory::EnsureCounter()':
SharedMemory.cpp:254:72: error: 'SHM_NORESERVE' was not declared in this scope; did you mean 'MAP_NORESERVE'?
254 | _sharedCounterID=shmget(_counterKey, 1, IPC_CREAT | IPC_EXCL | SHM_NORESERVE | 0666);
| ^~~~~~~~~~~~~
| MAP_NORESERVE
gmake: *** [Makefile:105: SharedMemory.o] Error 1
*** Error code 2
Stop.
bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star
*** Error code 1
Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star