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 <[email protected]> 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
