I have been trying to compile tophat from source on a Mac G5 running OSX 10.5.8.
Anyone know what I need to fix this?
Code:
mu-166163:tophat-1.3.2 $ make
make all-recursive
Making all in src
g++ -Wall -Wno-strict-aliasing -m64 -O3 -DNDEBUG -I/Users/xxxx/Desktop/software/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -DNDEBUG -I/Users/xxxx/Desktop/software/include -L/usr/lib -o prep_reads -L/Users/xxxx/Desktop/software/lib prep_reads.o ../src/libtophat.a -lbam -lz -lz
ld warning: in /Users/xxxx/Desktop/software/lib/libbam.a, file is not of required architecture
Undefined symbols:
"_bam_calend", referenced from:
GBamRecord::set_cigar(char const*)in libtophat.a(common.o)
"_bam_cigar2qlen", referenced from:
GBamRecord::add_sequence(char const*, int)in libtophat.a(common.o)
"_bam_nt16_table", referenced from:
_bam_nt16_table$non_lazy_ptr in libtophat.a(common.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [prep_reads] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
