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

2017-01-18 Thread Lincoln Stein
ense to remove this copy of bioperl > even in your distribution. What do you think? > > Kind regards > >Andreas. > > > -- > http://fam-tille.de > -- *Lincoln Stein* Scientific Director (Interim), Ontario Institute for Cancer Research Director, Informatics

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

2017-01-18 Thread Lincoln Stein
wrote: > Hi Lincoln, > > > > On Wed, Jan 18, 2017 at 07:07:55AM -0500, Lincoln Stein wrote: > > > > > > There appears to be a new dependency on libbio-coordinate. Probably best > to > > > add a "use Bio::Coordinate" and the dependency to Bio::

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

2017-01-18 Thread Lincoln Stein
inate" and the dependency to Bio::Graphics. Then the problem will disappear. Lincoln On Wed, Jan 18, 2017 at 7:00 AM, Lincoln Stein <lincoln.st...@gmail.com> wrote: > Ok, here is the last key piece of information. Replacing source-built > Bioperl with the debian bioperl-1.7.1-

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

2017-01-18 Thread Lincoln Stein
versions of bioperl), but this has no effect one way or another. Conclusion: something in the bioperl debian 1.7.1-1 package is causing the test failures. Lincoln On Wed, Jan 18, 2017 at 6:43 AM, Lincoln Stein <lincoln.st...@gmail.com> wrote: > Hi, > > Unfortunately I can't reprod

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

2017-01-18 Thread Lincoln Stein
-graphics package? In any case, I'm stuck in the "works for me" phase. Lincoln On Tue, Jan 17, 2017 at 2:07 AM, Andreas Tille <andr...@an3as.eu> wrote: > Hi Lincoln, > > On Mon, Jan 16, 2017 at 06:14:34PM -0500, Lincoln Stein wrote: > > I need a little help to reprodu

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

2017-01-17 Thread Lincoln Stein
at 6:27 PM gregor herrmann <gre...@debian.org> wrote: > On Tue, 17 Jan 2017 18:06:02 -0500, Lincoln Stein wrote: > > > > > Not good! But I believe that Gregor found that all these were caused by > the > > > testing suite not finding the proper dat

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

2017-01-17 Thread Lincoln Stein
to get up to the same point you got to? Lincoln On Tue, Jan 17, 2017 at 2:07 AM, Andreas Tille <andr...@an3as.eu> wrote: > Hi Lincoln, > > On Mon, Jan 16, 2017 at 06:14:34PM -0500, Lincoln Stein wrote: > > I need a little help to reproduce Gregor's failed tests, given th

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

2017-01-16 Thread Lincoln Stein
QTYX6uzpoAYZJqgYFAlh9Jo9fFIAALgAo > aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldEQx > RTEzMTZFOTNBNzYwQTgxMDREODVGQUJCM0E2ODAxODY0OUFBMDYACgkQuzpoAYZJ > qgbxjw//Q7gMuNwEYhst7aYXxZ6QcHqQf03cum5raXbXxSaDRrzllzV1g6PDC0k3 > Q5wlOrnMa3X9M+TflKolPSvAw2aUx+EttlRQbgFBitP8DqMqWwC3/6E

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

2017-01-16 Thread Lincoln Stein
Oh dear. What happens when you just "Build test" on the git checkout? Sounds like path issues. I can try applying the Deb patches and try to reproduce. Unfortunately I am a Deb packaging newbie. Lincoln On Mon, Jan 16, 2017 at 3:01 PM gregor herrmann wrote: > On Mon, 16

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

2017-01-15 Thread Lincoln Stein
to the security bug > > fix branch: > > > > https://github.com/GMOD/GBrowse/pull/59 > > > > Scott > > > > > > On Thu, Jan 12, 2017 at 1:57 PM, Lincoln Stein <lincoln.st...@gmail.com> > > wrote: > > > > > Hi Andreas, > >

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

2016-12-21 Thread Lincoln Stein
t; >> 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