Re: Tophat 1.4.0 fails to build on i386
Thanks Andreas, I just emailed debian-mentors. Let see if I can get
help from there.
I also emailed directly the author on the headers comments in the
specific file causing the issue. This file was newly created in this
version, so I'm guessing is safe to assume he might be the best person
to troubleshoot this issue.
I'll keep you posted.
On Fri, Jan 13, 2012 at 3:01 PM, Andreas Tille <andreas@an3as.eu> wrote:
> Hi Carlos,
>
> thanks for checking new upstream versions. In case you might not get a
> reasonable answer here (and I can't find any without deeper
> investigation a good address to foreward questions like this could be
> debian-mentors@lists.debian.org.
>
> Kind regards
>
> Andreas.
>
> On Fri, Jan 13, 2012 at 01:37:31PM -0500, Carlos Borroto wrote:
>> 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
>>
>>
>> --
>> To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
>> with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
>> Archive: [🔎] CABgGhBLoTHdjEiSX9S77y3H+TiXA5iAhMyQ7zvcnR74=thjThA@mail.gmail.com">http://lists.debian.org/[🔎] CABgGhBLoTHdjEiSX9S77y3H+TiXA5iAhMyQ7zvcnR74=thjThA@mail.gmail.com
>>
>>
>
> --
> http://fam-tille.de
>
>
> --
> To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
> with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
> Archive: [🔎] 20120113200100.GA20533@an3as.eu">http://lists.debian.org/[🔎] 20120113200100.GA20533@an3as.eu
>
Reply to: