make[2]: Entering directory `/home/adam/Fedora/tmp/tophat-1.2.0.test/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi
reads.cpp: In function 'void BWA_decode(const std::string&, const std::string&, const std::string&, std::string&)':
reads.cpp:434:54: warning: array subscript has type 'char'
if gcc -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include  -Wall -m64 -O3  -DNDEBUG -MT alphabet.o -MD -MP -MF ".deps/alphabet.Tpo" -c -o alphabet.o alphabet.c; \
then mv -f ".deps/alphabet.Tpo" ".deps/alphabet.Po"; else rm -f ".deps/alphabet.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT bwt_map.o -MD -MP -MF ".deps/bwt_map.Tpo" -c -o bwt_map.o bwt_map.cpp; \
then mv -f ".deps/bwt_map.Tpo" ".deps/bwt_map.Po"; else rm -f ".deps/bwt_map.Tpo"; exit 1; fi
bwt_map.cpp: In member function 'virtual bool SplicedBowtieHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)':
bwt_map.cpp:457:39: warning: comparison between signed and unsigned integer expressions
bwt_map.cpp:507:39: warning: comparison between signed and unsigned integer expressions
bwt_map.cpp:513:40: warning: comparison between signed and unsigned integer expressions
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \
then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT junctions.o -MD -MP -MF ".deps/junctions.Tpo" -c -o junctions.o junctions.cpp; \
then mv -f ".deps/junctions.Tpo" ".deps/junctions.Po"; else rm -f ".deps/junctions.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT insertions.o -MD -MP -MF ".deps/insertions.Tpo" -c -o insertions.o insertions.cpp; \
then mv -f ".deps/insertions.Tpo" ".deps/insertions.Po"; else rm -f ".deps/insertions.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT deletions.o -MD -MP -MF ".deps/deletions.Tpo" -c -o deletions.o deletions.cpp; \
then mv -f ".deps/deletions.Tpo" ".deps/deletions.Po"; else rm -f ".deps/deletions.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT align_status.o -MD -MP -MF ".deps/align_status.Tpo" -c -o align_status.o align_status.cpp; \
then mv -f ".deps/align_status.Tpo" ".deps/align_status.Po"; else rm -f ".deps/align_status.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT fragments.o -MD -MP -MF ".deps/fragments.Tpo" -c -o fragments.o fragments.cpp; \
then mv -f ".deps/fragments.Tpo" ".deps/fragments.Po"; else rm -f ".deps/fragments.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT tokenize.o -MD -MP -MF ".deps/tokenize.Tpo" -c -o tokenize.o tokenize.cpp; \
then mv -f ".deps/tokenize.Tpo" ".deps/tokenize.Po"; else rm -f ".deps/tokenize.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT inserts.o -MD -MP -MF ".deps/inserts.Tpo" -c -o inserts.o inserts.cpp; \
then mv -f ".deps/inserts.Tpo" ".deps/inserts.Po"; else rm -f ".deps/inserts.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT qual.o -MD -MP -MF ".deps/qual.Tpo" -c -o qual.o qual.cpp; \
then mv -f ".deps/qual.Tpo" ".deps/qual.Po"; else rm -f ".deps/qual.Tpo"; exit 1; fi
rm -f libtophat.a
ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o align_status.o fragments.o tokenize.o inserts.o qual.o 
ranlib libtophat.a
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT GBase.o -MD -MP -MF ".deps/GBase.Tpo" -c -o GBase.o GBase.cpp; \
then mv -f ".deps/GBase.Tpo" ".deps/GBase.Po"; else rm -f ".deps/GBase.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT codons.o -MD -MP -MF ".deps/codons.Tpo" -c -o codons.o codons.cpp; \
then mv -f ".deps/codons.Tpo" ".deps/codons.Po"; else rm -f ".deps/codons.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT gdna.o -MD -MP -MF ".deps/gdna.Tpo" -c -o gdna.o gdna.cpp; \
then mv -f ".deps/gdna.Tpo" ".deps/gdna.Po"; else rm -f ".deps/gdna.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT GStr.o -MD -MP -MF ".deps/GStr.Tpo" -c -o GStr.o GStr.cpp; \
then mv -f ".deps/GStr.Tpo" ".deps/GStr.Po"; else rm -f ".deps/GStr.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT GFaSeqGet.o -MD -MP -MF ".deps/GFaSeqGet.Tpo" -c -o GFaSeqGet.o GFaSeqGet.cpp; \
then mv -f ".deps/GFaSeqGet.Tpo" ".deps/GFaSeqGet.Po"; else rm -f ".deps/GFaSeqGet.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT GFastaIndex.o -MD -MP -MF ".deps/GFastaIndex.Tpo" -c -o GFastaIndex.o GFastaIndex.cpp; \
then mv -f ".deps/GFastaIndex.Tpo" ".deps/GFastaIndex.Po"; else rm -f ".deps/GFastaIndex.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT gff.o -MD -MP -MF ".deps/gff.Tpo" -c -o gff.o gff.cpp; \
then mv -f ".deps/gff.Tpo" ".deps/gff.Po"; else rm -f ".deps/gff.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT gtf_tracking.o -MD -MP -MF ".deps/gtf_tracking.Tpo" -c -o gtf_tracking.o gtf_tracking.cpp; \
then mv -f ".deps/gtf_tracking.Tpo" ".deps/gtf_tracking.Po"; else rm -f ".deps/gtf_tracking.Tpo"; exit 1; fi
rm -f libgc.a
ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gtf_tracking.o 
ranlib libgc.a
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT prep_reads.o -MD -MP -MF ".deps/prep_reads.Tpo" -c -o prep_reads.o prep_reads.cpp; \
then mv -f ".deps/prep_reads.Tpo" ".deps/prep_reads.Po"; else rm -f ".deps/prep_reads.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o prep_reads  prep_reads.o ../src/libtophat.a  -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT tophat_reports.o -MD -MP -MF ".deps/tophat_reports.Tpo" -c -o tophat_reports.o tophat_reports.cpp; \
then mv -f ".deps/tophat_reports.Tpo" ".deps/tophat_reports.Po"; else rm -f ".deps/tophat_reports.Tpo"; exit 1; fi
tophat_reports.cpp: In function ‘void print_sam_for_hits(const RefSequenceTable&, const HitsForRead&, const FragmentAlignmentGrade&, FragmentType, FILE*, FILE*)’:
tophat_reports.cpp:514:8: warning: unused variable ‘got_read’
tophat_reports.cpp: In function ‘void print_sam_for_hits(const RefSequenceTable&, const HitsForRead&, const HitsForRead&, const InsertAlignmentGrade&, FILE*, FILE*, FILE*)’:
tophat_reports.cpp:592:8: warning: unused variable ‘got_left_read’
tophat_reports.cpp:601:8: warning: unused variable ‘got_right_read’
tophat_reports.cpp: In function ‘void driver(FILE*, FILE*, FILE*, FILE*, FILE*, FILE*, FILE*, FILE*)’:
tophat_reports.cpp:950:35: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:981:35: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:1015:38: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:1037:37: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:1064:37: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:1064:85: warning: comparison between signed and unsigned integer expressions
tophat_reports.cpp:1094:23: warning: unused variable ‘stats’
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o tophat_reports  tophat_reports.o ../src/libtophat.a  -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT juncs_db.o -MD -MP -MF ".deps/juncs_db.Tpo" -c -o juncs_db.o juncs_db.cpp; \
then mv -f ".deps/juncs_db.Tpo" ".deps/juncs_db.Po"; else rm -f ".deps/juncs_db.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o juncs_db  juncs_db.o ../src/libtophat.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT gtf_juncs.o -MD -MP -MF ".deps/gtf_juncs.Tpo" -c -o gtf_juncs.o gtf_juncs.cpp; \
then mv -f ".deps/gtf_juncs.Tpo" ".deps/gtf_juncs.Po"; else rm -f ".deps/gtf_juncs.Tpo"; exit 1; fi
gtf_juncs.cpp: In function ‘uint32_t get_junctions_from_gff(FILE*, RefSequenceTable&)’:
gtf_juncs.cpp:57:13: warning: unused variable ‘ref_id’
gtf_juncs.cpp:39:11: warning: unused variable ‘num_juncs_reported’
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o gtf_juncs  gtf_juncs.o ../src/libtophat.a libgc.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT extract_reads.o -MD -MP -MF ".deps/extract_reads.Tpo" -c -o extract_reads.o extract_reads.cpp; \
then mv -f ".deps/extract_reads.Tpo" ".deps/extract_reads.Po"; else rm -f ".deps/extract_reads.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o extract_reads  extract_reads.o ../src/libtophat.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT segment_juncs.o -MD -MP -MF ".deps/segment_juncs.Tpo" -c -o segment_juncs.o segment_juncs.cpp; \
then mv -f ".deps/segment_juncs.Tpo" ".deps/segment_juncs.Po"; else rm -f ".deps/segment_juncs.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o segment_juncs  segment_juncs.o ../src/libtophat.a  -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT closures.o -MD -MP -MF ".deps/closures.Tpo" -c -o closures.o closures.cpp; \
then mv -f ".deps/closures.Tpo" ".deps/closures.Po"; else rm -f ".deps/closures.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o closure_juncs  closures.o ../src/libtophat.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT long_spanning_reads.o -MD -MP -MF ".deps/long_spanning_reads.Tpo" -c -o long_spanning_reads.o long_spanning_reads.cpp; \
then mv -f ".deps/long_spanning_reads.Tpo" ".deps/long_spanning_reads.Po"; else rm -f ".deps/long_spanning_reads.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o long_spanning_reads  long_spanning_reads.o ../src/libtophat.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT fix_map_ordering.o -MD -MP -MF ".deps/fix_map_ordering.Tpo" -c -o fix_map_ordering.o fix_map_ordering.cpp; \
then mv -f ".deps/fix_map_ordering.Tpo" ".deps/fix_map_ordering.Po"; else rm -f ".deps/fix_map_ordering.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o fix_map_ordering  fix_map_ordering.o ../src/libtophat.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT library_stats.o -MD -MP -MF ".deps/library_stats.Tpo" -c -o library_stats.o library_stats.cpp; \
then mv -f ".deps/library_stats.Tpo" ".deps/library_stats.Po"; else rm -f ".deps/library_stats.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o library_stats  library_stats.o ../src/libtophat.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT mask_sam.o -MD -MP -MF ".deps/mask_sam.Tpo" -c -o mask_sam.o mask_sam.cpp; \
then mv -f ".deps/mask_sam.Tpo" ".deps/mask_sam.Po"; else rm -f ".deps/mask_sam.Tpo"; exit 1; fi
mask_sam.cpp: In function ‘void driver(FILE*, FILE*)’:
mask_sam.cpp:109:73: warning: suggest parentheses around ‘&&’ within ‘||’
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o mask_sam  mask_sam.o ../src/libtophat.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT wiggles.o -MD -MP -MF ".deps/wiggles.Tpo" -c -o wiggles.o wiggles.cpp; \
then mv -f ".deps/wiggles.Tpo" ".deps/wiggles.Po"; else rm -f ".deps/wiggles.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o wiggles  wiggles.o ../src/libtophat.a -lbam -lz -lz 
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG  -MT sam_juncs.o -MD -MP -MF ".deps/sam_juncs.Tpo" -c -o sam_juncs.o sam_juncs.cpp; \
then mv -f ".deps/sam_juncs.Tpo" ".deps/sam_juncs.Po"; else rm -f ".deps/sam_juncs.Tpo"; exit 1; fi
g++ -Wall -m64 -O3  -DNDEBUG  -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG   -L/usr/lib -o sam_juncs  sam_juncs.o ../src/libtophat.a -lbam -lz -lz 
make[2]: Leaving directory `/home/adam/Fedora/tmp/tophat-1.2.0.test/src'
make[2]: Entering directory `/home/adam/Fedora/tmp/tophat-1.2.0.test'
make[2]: Leaving directory `/home/adam/Fedora/tmp/tophat-1.2.0.test'
make[1]: Leaving directory `/home/adam/Fedora/tmp/tophat-1.2.0.test'