Tophat 1.4.0 fails to build on i386

[Carlos Borroto <carlos.borroto@gmail.com>]

Hi all,

After updating the unreleased tophat package to a new upstream release
1.4.0, the i386 build if failing:
https://launchpadlibrarian.net/89589761/buildlog_ubuntu-oneiric-i386.tophat_1.4.0-1~oneiric1_FAILEDTOBUILD.txt.gz

The relevant part seems to be:
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
make[3]: Leaving directory `/build/buildd/tophat-1.4.0/src'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/build/buildd/tophat-1.4.0'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/build/buildd/tophat-1.4.0'
dh_auto_build: make -j1 returned exit code 2
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2

The same package for amd64 builds without problem.
https://launchpadlibrarian.net/89809979/buildlog_ubuntu-oneiric-amd64.tophat_1.4.0-1~oneiric2_BUILDING.txt.gz

I emailed tophat authors, but I was wondering is this is something any
of you have seen before?

Also, searching to see if I can find a solution, I found a similar
situation in this bu report:
https://bugs.launchpad.net/ubuntu/+source/glib2.0/+bug/121461

The interesting part that caught my attention was:
"For whatever reason, on i386, the linker expects to link against
"unsigned int", but on both i386 and amd64, the libgtkmm-2.4 libraries
only offer an "unsigned long" version"

I wonder if this is the problem here.

Thanks,
Carlos