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Re: Tophat 1.4.0 fails to build on i386



Hi,

I was able to solve this issue with the help of Peter Samuelson from
debian-mentors@lists.debian.org. It was a quick fix:
http://lists.debian.org/debian-mentors/2012/01/msg00362.html

I also received a respond from the developer involves in this
particular part of Tophat, he was kind enough to agree to look into
this issue. I forwarded Peter's solution to him. I'm guessing they
should be able to include it in the next upstream release.

I'll be working next on getting the package fully ready for submission.

Regards,
Carlos

On Tue, Jan 17, 2012 at 1:58 PM, Carlos Borroto
<carlos.borroto@gmail.com> wrote:
> 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
>>>
>>>
>>> --
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>>>
>>>
>>
>> --
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>>
>>
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