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Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)



Hi,

here is an update and a cal for help with gbrowse since I'm not an
experienced Perl programmer.  My guess is that its not really hard to
solve for somebody familiar with Perl and specifically with Bioperl.

On Sat, Dec 17, 2016 at 11:15:30PM +0100, Andreas Tille wrote:
> >   bioperl-run
> 
> Works with patch, Test suite runs at Build time

Just uploaded 1.7.1 after activating as much as possible unittest
at package build time.  Hope that this will not fire back ...
 
> >   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/..
> ...

Any help?
 
> 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?
 
I decided to go with version 1.7.1 for Stretch since all rdepends except
gbrowse are working and regarding popcon the other packages seem to be
more important.  Fixing gbrowse would be wanted for sure. 

Kind regards

      Andreas.

-- 
http://fam-tille.de


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