Re: Package fails to build on i386 with "undefined reference to"

[Peter Samuelson <peter@p12n.org>]

[Carlos Borroto]
> g++ -Wall -Wno-strict-aliasing -march=i686 -O3 -g -O2 -DNDEBUG
> -I/usr/include/seqan -Wall -Wno-strict-aliasing -march=i686 -O3 -g -O2
> -DNDEBUG   -Wl,-Bsymbolic-functions -L/usr/lib -o gtf_to_fasta
> GTFToFasta.o FastaTools.o ../src/libtophat.a libgc.a -lbam -lz -lz
> GTFToFasta.o: In function `GFaSeqGet':
> /build/buildd/tophat-1.4.0/src/GFaSeqGet.h:66: undefined reference to
> `GFaSeqGet::finit(char const*, long, bool)'
> collect2: ld returned 1 exit status
> make[3]: *** [gtf_to_fasta] Error 1

Try adding a line to the top of GTFToFasta.h right after the include
guard (#ifndef GTFToFasta_H, #define GTFToFasta_H):

    #include "config.h"

What appears to be happening is that "config.h" wants to define some
stuff that affects how the off_t data type is interpreted, but this
fails to happen if you include certain system headers before you define
the LFS symbols (I'm talking about the _LARGE_FILES and _FILE_OFFSET_BITS
at the bottom of config.h.in).

Peter