Re: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: Fails to build from source since bioperl upgrade has broken libbio-graphics-perl)

[Sascha Steinbiss <satta@debian.org>]

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