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

On Wed, Jan 18, 2017 at 02:21:04PM -0500, Lincoln Stein wrote: > Yes, I'll remove it immediately and apply the patches to bio::graphics as > well. Fine. Do you intend to do a micro release (say 2.56.1) after this change or should I remove the file here locally for the time beeing? Both would be

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

Yes, I'll remove it immediately and apply the patches to bio::graphics as well. Lincoln On Wed, Jan 18, 2017 at 11:58 AM, Andreas Tille wrote: > On Wed, Jan 18, 2017 at 05:39:05PM +0100, gregor herrmann wrote: > > > > > >

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

On Wed, Jan 18, 2017 at 05:39:05PM +0100, gregor herrmann wrote: > > > > > > https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/patches > > Oh, cool, adding the (build)-dep is really enough, no patching > required. Nice. Yes, we needed this for another package ... > For

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

On Wed, 18 Jan 2017 17:27:21 +0100, Andreas Tille wrote: > > Cool. In Debian terminology this means a new "Build-Depends" and after > > adding > > libbio-coordinate-perl package to this the tests succeeded. Thanks a lot > > for > > your help and patience! > > > > I now need to sort out some

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

[droping debian-perl list from CC] On Wed, Jan 18, 2017 at 02:30:32PM +0100, Andreas Tille 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"

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

On Wed, 18 Jan 2017 14:00:47 +, Lincoln Stein wrote: > Glad to be of help. No source changes to bio::graphics needed then? Probably that too :) I'll take a look later today. Thanks for your efforts and your enormous help! Cheers, gregor -- .''`. https://info.comodo.priv.at/ - Debian

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

Glad to be of help. No source changes to bio::graphics needed then? At some point in near future I will be making changes to the exception reporting in bio::graphics so that the error messages are more informative. Lincoln On Wed, Jan 18, 2017 at 8:30 AM Andreas Tille wrote:

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

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::Graphics. Then the > problem will disappear. Cool. In Debian terminology this

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

Ok, and here is a little command-line test that takes the problem a bit deeper. I'm sending this out because I have to go to work now and can't get back to this again today: perl -MBio::Perl -MBio::Graphics -MBio::Graphics::Glyph::span Can't locate Bio/Coordinate/Pair.pm in @INC (you may need to

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

Ok, here is the last key piece of information. Replacing source-built Bioperl with the debian bioperl-1.7.1-1 package from https://packages.debian.org/sid/bioperl reproduced Gregor's test errors exactly. I also tried swapping in libbio-graphics-perl 2.40-1 from the same repository (with both

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

Hi, Unfortunately I can't reproduce the testing failures, and the build got all the way to the signature generation, at which point it aborted because I do not have the proper gpg signing key. Bear with me, because I am new at this. Here is what I did: 1. git clone

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

That would have been my guess too, but Bio:: Graphics 2.40 is the right version. When running build test on a virgin Mint 18.2 system with Bio::Perl 1.7.1 and Bio::Graphics 2.40 I'm getting 100% test success. This is very puzzling. I'll take a closer look tonight. Lincoln On Tue, Jan 17, 2017

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

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 data files due to an assumption about > the current working directory. When he fixed this, there were just a > handful of

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

Not good! But I believe that Gregor found that all these were caused by the testing suite not finding the proper data files due to an assumption about the current working directory. When he fixed this, there were just a handful of tests still failing. Gregor, is there a patch file that I can apply

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

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 that I'm a > complete newbie wrt the Debian packaging system. I have cloned gbrowse > 2.56+dfsg-1 from the Debian Med repository, but I don't know what

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

Hi, I need a little help to reproduce Gregor's failed tests, given that I'm a complete newbie wrt the Debian packaging system. I have cloned gbrowse 2.56+dfsg-1 from the Debian Med repository, but I don't know what command line to use to attempt the build. What is the next step? I'm guessing it

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

On Mon, 16 Jan 2017 21:38:14 +0100, Andreas Tille wrote: > thanks a lot for you detailed analysis. BTW, you should be able to `git > push` into Debian Med repository - no need to do the attachment detour > if this might be more convenient for you. Ack, will do so next time. > Hmmm, may be I

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

On Mon, 16 Jan 2017 20:23:37 +, Lincoln Stein wrote: > Oh dear. What happens when you just "Build test" on the git checkout? Voilà: [..] t/03.render.t . 1/150 - EXCEPTION: Bio::Root::Exception - MSG: The requested glyph class, ``arrow'' is not available:

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

Hi Gregor, thanks a lot for you detailed analysis. BTW, you should be able to `git push` into Debian Med repository - no need to do the attachment detour if this might be more convenient for you. On Mon, Jan 16, 2017 at 09:01:11PM +0100, gregor herrmann wrote: > On Mon, 16 Jan 2017 16:45:52

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

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: ...)

On Mon, 16 Jan 2017 16:45:52 +0100, Andreas Tille wrote: > > If you want to use the same list of tests to skip during build, you > > can do something like > > https://sources.debian.net/src/libipc-sharelite-perl/0.17-4/debian/rules > Ahhh, OK. I wrongly assumed that would be some magic since in

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

On Mon, Jan 16, 2017 at 12:04:31PM +0100, gregor herrmann wrote: > That's not unexpected since debian/tests/pkg-perl/smoke-skip is an > (optional) configuration file for the autopkgtest-pkg-perl framework > and is not related to building the package. > > If you want to use the same list of tests

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

On Mon, 16 Jan 2017 05:55:20 +0100, Andreas Tille wrote: > Since I learned from Perl team (in CC) that I can exclude tests via > >debian/tests/pkg-perl/smoke-skip > > I tried to use this feature. Unfortunately this does not work as > expected - at least in the build process. That's not

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

Hi Lincoln, On Sun, Jan 15, 2017 at 04:25:46PM -0500, Lincoln Stein wrote: > The bug in the memory adaptor that Scott found turns out to have been from > using the old perl 1.6.9 installed by the Debian package. Updating to 1.7.1 > (1.007001) fixes the problem. > > I have merged all GBrowse

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

>>, Carnë Draug <carandraug+...@gmail.com<mailto:carandraug+...@gmail.com>> Subject: Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...) Hi, The bug in the memory adaptor that Scott found turns out to have been fro

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

Hi, The bug in the memory adaptor that Scott found turns out to have been from using the old perl 1.6.9 installed by the Debian package. Updating to 1.7.1 (1.007001) fixes the problem. I have merged all GBrowse changes into git version 2.56 and have made a CPAN release. I think you can go ahead

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

Thanks to you both. I think the only question targeted directly at my was the "how much time question": On Februrar 5 is full freeze. You need to cut 10 days from this since a package has a 10 day migration time until it makes it from unstable to the release candidates in testing. So this

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

I made a few changes in a branch off that security-bug-fixes branch that quieted several warning messages, though I still need to sort out at least one problem (the memory adaptor doesn't seem to be reading fasta files, but also doesn't emit a warning about a problem). Lincoln, if you want to

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

Hi Lincoln, On Wed, Dec 21, 2016 at 06:25:46PM -0500, Lincoln Stein wrote: > I am devoting several days over the Christmas holidays to fixing the > various outstanding bugs in gbrowse. Stay tuned! Did you managed to managed to work on this? If not we probably can not include gbrowse in the next

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

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 < cjfie...@illinois.edu> wrote: > This may be something to pass by Lincoln or Scott Cain(CC'd). Lincoln I > did