make all-recursive make[1]: Entering directory `/home/adam/rpmbuild/BUILD/tophat-1.2.0' Making all in src make[2]: Entering directory `/home/adam/rpmbuild/BUILD/tophat-1.2.0/src' g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o reads.o reads.cpp gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c alphabet.c g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o bwt_map.o bwt_map.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o common.o common.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o junctions.o junctions.cpp 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' g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o insertions.o insertions.cpp bwt_map.h: In member function 'bool HitStream::next_read_hits(HitsForRead&)': bwt_map.h:680:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o deletions.o deletions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o align_status.o align_status.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o fragments.o fragments.cpp 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 g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o tokenize.o tokenize.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o inserts.o inserts.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o qual.o qual.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o GBase.o GBase.cpp GBase.cpp: In function 'void writeFasta(FILE*, const char*, const char*, const char*, int, int)': GBase.cpp:651:52: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o codons.o codons.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o gdna.o gdna.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o GStr.o GStr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o GFaSeqGet.o GFaSeqGet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o GFastaIndex.o GFastaIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o gff.o gff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o gtf_tracking.o gtf_tracking.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o prep_reads.o prep_reads.cpp make[2]: *** No rule to make target `../src/libtophat.a', needed by `prep_reads'. Stop. make[2]: *** Waiting for unfinished jobs.... make[2]: Leaving directory `/home/adam/rpmbuild/BUILD/tophat-1.2.0/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/adam/rpmbuild/BUILD/tophat-1.2.0' make: *** [all] Error 2 error: Bad exit status from /var/tmp/rpm-tmp.cEs4nj (%build) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.cEs4nj (%build)