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

[Andreas Tille <andreas@an3as.eu>]

Hi,

I checked all rdepends of BioPerl.  In summary there are no real new
BioPerl related issues (Sascha, could you please check roary - see
below).

On Fri, Dec 16, 2016 at 01:06:35PM +0100, Andreas Tille wrote:
> 
> $ apt-cache rdepends bioperl | grep "^ " | sort | uniq | grep -v -e alien-hunter -e libbio-perl-perl -e med-
>   arb

Not tested yet (non-free)

>   bioperl-run

Works with patch, Test suite runs at Build time

>   gbrowse

Fails - help is urgently needed:

...
syntax error at /home/andreas/debian-maintain/alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 963, near "$ENV\"
syntax error at /home/andreas/debian-maintain/alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 963, near "''}"
Global symbol "$self" requires explicit package name (did you forget to declare "my $self"?) at /home/andreas/debian-maintain/alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 971, <DATA> line 192.
Global symbol "$symbolic_db_name" requires explicit package name (did you forget to declare "my $symbolic_db_name"?) at /home/andreas/debian-maintain/alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 971, <DATA> line 192.
Global symbol "$length" requires explicit package name (did you forget to declare "my $length"?) at /home/andreas/debian-maintain/alioth/debian-med_git/build-area/gbrowse-2.54+dfsg/t/..
...

>   iva

Build + Testsuite OK.

>   libbio-graphics-perl

Builds when using libbio-coordinate-perl #848509

>   libchado-perl

Build + Testsuite OK. 

>   libgo-perl

Build + Testsuite OK. 

>   libtfbs-perl

Build + Testsuite OK. 

>   ncbi-epcr

Builds

>   predictprotein

Builds

>   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.


>   velvetoptimiser

Builds
 

So as far as I can see if we can solve the gbrowse issue the migration
to 1.7.1 seems possible.

What do you think?

Kind regards

      Andreas.

-- 
http://fam-tille.de