Package fails to build on i386 with "undefined reference to"
Hi all,
My name is Carlos Borroto. I recently joined Debian Med's team to help
packaging several bioinformatics tools. I ran into a problem I would
like get help on.
I'm working in a tool named TopHat[1]. It builds correctly on amd64:
https://launchpadlibrarian.net/89809979/buildlog_ubuntu-oneiric-amd64.tophat_1.4.0-1~oneiric2_BUILDING.txt.gz
But fails on i386:
https://launchpadlibrarian.net/89813979/buildlog_ubuntu-oneiric-i386.tophat_1.4.0-1~oneiric2_FAILEDTOBUILD.txt.gz
The same happens in a local cowbuilder environment for Debian Sid. 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
I contacted the authors about this issue, but I haven't received a
response yet. With my limited knowledge I did some digging and it
seems I'm running into an issue similar to:
https://bugs.launchpad.net/ubuntu/+source/glib2.0/+bug/121461
>From that bug:
"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"
Still, I haven't found a way to resolve this issue. Is there anything
I could do beside waiting to see if the authors respond?
Kind regards,
Carlos
[1]http://tophat.cbcb.umd.edu/
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