sci-biology:STAR-2.7.10a:20220802-145349.log

sci-biology:STAR-2.7.10a:20220802-145349.log (text/plain), 29.64 KB, created by Toralf Förster on 2022-08-02 14:55:34 UTC

 * Package:    sci-biology/STAR-2.7.10a
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_musl kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking STAR-2.7.10a.tar.gz to /var/tmp/portage/sci-biology/STAR-2.7.10a/work
>>> Source unpacked in /var/tmp/portage/sci-biology/STAR-2.7.10a/work
>>> Preparing source in /var/tmp/portage/sci-biology/STAR-2.7.10a/work/STAR-2.7.10a ...
 * Applying STAR-2.7.10a-fix-build-system.patch ...
 [ ok ]
 * Applying STAR-2.7.10a-missing-include.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/STAR-2.7.10a/work/STAR-2.7.10a ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/STAR-2.7.10a/work/STAR-2.7.10a ...
make -j4 -C source STAR 
make: Entering directory '/var/tmp/portage/sci-biology/STAR-2.7.10a/work/STAR-2.7.10a/source'
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_multiMappers.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 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_multiMappers.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 twoPassRunPass1.cpp bam_cat.c
'rm' -f ./Depend.list
x86_64-gentoo-linux-musl-g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -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_multiMappers.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 twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list
x86_64-gentoo-linux-musl-g++: warning: parametersDefault.xxd: linker input file unused because linking not done
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_collapseUMI_Graph.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_collapseUMIall_multiMappers.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ParametersClip_initialize.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ClipMate_clip.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ClipCR4.cpp
cd opal && \
x86_64-gentoo-linux-musl-g++ -c -I./ -std=c++11   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS  -mavx2 opal.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ClipMate_clipChunk.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ClipMate_initialize.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_loadRawMatrix.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_emptyDrops_CR.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS soloInputFeatureUMI.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_countSmartSeq.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_redistributeReadsByCB.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_quantTranscript.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_sumThreads.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_countVelocyto.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_countCBgeneUMI.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS Transcriptome_classifyAlign.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_cellFiltering.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_statsOutput.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS bamSortByCoordinate.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloBarcode.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ParametersSolo.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloRead.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloRead_record.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloReadBarcode.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloReadBarcode_getCBandUMI.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloBarcode_extractBarcode.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloReadFeature.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloReadFeature_record.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloReadFeature_inputRecords.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS Solo.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_outputResults.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_processRecords.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SoloFeature_addBAMtags.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ReadAlign_transformGenome.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS Genome_transformGenome.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS Transcript_convertGenomeCigar.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS twoPassRunPass1.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS samHeaders.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS Genome_genomeLoad.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS Genome_genomeOutLoad.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS Transcript_transformGenome.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ReadAlign_outputSpliceGraphSAM.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ReadAlign_mapOneReadSpliceGraph.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SpliceGraph.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SpliceGraph_swScoreSpliced.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SpliceGraph_swTraceBack.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SpliceGraph_findSuperTr.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS sjAlignSplit.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS GTF.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS GTF_transcriptGeneSJ.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS GTF_superTranscript.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SuperTranscriptome.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ReadAlign_outputAlignments.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS ReadAlign.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS STAR.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SharedMemory.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS PackedArray.cpp
x86_64-gentoo-linux-musl-g++ -c   -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=""' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS SuffixArrayFuns.cpp
In file included from SharedMemory.cpp:5:
SharedMemory.h:142:27: error: expected ')' before 'key'
  142 |         SharedMemory(key_t key, bool unloadLast);
      |                     ~     ^~~~
      |                           )
SharedMemory.h:160:9: error: 'key_t' does not name a type
  160 |         key_t _key;
      |         ^~~~~
SharedMemory.h:161:9: error: 'key_t' does not name a type
  161 |         key_t _counterKey;
      |         ^~~~~
SharedMemory.cpp:21:1: error: no declaration matches 'SharedMemory::SharedMemory(key_t, bool)'
   21 | SharedMemory::SharedMemory(key_t key, bool unloadLast): _key(key), _counterKey(key+1), _unloadLast(unloadLast), _err(&cerr)
      | ^~~~~~~~~~~~
SharedMemory.h:85:7: note: candidates are: 'constexpr SharedMemory::SharedMemory(const SharedMemory&)'
   85 | class SharedMemory
      |       ^~~~~~~~~~~~
SharedMemory.h:85:7: note:                 'SharedMemory::SharedMemory()'
SharedMemory.h:85:7: note: 'class SharedMemory' defined here
SharedMemory.cpp: In member function 'std::string SharedMemory::GetPosixObjectKey()':
SharedMemory.cpp:89:19: error: '_key' was not declared in this scope; did you mean 'key'?
   89 |     key << "/" << _key;
      |                   ^~~~
      |                   key
SharedMemory.cpp: In member function 'std::string SharedMemory::CounterName()':
SharedMemory.cpp:96:45: error: '_key' was not declared in this scope
   96 |     counterName << "/shared_use_counter" << _key;
      |                                             ^~~~
SharedMemory.cpp: In member function 'void SharedMemory::CreateAndInitSharedObject(size_t)':
SharedMemory.cpp:108:19: error: '_key' was not declared in this scope
  108 |     _shmID=shmget(_key, toReserve, IPC_CREAT | IPC_EXCL | SHM_NORESERVE | 0666); //        _shmID = shmget(shmKey, shmSize, IPC_CREAT | SHM_NORESERVE | SHM_HUGETLB | 0666);
      |                   ^~~~
SharedMemory.cpp: In member function 'void SharedMemory::OpenIfExists()':
SharedMemory.cpp:140:23: error: '_key' was not declared in this scope
  140 |         _shmID=shmget(_key,0,0);
      |                       ^~~~
SharedMemory.cpp: In member function 'void SharedMemory::EnsureCounter()':
SharedMemory.cpp:246:33: error: '_counterKey' was not declared in this scope; did you mean '_counterMem'?
  246 |         _sharedCounterID=shmget(_counterKey,0,0);
      |                                 ^~~~~~~~~~~
      |                                 _counterMem
SharedMemory.cpp:253:33: error: '_counterKey' was not declared in this scope; did you mean '_counterMem'?
  253 |         _sharedCounterID=shmget(_counterKey, 1, IPC_CREAT | IPC_EXCL | SHM_NORESERVE | 0666);
      |                                 ^~~~~~~~~~~
      |                                 _counterMem
make: *** [Makefile:95: SharedMemory.o] Error 1
make: *** Waiting for unfinished jobs....
STAR.cpp: In function 'int main(int, char**)':
STAR.cpp:189:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  189 |         bgzf_flush(P.inOut->outBAMfileUnsorted);
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
STAR.cpp:193:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  193 |         bgzf_flush(P.inOut->outQuantBAMfile);
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
make: Leaving directory '/var/tmp/portage/sci-biology/STAR-2.7.10a/work/STAR-2.7.10a/source'
 * ERROR: sci-biology/STAR-2.7.10a::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/STAR-2.7.10a::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/STAR-2.7.10a::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:STAR-2.7.10a:20220802-145349.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/STAR-2.7.10a/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/STAR-2.7.10a/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/STAR-2.7.10a/work/STAR-2.7.10a'
 * S: '/var/tmp/portage/sci-biology/STAR-2.7.10a/work/STAR-2.7.10a'