Bug#812062: ICE: in dwarf2out_finish, at dwarf2out.c:27175 (lto)

[Martin Michlmayr <tbm@hpe.com>]

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