{"action":"closed","issue":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/71","labels_url":"https://api.github.com/repos/alexdobin/STAR/issues/71/labels{/name}","comments_url":"https://api.github.com/repos/alexdobin/STAR/issues/71/comments","events_url":"https://api.github.com/repos/alexdobin/STAR/issues/71/events","html_url":"https://github.com/alexdobin/STAR/issues/71","id":104481387,"number":71,"title":"make fails","user":{"login":"macmanes","id":164752,"avatar_url":"https://avatars.githubusercontent.com/u/164752?v=3","gravatar_id":"","url":"https://api.github.com/users/macmanes","html_url":"https://github.com/macmanes","followers_url":"https://api.github.com/users/macmanes/followers","following_url":"https://api.github.com/users/macmanes/following{/other_user}","gists_url":"https://api.github.com/users/macmanes/gists{/gist_id}","starred_url":"https://api.github.com/users/macmanes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macmanes/subscriptions","organizations_url":"https://api.github.com/users/macmanes/orgs","repos_url":"https://api.github.com/users/macmanes/repos","events_url":"https://api.github.com/users/macmanes/events{/privacy}","received_events_url":"https://api.github.com/users/macmanes/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-09-02T13:29:34Z","updated_at":"2015-09-03T19:16:04Z","closed_at":"2015-09-03T19:16:04Z","body":"with a `git clone` this AM (2 Sept)\r\n\r\n`gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4`\r\n\r\n\r\n```\r\nmake\r\n\r\ncd source && make STAR\r\nmake[1]: Entering directory `/share/STAR/source'\r\nMakefile:86: Depend.list: No such file or directory\r\necho alignSmithWaterman.cpp BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp ErrorWarning.cpp extendAlign.cpp Genome.cpp genomeGenerate.cpp genomeParametersWrite.cpp GlobalVariables.cpp InOutStreams.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp OutSJ.cpp PackedArray.cpp Parameters_closeReadsFiles.cpp Parameters.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign.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 readLoad.cpp SequenceFuns.cpp serviceFuns.cpp SharedMemory.cpp signalFromBAM.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sjSplitAlign.cpp STAR.cpp Stats.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp SuffixArrayFuns.cpp sysRemoveDir.cpp ThreadControl.cpp TimeFunctions.cpp Transcript_alignScore.cpp Transcript.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp bam_cat.c\r\nalignSmithWaterman.cpp BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp ErrorWarning.cpp extendAlign.cpp Genome.cpp genomeGenerate.cpp genomeParametersWrite.cpp GlobalVariables.cpp InOutStreams.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp OutSJ.cpp PackedArray.cpp Parameters_closeReadsFiles.cpp Parameters.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign.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 readLoad.cpp SequenceFuns.cpp serviceFuns.cpp SharedMemory.cpp signalFromBAM.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sjSplitAlign.cpp STAR.cpp Stats.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp SuffixArrayFuns.cpp sysRemoveDir.cpp ThreadControl.cpp TimeFunctions.cpp Transcript_alignScore.cpp Transcript.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp bam_cat.c\r\n/bin/rm -f ./Depend.list\r\ng++ -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=\"Wed Sep 2 09:32:30 EDT 2015 :/share/STAR/source\"' -MM alignSmithWaterman.cpp BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp ErrorWarning.cpp extendAlign.cpp Genome.cpp genomeGenerate.cpp genomeParametersWrite.cpp GlobalVariables.cpp InOutStreams.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp OutSJ.cpp PackedArray.cpp Parameters_closeReadsFiles.cpp Parameters.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign.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 readLoad.cpp SequenceFuns.cpp serviceFuns.cpp SharedMemory.cpp signalFromBAM.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sjSplitAlign.cpp STAR.cpp Stats.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp SuffixArrayFuns.cpp sysRemoveDir.cpp ThreadControl.cpp TimeFunctions.cpp Transcript_alignScore.cpp Transcript.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list\r\ng++: warning: parametersDefault.xxd: linker input file unused because linking not done\r\ng++: warning: htslib: linker input file unused because linking not done\r\nmake[1]: Leaving directory `/share/STAR/source'\r\nmake[1]: Entering directory `/share/STAR/source'\r\ng++ -c  -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=\"Wed Sep 2 09:32:34 EDT 2015 :/share/STAR/source\"' SharedMemory.cpp\r\ng++ -c  -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=\"Wed Sep 2 09:32:34 EDT 2015 :/share/STAR/source\"' PackedArray.cpp\r\ng++ -c  -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=\"Wed Sep 2 09:32:34 EDT 2015 :/share/STAR/source\"' SuffixArrayFuns.cpp\r\nSuffixArrayFuns.cpp:191:6: warning: unused parameter ‘dirR’ [-Wunused-parameter]\r\n uint suffixArraySearch(char** s2, uint S, uint N, char* G, PackedArray& SA, bool dirR, uint i1, uint i2, uint L, Parameters* P) {\r\n      ^\r\nSuffixArrayFuns.cpp: In function ‘long long unsigned int suffixArraySearch(char**, long long unsigned int, long long unsigned int, char*, PackedArray&, bool, long long unsigned int, long long unsigned int, long long unsigned int, Parameters*)’:\r\nSuffixArrayFuns.cpp:264:9: warning: ‘compRes’ may be used uninitialized in this function [-Wmaybe-uninitialized]\r\n         if (compRes) { //move 1 to 3\r\n         ^\r\ng++ -c  -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=\"Wed Sep 2 09:32:34 EDT 2015 :/share/STAR/source\"' STAR.cpp\r\ng++ -c  -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=\"Wed Sep 2 09:32:34 EDT 2015 :/share/STAR/source\"' Parameters.cpp\r\nParameters.cpp: In member function ‘void Parameters::inputParameters(int, char**)’:\r\nParameters.cpp:832:25: error: assigning to an array from an initializer list\r\n     alignEndsType.ext[0]={false, false};\r\n                         ^\r\nParameters.cpp:833:25: error: assigning to an array from an initializer list\r\n     alignEndsType.ext[1]={false, false};\r\n                         ^\r\nParameters.cpp:836:29: error: assigning to an array from an initializer list\r\n         alignEndsType.ext[0]={true, true};\r\n                             ^\r\nParameters.cpp:837:29: error: assigning to an array from an initializer list\r\n         alignEndsType.ext[1]={true, true};\r\n                             ^\r\nParameters.cpp:1036:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n     for (int ii=0; ii<chimFilter.size(); ii++)\r\n                                       ^\r\nParameters.cpp:1054:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n     for (int ii=0; ii<readNameSeparator.size(); ii++)\r\n                                              ^\r\nmake[1]: *** [Parameters.o] Error 1\r\nmake[1]: Leaving directory `/share/STAR/source'\r\nmake: *** [STAR] Error 2\r\n```"}}