sci-biology:STAR-2.5.3a:20200405-103850.log

sci-biology:STAR-2.5.3a:20200405-103850.log (text/plain), 10.64 KB, created by Toralf Förster on 2020-04-05 11:19:41 UTC

 * Package:    sci-biology/STAR-2.5.3a
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail],[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-2.5.3a.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-gentoo-linux-musl-g++ -Wall -Wextra -pthread `x86_64-gentoo-linux-musl-pkg-config --cflags htslib` `x86_64-gentoo-linux-musl-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Sun Apr 5 12:38:53 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-gentoo-linux-musl-g++: warning: parametersDefault.xxd: linker input file unused because linking not done
x86_64-gentoo-linux-musl-g++ -c  -O2 -pipe -march=native -Wall -Wextra -pthread `x86_64-gentoo-linux-musl-pkg-config --cflags htslib` `x86_64-gentoo-linux-musl-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Sun Apr 5 12:38:59 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' SharedMemory.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)
      | ^~~~~~~~~~~~
In file included from SharedMemory.cpp:5:
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:45: SharedMemory.o] 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:20200405-103850.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'