Re: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: Fails to build from source since bioperl upgrade has broken libbio-graphics-perl)
BTW, [1] here was:
https://github.com/sanger-pathogens/Roary/issues/196
Cheers
Sascha
> On 17 Dec 2016, at 23:28, Sascha Steinbiss <satta@debian.org> wrote:
>
> Hi all,
>
> thanks for checking these.
>
>>> roary
>>
>> Build, however when trying to simulate the test suite via
>>
>> cd t/data/genbank_gbff
>> roary -f out *.gff
>>
>> Please cite Roary if you use any of the results it produces:
>> Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
>> "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693
>> doi: http://doi.org/10.1093/bioinformatics/btv421
>> Pubmed: 26198102
>>
>> Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl/5.24/Encode.pm line 61.
>>
>>
>> This does not look good even if it does not look related to BioPerl.
>
> In fact, it doesn’t look related to Roary either. It’s apparently a missing Encode/ConfigLocal.pm in the coded provided by libencode-perl, but not a fatal issue here as it doesn’t seem to impact the result or performance of Roary. It’s been reported before [1] and I will let upstream know that the warning is back. Not a blocker AFAICS.
>
> Cheers
> Sascha
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