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

[Lincoln Stein]

I am devoting several days over the Christmas holidays to fixing the
various outstanding bugs in gbrowse. Stay tuned!

Lincoln

On Wed, Dec 21, 2016 at 5:23 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> This may be something to pass by Lincoln or Scott Cain(CC'd).  Lincoln I
> did manage to get a new Bio-Graphics out (as well as BioPerl-Run), which
> seems to have addressed the latest, but I'm unable to look at gbrowse until
> well into the new year.
>
> Chris
>
> Chris
>
> Sent from my iPhone
>
> > On Dec 21, 2016, at 3:42 PM, Andreas Tille <andreas at an3as.eu> wrote:
> >
> > 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
>



-- 
*Lincoln Stein*

Scientific Director (Interim), Ontario Institute for Cancer Research
Director, Informatics and Bio-computing Program, OICR
Senior Principal Investigator, OICR
Professor, Department of Molecular Genetics, University of Toronto

<http://goog_1828306398>
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