Question: SpliceJumper installation issues. Particularly with make
0
gravatar for njbernstein
3.1 years ago by
njbernstein40
United States
njbernstein40 wrote:

 

I'm attempting to install splice jumper (http://www.biomedcentral.com/1471-2105/16/S17/S10, https://github.com/Reedwarbler/SpliceJumper)

So I downloaded the zip, and unzipped it. Then ran make, but there is still no SpliceJumper (I have bamtools installed). 

Here is the output from make:

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c bam_parse.cpp

bam_parse.cpp: In member function ‘void BamParse::parseCigar(std::vector<BamTools::CigarOp, std::allocator<BamTools::CigarOp> >&, BamAlignmentRecord*&)’:

bam_parse.cpp:57: warning: comparison between signed and unsigned integer expressions

bam_parse.cpp: In member function ‘bool BamParse::parseAlignment(int, int, int, int)’:

bam_parse.cpp:121: warning: unused variable ‘is_set’

bam_parse.cpp: In member function ‘void BamParse::getChromNameLength(int, std::string&, int&)’:

bam_parse.cpp:275: warning: comparison between signed and unsigned integer expressions

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c Coverage.cpp

Coverage.cpp:454:5: warning: multi-line comment

Coverage.cpp: In member function ‘void Coverage::pileupRegion(int, int, int, BamParse&, int*&, Brkpnt*&, int*&, int*&, int*&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&, std::string&)’:

Coverage.cpp:405: warning: ‘clip_pos1’ may be used uninitialized in this function

Coverage.cpp:405: warning: ‘clip_pos2’ may be used uninitialized in this function

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c fai_parser.cpp

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c fasta_parser.cpp

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c ReferenceSeq.cpp

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c algorithms/local_alignment.cpp

algorithms/local_alignment.cpp:29: warning: deprecated conversion from string constant to ‘char*’

algorithms/local_alignment.cpp:50: warning: deprecated conversion from string constant to ‘char*’

algorithms/local_alignment.cpp:71: warning: deprecated conversion from string constant to ‘char*’

algorithms/local_alignment.cpp:81: warning: deprecated conversion from string constant to ‘char*’

algorithms/local_alignment.cpp: In member function ‘void LocalAlignment::align(int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&)’:

algorithms/local_alignment.cpp:1071: warning: comparison between signed and unsigned integer expressions

algorithms/local_alignment.cpp:1071: warning: comparison between signed and unsigned integer expressions

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c CandidateSitesCaller.cpp

CandidateSitesCaller.cpp: In member function ‘void CandidateSitesCaller::loadBrkpntInfo(int*&, int*&, int*&, int*&)’:

CandidateSitesCaller.cpp:57: warning: unused variable ‘clip’

CandidateSitesCaller.cpp: In member function ‘void CandidateSitesCaller::callCandidateSites()’:

CandidateSitesCaller.cpp:187: warning: unused variable ‘idx_start’

CandidateSitesCaller.cpp:137: warning: unused variable ‘lclip’

CandidateSitesCaller.cpp:137: warning: unused variable ‘rclip’

CandidateSitesCaller.cpp:138: warning: unused variable ‘clip’

CandidateSitesCaller.cpp:140: warning: unused variable ‘local_cov’

CandidateSitesCaller.cpp: In member function ‘void CandidateSitesCaller::outputFeatures(std::string)’:

CandidateSitesCaller.cpp:311: warning: comparison between signed and unsigned integer expressions

CandidateSitesCaller.cpp:272: warning: unused variable ‘nsplit_map’

CandidateSitesCaller.cpp: In member function ‘bool CandidateSitesCaller::searchMapSite(std::string, ReferenceSeq&, std::string, int, int, bool)’:

CandidateSitesCaller.cpp:652: warning: comparison between signed and unsigned integer expressions

CandidateSitesCaller.cpp:700: warning: comparison between signed and unsigned integer expressions

CandidateSitesCaller.cpp:753: warning: comparison between signed and unsigned integer expressions

CandidateSitesCaller.cpp: In member function ‘void CandidateSitesCaller::getCigarPosLen(std::vector<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int>, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int> > >&, int, int&, int&, int&, int&)’:

CandidateSitesCaller.cpp:824: warning: unused variable ‘cnt’

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c TrainingSet.cpp

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c HardClipReads.cpp

HardClipReads.cpp:138: warning: deprecated conversion from string constant to ‘char*’

HardClipReads.cpp: In function ‘void stk_printstr(const kstring_t*, unsigned int)’:

HardClipReads.cpp:157: warning: comparison between signed and unsigned integer expressions

HardClipReads.cpp:159: warning: comparison between signed and unsigned integer expressions

HardClipReads.cpp: In function ‘int stk_subseq(const char*, const char*, const char*)’:

HardClipReads.cpp:274: warning: comparison between signed and unsigned integer expressions

HardClipReads.cpp:278: warning: comparison between signed and unsigned integer expressions

HardClipReads.cpp:290: warning: comparison between signed and unsigned integer expressions

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c main.cpp

main.cpp: In function ‘int main(int, char**)’:

main.cpp:26: warning: unused variable ‘refsize’

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -o JunctionClassifier_1 public_func.o Alignment.o bam_parse.o Coverage.o fai_parser.o fasta_parser.o ReferenceSeq.o local_alignment.o CandidateSitesCaller.o TrainingSet.o HardClipReads.o main.o \

    -lbamtools -lz -lm

 

Here is the output from ls: 

algorithms     bam_alignment_record.h  bam_parse.o               Coverage.cpp    fai_parser.h      fasta_parser.o     JunctionCaller.cpp    kseq.h             Makefile         public_func.o        ReferenceSeq.h    TrainingSet.cpp

Alignment.cpp  bam_header_record.h     CandidateSitesCaller.cpp  Coverage.h      fai_parser.o      HardClipReads.cpp  JunctionCaller.h      local_alignment.o  Makefile.bak     public_parameters.h  ReferenceSeq.o    TrainingSet.h

Alignment.h    bam_parse.cpp           CandidateSitesCaller.h    Coverage.o      fasta_parser.cpp  HardClipReads.h    JunctionClassifier_1  main.cpp           public_func.cpp  readme.txt           ResultAnalyze     TrainingSet.o

Alignment.o    bam_parse.h             CandidateSitesCaller.o    fai_parser.cpp  fasta_parser.h    HardClipReads.o    khash.h               main.o             public_func.h    ReferenceSeq.cpp

 

Any Ideas?

rna-seq • 905 views
ADD COMMENTlink modified 3.1 years ago by Jean-Karim Heriche18k • written 3.1 years ago by njbernstein40
3
gravatar for Jean-Karim Heriche
3.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

I don't see any error, only warnings in the output you provided. Also object files have been generated so it looks like the compilation worked. From the last line of the make output, it looks like the program is named JunctionClassifier_1 which you  have in your ls output so I think it all worked fine.

ADD COMMENTlink written 3.1 years ago by Jean-Karim Heriche18k

Great Thanks!

ADD REPLYlink written 3.1 years ago by njbernstein40
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