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?