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

[Andreas Tille]

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

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>
> 
> 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