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 <[email protected]> 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 <[email protected]> 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 >>>> [email protected] >>>> 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.
