sci-biology:STAR-2.5.3a:20200805-064032.log

sci-biology:STAR-2.5.3a:20200805-064032.log (text/plain), 40.84 KB, created by Toralf Förster on 2020-08-05 16:12:51 UTC

 * Package:    sci-biology/STAR-2.5.3a
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking STAR-2.5.3a.tar.gz to /var/tmp/portage/sci-biology/STAR-2.5.3a/work
>>> Source unpacked in /var/tmp/portage/sci-biology/STAR-2.5.3a/work
>>> Preparing source in /var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a ...
 * Applying STAR-2.5.3a-fix-build-system.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a ...
make -j1 -C source STAR 
make: Entering directory '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source'
echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeGenerate.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sortSuffixesBucket.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c
BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeGenerate.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sortSuffixesBucket.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c
/bin/rm -f ./Depend.list
x86_64-pc-linux-gnu-g++ -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:34 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeGenerate.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sortSuffixesBucket.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c parametersDefault.xxd >> Depend.list
x86_64-pc-linux-gnu-g++: warning: parametersDefault.xxd: linker input file unused because linking not done
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' SharedMemory.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' PackedArray.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' SuffixArrayFuns.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' STAR.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Parameters.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' InOutStreams.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' SequenceFuns.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Genome.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Chain.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Stats.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Transcript.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Transcript_alignScore.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_storeAligns.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_stitchPieces.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_multMapSelect.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_mapOneRead.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' readLoad.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlignChunk.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlignChunk_processChunks.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlignChunk_mapChunk.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' OutSJ.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' outputSJ.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' blocksOverlap.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ThreadControl.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sysRemoveDir.cpp
sysRemoveDir.cpp: In function ‘int removeFileOrDir(const char*, const stat*, int, FTW*)’:
sysRemoveDir.cpp:7:58: warning: unused parameter ‘sb’ [-Wunused-parameter]
    7 | int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
      |                                       ~~~~~~~~~~~~~~~~~~~^~
sysRemoveDir.cpp:7:88: warning: unused parameter ‘ftwbuf’ [-Wunused-parameter]
    7 |  char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
      |                                                   ~~~~~~~~~~~~^~~~~~

x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_maxMappableLength2strands.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' binarySearch2.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_outputAlignments.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_outputTranscriptSAM.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_outputTranscriptSJ.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_outputTranscriptCIGARp.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_createExtendWindowsWithAlign.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_assignAlignToWindow.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_oneRead.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_stitchWindowSeeds.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_chimericDetection.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' stitchWindowAligns.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' extendAlign.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' stitchAlignToTranscript.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' alignSmithWaterman.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' genomeGenerate.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' genomeParametersWrite.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' genomeScanFastaFiles.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' genomeSAindex.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Genome_insertSequences.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' insertSeqSA.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' funCompareUintAndSuffixes.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sortSuffixesBucket.cpp
sortSuffixesBucket.cpp: In function ‘void sortSuffixesBucket(char*, void*, int, int)’:
sortSuffixesBucket.cpp:27:40: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   27 |         uint64_t iprev=*(uint64_t*)(ind+0*indSkip);
      |                                     ~~~^~~~~~~~~~
sortSuffixesBucket.cpp:31:33: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   31 |             if (*(uint64_t*)(ind+id*indSkip)==iprev)
      |                              ~~~^~~~~~~~~~~
sortSuffixesBucket.cpp:43:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   43 |                 iprev=*(uint64_t*)(ind+id*indSkip);
      |                                    ~~~^~~~~~~~~~~
sortSuffixesBucket.cpp:62:45: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   62 |                 charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t
      |                                          ~~~^~~~~~~~~~~
sortSuffixesBucket.cpp:62:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   62 |                 charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t
      |                                          ~~~~~~~~~~~~~~^~
sortSuffixesBucket.cpp:62:71: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   62 |       charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^

sortSuffixesBucket.cpp:85:46: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   85 |                     char c=G[*(uint64_t*)(ind+id*indSkip+8) + charShift];
      |                                           ~~~^~~~~~~~~~~
sortSuffixesBucket.cpp:85:57: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   85 |                     char c=G[*(uint64_t*)(ind+id*indSkip+8) + charShift];
      |                                           ~~~~~~~~~~~~~~^~
sortSuffixesBucket.cpp:86:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   86 |                     memcpy(ind1+charStart[c]*indSkip, ind+id*indSkip, indSkip);
      |                                           ^
sortSuffixesBucket.cpp:86:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   86 |                     memcpy(ind1+charStart[c]*indSkip, ind+id*indSkip, indSkip);
      |                                                       ~~~^~~~~~~~~~~
sortSuffixesBucket.cpp:87:31: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   87 |                     charStart[c]++;
      |                               ^
sortSuffixesBucket.cpp:89:27: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith]
   89 |                 memcpy(ind+uB1[iu]*indSkip, ind1+uB1[iu]*indSkip, (uB2[iu]-uB1[iu])*indSkip);
      |                        ~~~^~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' funCompareUintAndSuffixesMemcmp.cpp
funCompareUintAndSuffixesMemcmp.cpp: In function ‘int funCompareUintAndSuffixesMemcmp(const void*, const void*)’:
funCompareUintAndSuffixesMemcmp.cpp:21:15: warning: unused variable ‘p5’ [-Wunused-variable]
   21 |         char *p5=g_funCompareUintAndSuffixesMemcmp_G+va[1]+g_funCompareUintAndSuffixesMemcmp_L;
      |               ^~
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' TimeFunctions.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ErrorWarning.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' loadGTF.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' streamFuns.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' stringSubstituteAll.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Transcriptome.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Transcriptome_quantAlign.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_quantTranscriptome.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Quantifications.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Transcriptome_geneCountsAddAlign.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sjdbLoadFromFiles.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sjdbLoadFromStream.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sjdbPrepare.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sjdbBuildIndex.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sjdbInsertJunctions.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' mapThreadsSpawn.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' BAMoutput.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' BAMfunctions.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_alignBAM.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' BAMbinSortByCoordinate.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' signalFromBAM.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' bamRemoveDuplicates.cpp
x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' BAMbinSortUnmapped.cpp
BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, BGZF*, Parameters*)’:
BAMbinSortUnmapped.cpp:5:78: warning: unused parameter ‘bgzfBAM’ [-Wunused-parameter]
    5 | mapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P) {
      |                                                       ~~~~~~^~~~~~~

x86_64-pc-linux-gnu-g++ -c  -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` bam_cat.c
x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color  -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Wed Aug 5 08:40:41 AM CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o STAR SharedMemory.o PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Chain.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o sortSuffixesBucket.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o bam_cat.o GlobalVariables.cpp  -pthread `x86_64-pc-linux-gnu-pkg-config --libs htslib` `x86_64-pc-linux-gnu-pkg-config --libs zlib` -lrt
Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’:
Parameters_openReadsFiles.cpp:58:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   58 |                 system(("ls -lL " + file1 + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str());
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Parameters_openReadsFiles.cpp:30:20: warning: variable ‘imate’ might be clobbered by ‘longjmp’ or ‘vfork’ [-Wclobbered]
   30 |          for (uint imate=0;imate<readNmates;imate++) {//open readIn files
      |                    ^~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: bam_cat.o: in function `bam_cat(int, char* const*, bam_hdr_t const*, char const*)':
bam_cat.c:(.text+0x310): undefined reference to `bam_hdr_destroy'
collect2: error: ld returned 1 exit status
make: *** [Makefile:90: STAR] Error 1
make: Leaving directory '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source'
 * ERROR: sci-biology/STAR-2.5.3a::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/STAR-2.5.3a::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/STAR-2.5.3a::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:STAR-2.5.3a:20200805-064032.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/STAR-2.5.3a/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/STAR-2.5.3a/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a'
 * S: '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a'