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/ -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CABgGhBK=FBU19cbzF_e8oGUe23r15hG_Sf4XS2861R_7rYG=x...@mail.gmail.com
