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