[Debian-med-packaging] Bug#807150: gubbins: FTBFS on i386: Invalid ALN file for multiple lines per seq

[Andrew Page]

Hi Andreas,
Sascha and I had a look at -lsubunit the other day and he’s going to put in a patch. Its not needed in the gubbins or snp_sites build files, it appears to be an issue with the dependancies in check in Debian.
Regards,
Andrew


> On 9 Dec 2015, at 16:36, Andreas Tille <tille at debian.org> wrote:
> 
> Hi Andrew,
> 
> I just uploaded the new version to Debian unstable.  Please note that you somehow
> missed to add -lsubunit to src/Makefile.am.  I adapted the Debian patch for the
> new version:
> 
>   https://anonscm.debian.org/cgit/debian-med/gubbins.git/tree/debian/patches/add_missing_lib_for_check.patch <https://anonscm.debian.org/cgit/debian-med/gubbins.git/tree/debian/patches/add_missing_lib_for_check.patch>
> 
> Thanks for your support
> 
>      Andreas.
> 
> On Wed, Dec 09, 2015 at 03:57:41PM +0000, Andrew Page wrote:
>> Hi,
>> I have pushed a fix for the build error on i386 as version 1.4.4
>> Details are here:
>> https://github.com/sanger-pathogens/gubbins/pull/158 <https://github.com/sanger-pathogens/gubbins/pull/158> <https://github.com/sanger-pathogens/gubbins/pull/158 <https://github.com/sanger-pathogens/gubbins/pull/158>>
>> 
>> I replicated the bug on i386 and fixed it. The tests also pass on amd64 & OSX 10.10
>> 
>> Regards,
>> Andrew
>> 
>> 
>>> On 6 Dec 2015, at 06:40, Andreas Tille <andreas at an3as.eu> wrote:
>>> 
>>> Hi Andrew,
>>> 
>>> I hereby forward a build issue on i386 architecture.
>>> 
>>> Kind regards
>>> 
>>>      Andreas.
>>> 
>>> On Sat, Dec 05, 2015 at 10:30:32PM -0500, Aaron M. Ucko wrote:
>>>> Source: gubbins
>>>> Version: 1.4.3-1
>>>> Severity: important
>>>> Justification: fails to build from source
>>>> 
>>>> The i386 build of gubbins failed:
>>>> 
>>>> FAIL: run_all_tests
>>>> ============================================================================
>>>> Testsuite summary for gubbins 1.4.3
>>>> ============================================================================
>>>> # TOTAL: 1
>>>> # PASS:  0
>>>> # SKIP:  0
>>>> # XFAIL: 0
>>>> # FAIL:  1
>>>> # XPASS: 0
>>>> # ERROR: 0
>>>> ============================================================================
>>>> See src/test-suite.log
>>>> 
>>>> I was able to reproduce the error in an i386 chroot, yielding the following
>>>> details:
>>>> 
>>>> FAIL: run_all_tests
>>>> ===================
>>>> 
>>>> Running suite(s): Creating_SNP_Sites
>>>>  Parsing a phylip file
>>>>  Parsing a vcf file
>>>>  checking branch sequences
>>>>  Checking the gubbins functionality
>>>>  snp_searching
>>>> 94%: Checks: 39, Failures: 2, Errors: 0
>>>> ../tests/check_snp_sites.c:73:F:snp_sites:valid_alignment_with_multiple_lines_per_sequence:0: Invalid ALN file for multiple lines per seq
>>>> ../tests/check_snp_sites.c:85:F:snp_sites:two_sequences:0: Invalid ALN file for multiple lines per seq
>>>> FAIL run_all_tests (exit status: 1)
>>>> 
>>>> Could you please take a look?
>>>> 
>>>> Thanks!
>>>> 
>>>> _______________________________________________
>>>> Debian-med-packaging mailing list
>>>> Debian-med-packaging at lists.alioth.debian.org
>>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>>>> 
>>> 
>>> -- 
>>> http://fam-tille.de
>> 
>> 
>> 
>> 
>> -- 
>> The Wellcome Trust Sanger Institute is operated by Genome Research 
>> Limited, a charity registered in England with number 1021457 and a 
>> company registered in England with number 2742969, whose registered 
>> office is 215 Euston Road, London, NW1 2BE. 
>> 
>> 
> 
> -- 
> http://fam-tille.de <http://fam-tille.de/>



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


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