Package: g++-6 Version: 6-20160117-1 I get this ICE when building the package but not when running the command manually.
Oh, because some command line options, including -flto, get dropped. I can reproduce it now. How do I generate a testcase for an LTO bug? > Package: rna-star > Version: 2.5.0a+dfsg-1 ... > g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -Wall -Wextra -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security > -D'COMPILATION_TIME_PLACE="Tue Jan 19 11:34:24 UTC 2016 > :/<<BUILDDIR>>/rna-star-2.5.0a+dfsg/source"' bam_cat.c > g++ -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp > -D'COMPILATION_TIME_PLACE="Tue Jan 19 11:34:24 UTC 2016 > :/<<BUILDDIR>>/rna-star-2.5.0a+dfsg/source"' -flto -flto -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fstack-protector-strong -Wformat > -Werror=format-security SharedMemory.o PackedArray.o SuffixArrayFuns.o STAR.o > Parameters.o InOutStreams.o SequenceFuns.o Genome.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_ass > ignAlignToWindow.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 > 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 -Bstatic -lhts -Bdynamic -Wl,-z,relro -Wl,-z,relro > Parameters_openReadsFiles.cpp: In member function 'void > Parameters::openReadsFiles()': > Parameters_openReadsFiles.cpp:58:97: warning: ignoring return value of 'int > system(const char*)', declared with attribute warn_unused_result > [-Wunused-result] > system(("ls -lL " + file1 + " > "+ > outFileTmp+"/readFilesIn.info 2>&1").c_str()); > > ^ > > lto1: internal compiler error: in dwarf2out_finish, at dwarf2out.c:27175 > 0x6a2e00 dwarf2out_finish > ../../src/gcc/dwarf2out.c:27175 > Please submit a full bug report, > with preprocessed source if appropriate. > Please include the complete backtrace with any bug report. > See <file:///usr/share/doc/gcc-6/README.Bugs> for instructions. > lto-wrapper: fatal error: g++ returned 1 exit status > compilation terminated. > /usr/bin/ld: error: lto-wrapper failed > collect2: error: ld returned 1 exit status > Makefile:98: recipe for target 'STAR' failed > make[2]: *** [STAR] Error 1 -- Martin Michlmayr Linux for HPE Helion, Hewlett Packard Enterprise