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Id: 119235
Status: resolved
Priority: 0/
Queue: bioperl
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Owner: Nobody in particular
Requestors: andreas [...] an3as.eu
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History Show all quoted text
  Wed Dec 14 03:58:41 2016 andreas [...] an3as.eu - Ticket created
Subject: Bio/Coordinate/Pair.pm removed from BioPerl in version 1.00070001
Date: Wed, 14 Dec 2016 09:58:23 +0100
To: 848105 [...] bugs.debian.org, bug-bioperl [...] rt.cpan.org
From: Andreas Tille <andreas [...] an3as.eu>
Hi, since I uploaded a Debian package of the latest version of BioPerl which has removed Bio::Coordinate::Pair which was available in 1.6.924[1] the test suite of at least one depending package in Debian are failing due to missing Bio/Coordinate/Pair.pm. I wonder whether there is a sensible migration path for those projects that are relying on the old code version. Kind regards Andreas. [1] http://search.cpan.org/dist/BioPerl-1.6.924/Bio/Coordinate/Pair.pm On Wed, Dec 14, 2016 at 08:46:23AM +0100, Chris Lamb wrote: Show quoted text
> perl Build test --verbose 1 > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: The requested glyph class, ``arrow'' is not available: Can't locate Bio/Coordinate/Pair.pm in @INC (you may need to install the Bio::Coordinate::Pair module) (@INC contains: . «BUILDDIR»/t/../lib /home/lamby/temp/cdt.20161214084524.WfwH8dO4Qj.db.libbio-graphics-perl/libbio-graphics-perl-2.39/blib/lib /home/lamby/temp/cdt.20161214084524.WfwH8dO4Qj.db.libbio-graphics-perl/libbio-graphics-perl-2.39/blib/arch /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.24.1 /usr/local/share/perl/5.24.1 /usr/lib/x86_64-linux-gnu/perl5/5.24 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.24 /usr/share/perl/5.24 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /home/lamby/temp/cdt.20161214084524.WfwH8dO4Qj.db.libbio-graphics-perl/libbio-graphics-perl-2.39/t/../lib/Bio/Graphics/Glyph/arrow.pm line 13. > BEGIN failed--compilation aborted at «BUILDDIR»/t/../lib/Bio/Graphics/Glyph/arrow.pm line 13. > Compilation failed in require at (eval 43) line 2. > > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447 > STACK: Bio::Graphics::Glyph::Factory::make_glyph «BUILDDIR»/t/../lib/Bio/Graphics/Glyph/Factory.pm:342 > STACK: Bio::Graphics::Glyph::make_subglyph «BUILDDIR»/t/../lib/Bio/Graphics/Glyph.pm:310 > STACK: Bio::Graphics::Glyph::new «BUILDDIR»/t/../lib/Bio/Graphics/Glyph.pm:270 > STACK: Bio::Graphics::Glyph::Factory::make_glyph «BUILDDIR»/t/../lib/Bio/Graphics/Glyph/Factory.pm:346 > STACK: Bio::Graphics::Panel::_add_track «BUILDDIR»/t/../lib/Bio/Graphics/Panel.pm:414 > STACK: Bio::Graphics::Panel::_do_add_track «BUILDDIR»/t/../lib/Bio/Graphics/Panel.pm:386 > STACK: Bio::Graphics::Panel::add_track «BUILDDIR»/t/../lib/Bio/Graphics/Panel.pm:312 > STACK: Bio::Graphics::FeatureFile::render «BUILDDIR»/t/../lib/Bio/Graphics/FeatureFile.pm:675 > STACK: t/BioGraphics.t:53 > ----------------------------------------------------------- > # Looks like you planned 49 tests but ran 4. > # Looks like your test exited with 2 just after 4. > t/BioGraphics.t .. > 1..49 > ok 1 - use GD::Image; > ok 2 - use Bio::Graphics::FeatureFile; > ok 3 - use Bio::Graphics::Panel; > ok 4 > Dubious, test returned 2 (wstat 512, 0x200) > Failed 45/49 subtests > t/Wiggle.t ....... > 1..11 > ok 1 > ok 2 > ok 3 > ok 4 > ok 5 > ok 6 > ok 7 > ok 8 > ok 9 > ok 10 > ok 11 > ok > > Test Summary Report > ------------------- > t/BioGraphics.t (Wstat: 512 Tests: 4 Failed: 0) > Non-zero exit status: 2 > Parse errors: Bad plan. You planned 49 tests but ran 4. > Files=2, Tests=15, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.50 cusr 0.04 csys = 0.57 CPU) > Result: FAIL > Failed 1/2 test programs. 0/15 subtests failed. > dh_auto_test: perl Build test --verbose 1 returned exit code 255 > debian/rules:4: recipe for target 'build' failed > make: *** [build] Error 2 > dpkg-buildpackage: error: debian/rules build gave error exit status 2 > > […] > > The full build log is attached. > > > Regards, > > -- > ,''`. > : :' : Chris Lamb > `. `'` lamby@debian.org / chris-lamb.co.uk > `-
Show quoted text
> _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
-- http://fam-tille.de
  Wed Dec 14 23:57:49 2016 cjfields [...] cpan.org - Correspondence added
From: cjfields [...] cpan.org
On Wed Dec 14 03:58:41 2016, andreas@an3as.eu wrote: Show quoted text
> Hi, > > since I uploaded a Debian package of the latest version of BioPerl > which > has removed Bio::Coordinate::Pair which was available in 1.6.924[1] > the > test suite of at least one depending package in Debian are failing due > to missing Bio/Coordinate/Pair.pm. > > I wonder whether there is a sensible migration path for those projects > that are relying on the old code version. > > Kind regards > > Andreas. > > [1] http://search.cpan.org/dist/BioPerl-1.6.924/Bio/Coordinate/Pair.pm > > On Wed, Dec 14, 2016 at 08:46:23AM +0100, Chris Lamb wrote:
> > perl Build test --verbose 1 > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: The requested glyph class, ``arrow'' is not available: Can't > > locate Bio/Coordinate/Pair.pm in @INC (you may need to install the > > Bio::Coordinate::Pair module) (@INC contains: . «BUILDDIR»/t/../lib > > /home/lamby/temp/cdt.20161214084524.WfwH8dO4Qj.db.libbio-graphics- > > perl/libbio-graphics-perl-2.39/blib/lib > > /home/lamby/temp/cdt.20161214084524.WfwH8dO4Qj.db.libbio-graphics- > > perl/libbio-graphics-perl-2.39/blib/arch /etc/perl > > /usr/local/lib/x86_64-linux-gnu/perl/5.24.1 > > /usr/local/share/perl/5.24.1 /usr/lib/x86_64-linux-gnu/perl5/5.24 > > /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.24 > > /usr/share/perl/5.24 /usr/local/lib/site_perl /usr/lib/x86_64-linux- > > gnu/perl-base) at > > /home/lamby/temp/cdt.20161214084524.WfwH8dO4Qj.db.libbio-graphics- > > perl/libbio-graphics-perl-2.39/t/../lib/Bio/Graphics/Glyph/arrow.pm > > line 13. > > BEGIN failed--compilation aborted at > > «BUILDDIR»/t/../lib/Bio/Graphics/Glyph/arrow.pm line 13. > > Compilation failed in require at (eval 43) line 2. > > > > STACK: Error::throw > > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447 > > STACK: Bio::Graphics::Glyph::Factory::make_glyph > > «BUILDDIR»/t/../lib/Bio/Graphics/Glyph/Factory.pm:342 > > STACK: Bio::Graphics::Glyph::make_subglyph > > «BUILDDIR»/t/../lib/Bio/Graphics/Glyph.pm:310 > > STACK: Bio::Graphics::Glyph::new > > «BUILDDIR»/t/../lib/Bio/Graphics/Glyph.pm:270 > > STACK: Bio::Graphics::Glyph::Factory::make_glyph > > «BUILDDIR»/t/../lib/Bio/Graphics/Glyph/Factory.pm:346 > > STACK: Bio::Graphics::Panel::_add_track > > «BUILDDIR»/t/../lib/Bio/Graphics/Panel.pm:414 > > STACK: Bio::Graphics::Panel::_do_add_track > > «BUILDDIR»/t/../lib/Bio/Graphics/Panel.pm:386 > > STACK: Bio::Graphics::Panel::add_track > > «BUILDDIR»/t/../lib/Bio/Graphics/Panel.pm:312 > > STACK: Bio::Graphics::FeatureFile::render > > «BUILDDIR»/t/../lib/Bio/Graphics/FeatureFile.pm:675 > > STACK: t/BioGraphics.t:53 > > ----------------------------------------------------------- > > # Looks like you planned 49 tests but ran 4. > > # Looks like your test exited with 2 just after 4. > > t/BioGraphics.t .. > > 1..49 > > ok 1 - use GD::Image; > > ok 2 - use Bio::Graphics::FeatureFile; > > ok 3 - use Bio::Graphics::Panel; > > ok 4 > > Dubious, test returned 2 (wstat 512, 0x200) > > Failed 45/49 subtests > > t/Wiggle.t ....... > > 1..11 > > ok 1 > > ok 2 > > ok 3 > > ok 4 > > ok 5 > > ok 6 > > ok 7 > > ok 8 > > ok 9 > > ok 10 > > ok 11 > > ok > > > > Test Summary Report > > ------------------- > > t/BioGraphics.t (Wstat: 512 Tests: 4 Failed: 0) > > Non-zero exit status: 2 > > Parse errors: Bad plan. You planned 49 tests but ran 4. > > Files=2, Tests=15, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.50 > > cusr 0.04 csys = 0.57 CPU) > > Result: FAIL > > Failed 1/2 test programs. 0/15 subtests failed. > > dh_auto_test: perl Build test --verbose 1 returned exit code 255 > > debian/rules:4: recipe for target 'build' failed > > make: *** [build] Error 2 > > dpkg-buildpackage: error: debian/rules build gave error exit status 2 > > > > […] > > > > The full build log is attached. > > > > > > Regards, > > > > -- > > ,''`. > > : :' : Chris Lamb > > `. `'` lamby@debian.org / chris-lamb.co.uk > > `-
> >
> > _______________________________________________ > > Debian-med-packaging mailing list > > Debian-med-packaging@lists.alioth.debian.org > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med- > > packaging
I will work on a separate CPAN release of Bio::Coordinate modules. A key issue may be that Bio::Graphics would need a release to add Bio::Coordinate::Pair as a direct dependency, if it isn't already present.
  Wed Dec 14 23:57:50 2016 The RT System itself - Status changed from 'new' to 'open'
  Thu Dec 15 02:33:55 2016 andreas [...] an3as.eu - Correspondence added
Subject: Re: [rt.cpan.org #119235] Bio/Coordinate/Pair.pm removed from BioPerl in version 1.00070001
Date: Thu, 15 Dec 2016 08:33:40 +0100
To: Chris Fields via RT <bug-bioperl [...] rt.cpan.org>, 848105 [...] bugs.debian.org
From: Andreas Tille <andreas [...] an3as.eu>
Hi Chris, On Wed, Dec 14, 2016 at 11:57:50PM -0500, Chris Fields via RT wrote: Show quoted text
> > I will work on a separate CPAN release of Bio::Coordinate modules. A key issue may be that Bio::Graphics would need a release to add Bio::Coordinate::Pair as a direct dependency, if it isn't already present.
Thanks for your quick response. Would you mind giving us a notification once Bio::Coordinate would be available? This would help fixing the bug in the Debian bug tracking system. Do you have a rough estimation of the time you might need for this? Kind regards Andreas. -- http://fam-tille.de
  Thu Dec 15 10:08:51 2016 cjfields [...] cpan.org - Correspondence added
From: cjfields [...] cpan.org
Hi Andreas, It's now on CPAN: https://metacpan.org/pod/Bio::Coordinate I had actually pushed a release out a month ago but it apparently didn't index correctly (it needed a module with the same name as the distribution). Let me know if this works! chris On Thu Dec 15 02:33:55 2016, andreas@an3as.eu wrote: Show quoted text
> Hi Chris, > > On Wed, Dec 14, 2016 at 11:57:50PM -0500, Chris Fields via RT wrote:
> > > > I will work on a separate CPAN release of Bio::Coordinate modules. A > > key issue may be that Bio::Graphics would need a release to add > > Bio::Coordinate::Pair as a direct dependency, if it isn't already > > present.
> > Thanks for your quick response. Would you mind giving us a > notification > once Bio::Coordinate would be available? This would help fixing the > bug > in the Debian bug tracking system. Do you have a rough estimation of > the > time you might need for this? > > Kind regards > > Andreas.
  Thu Dec 15 11:49:23 2016 tille [...] debian.org - Correspondence added
CC: 848105 [...] bugs.debian.org
Subject: Re: [rt.cpan.org #119235] Bio/Coordinate/Pair.pm removed from BioPerl in version 1.00070001
Date: Thu, 15 Dec 2016 17:49:10 +0100
To: Chris Fields via RT <bug-bioperl [...] rt.cpan.org>
From: Andreas Tille <tille [...] debian.org>
Hi Chris, On Thu, Dec 15, 2016 at 10:08:53AM -0500, Chris Fields via RT wrote: Show quoted text
> It's now on CPAN: > > https://metacpan.org/pod/Bio::Coordinate
Thanks a lot for the quick confirmation. Show quoted text
> I had actually pushed a release out a month ago but it apparently didn't index correctly (it needed a module with the same name as the distribution). > > Let me know if this works!
I just noticed that the issue with libbio-graphics-perl is even more complex than just a missing Bio::Coordinate. I noticed that other packages that are depending from libbio-graphics-perl are failing to build[1]. May be the only quick solution is to revert the bump of BioPerl version for the moment (= before the next stable release of Debian) and try upgrading later. I'll keep you informed if I might find any problem with Bio::Coordinate. Just for the sake of interest: Is there any specific reason to outsource Bio::Coordinate from BioPerl? Kind regards Andreas. [1] https://bugs.debian.org/848236 -- http://fam-tille.de
  Thu Dec 15 12:18:37 2016 cjfields [...] cpan.org - Correspondence added
From: cjfields [...] cpan.org
On Thu Dec 15 11:49:23 2016, tille@debian.org wrote: Show quoted text
> Hi Chris, > > On Thu, Dec 15, 2016 at 10:08:53AM -0500, Chris Fields via RT wrote:
> > It's now on CPAN: > > > > https://metacpan.org/pod/Bio::Coordinate
> > Thanks a lot for the quick confirmation. >
> > I had actually pushed a release out a month ago but it apparently > > didn't index correctly (it needed a module with the same name as the > > distribution). > > > > Let me know if this works!
> > I just noticed that the issue with libbio-graphics-perl is even more > complex than just a missing Bio::Coordinate. I noticed that other > packages that are depending from libbio-graphics-perl are failing to > build[1]. May be the only quick solution is to revert the bump of > BioPerl version for the moment (= before the next stable release of > Debian) and try upgrading later. > > I'll keep you informed if I might find any problem with > Bio::Coordinate. > > Just for the sake of interest: Is there any specific reason to > outsource > Bio::Coordinate from BioPerl? > > Kind regards > > Andreas. > > [1] https://bugs.debian.org/848236
Yes. The main BioPerl distribution contains ~800 modules, the vast majority of which are rarely utilized on a day-to-day basis. However, these modules also add (1) a significant number of additional dependencies and/or (2) a fair amount of technical debt to the main distribution. Bio::Coordinate doesn't fall as much into the former category but it does fall into the latter, primarily since it doesn't get utilized very often in the wild. Also, the main developers who have contributed the code have moved on, it's had very little in the way of updates (which could be for many varied reasons). Another argument is whether there are some potential overlaps or redundancies with other modules in the BioPerl distribution, in particular the Bio::Map modules. As this was an easy set of modules to split out, with very little apparent usage, a very centralized specific use-case, was not well documented with regards to utilization, and may have redundancy issues, we (well, Rob Buels and I) decided to move this out of master several years back. Problem is, we can't easily predict which CPAN modules will break if they aren't setting dependencies correctly (as with Bio:Graphics). For instance, the proper dependency for Bio::Graphics in this case would be Bio::Coordinate::Pair. If this was set correctly, CPAN would search for Bio::Coordinate::Pair, find the last indexed (even if it's an older version of BioPerl), and install it. Once a new version of Bio::Coordinate::Pair is available, CPAN can then resolve the additional downstream dependencies (namely the latest Bioperl release). But, if the dependency listed is something like Bio::Root::Root or Bio::Perl, then installation will fail since the latest BioPerl release has removed the code. My opinion is this is a bug within Bio::Graphics (e.g. listing the wrong module dependency), not BioPerl. The lesson for us is that we never know who uses modules we have. But maybe we (BioPerl devs) would like to avoid these issues in the future, or at least try to help correct for them? Problem is, the only way to resolve these 'reverse dependency' issues is to literally set up testing on CPAN dists listing any dependencies on BioPerl to see what happens when we remove modules (https://github.com/bioperl/bioperl-live/issues/203). Not an easy fix to set up, and it only tests CPAN modules. So, it's a bit complicated :) But I do think it's worth slimming down the code base just from a maintenance perspective, and this may actually improve the core code even more over time.
  Thu Dec 15 12:40:00 2016 cjfields [...] cpan.org - Correspondence added
From: cjfields [...] cpan.org
On Thu Dec 15 11:49:23 2016, tille@debian.org wrote: Show quoted text
> Hi Chris, > > On Thu, Dec 15, 2016 at 10:08:53AM -0500, Chris Fields via RT wrote:
> > It's now on CPAN: > > > > https://metacpan.org/pod/Bio::Coordinate
> > Thanks a lot for the quick confirmation. >
> > I had actually pushed a release out a month ago but it apparently > > didn't index correctly (it needed a module with the same name as the > > distribution). > > > > Let me know if this works!
> > I just noticed that the issue with libbio-graphics-perl is even more > complex than just a missing Bio::Coordinate. I noticed that other > packages that are depending from libbio-graphics-perl are failing to > build[1]. May be the only quick solution is to revert the bump of > BioPerl version for the moment (= before the next stable release of > Debian) and try upgrading later. > > I'll keep you informed if I might find any problem with > Bio::Coordinate. > > Just for the sake of interest: Is there any specific reason to > outsource > Bio::Coordinate from BioPerl? > > Kind regards > > Andreas. > > [1] https://bugs.debian.org/848236
Just a last minute addition, I'm checking in with Lincoln to see if I can attempt a new Bio-Graphics CPAN release (I am apparently still listed as a co-maintainer on PAUSE).
  Thu Dec 15 17:01:36 2016 andreas [...] an3as.eu - Correspondence added
CC: 848105 [...] bugs.debian.org
Subject: Re: [rt.cpan.org #119235] Bio/Coordinate/Pair.pm removed from BioPerl in version 1.00070001
Date: Thu, 15 Dec 2016 23:01:20 +0100
To: Chris Fields via RT <bug-bioperl [...] rt.cpan.org>
From: Andreas Tille <andreas [...] an3as.eu>
On Thu, Dec 15, 2016 at 12:40:01PM -0500, Chris Fields via RT wrote: Show quoted text
> > Just a last minute addition, I'm checking in with Lincoln to see if I can attempt a new Bio-Graphics CPAN release (I am apparently still listed as a co-maintainer on PAUSE).
OK, if you would confirm that Bio-Graphics could be brought into a state that it works with Bio-Coordinate I would reconsider my plan to switch the Debian packages back to the old series of BioPerl since this would have been the safest way to ensure that all depenencies in Debian will work properly. Kind regards Andreas. -- http://fam-tille.de
  Thu Dec 15 17:04:57 2016 andreas [...] an3as.eu - Correspondence added
Subject: Re: [rt.cpan.org #119235] Bio/Coordinate/Pair.pm removed from BioPerl in version 1.00070001
Date: Thu, 15 Dec 2016 23:04:46 +0100
To: Chris Fields via RT <bug-bioperl [...] rt.cpan.org>
From: Andreas Tille <andreas [...] an3as.eu>
On Thu, Dec 15, 2016 at 12:40:01PM -0500, Chris Fields via RT wrote: Show quoted text
> > Just a last minute addition, I'm checking in with Lincoln to see if I can attempt a new Bio-Graphics CPAN release (I am apparently still listed as a co-maintainer on PAUSE).
Another question: To create a package of Bio-Coordinate I'd need at least some rudimentary description. Would you mind enhancing README.md slightly to have some short synopsis and a description of say 3-4 lines of text? This would be really helpful. Kind regards Andreas. -- http://fam-tille.de
  Fri Dec 16 15:48:04 2016 cjfields [...] cpan.org - Correspondence added
From: cjfields [...] cpan.org
On Thu Dec 15 11:49:23 2016, tille@debian.org wrote: Show quoted text
> Hi Chris, > > On Thu, Dec 15, 2016 at 10:08:53AM -0500, Chris Fields via RT wrote:
> > It's now on CPAN: > > > > https://metacpan.org/pod/Bio::Coordinate
> > Thanks a lot for the quick confirmation. >
> > I had actually pushed a release out a month ago but it apparently > > didn't index correctly (it needed a module with the same name as the > > distribution). > > > > Let me know if this works!
> > I just noticed that the issue with libbio-graphics-perl is even more > complex than just a missing Bio::Coordinate. I noticed that other > packages that are depending from libbio-graphics-perl are failing to > build[1]. May be the only quick solution is to revert the bump of > BioPerl version for the moment (= before the next stable release of > Debian) and try upgrading later. > > I'll keep you informed if I might find any problem with > Bio::Coordinate. > > Just for the sake of interest: Is there any specific reason to > outsource > Bio::Coordinate from BioPerl? > > Kind regards > > Andreas. > > [1] https://bugs.debian.org/848236
Hi Andreas, A new Bio-Graphics release was posted yesterday and (despite initial problems) has been added to CPAN: https://metacpan.org/pod/Bio::Graphics Can you test to see if this issue is resolved? I can work on updating the README.md for Bio::Coordinate in the meantime.
  Tue Dec 20 13:42:42 2016 andreas [...] an3as.eu - Correspondence added
Subject: Re: [rt.cpan.org #119235] Bio/Coordinate/Pair.pm removed from BioPerl in version 1.00070001
Date: Tue, 20 Dec 2016 19:42:24 +0100
To: Chris Fields via RT <bug-bioperl [...] rt.cpan.org>
From: Andreas Tille <andreas [...] an3as.eu>
Hi Chris, On Fri, Dec 16, 2016 at 03:48:10PM -0500, Chris Fields via RT wrote: Show quoted text
> A new Bio-Graphics release was posted yesterday and (despite initial problems) has been added to CPAN: > > https://metacpan.org/pod/Bio::Graphics > > Can you test to see if this issue is resolved? I can work on updating the README.md for Bio::Coordinate in the meantime.
Uploaded to Debian, thanks for your support Andreas. -- http://fam-tille.de
  Tue Feb 05 11:51:36 2019 CDRAUG [...] cpan.org - Status changed from 'open' to 'resolved'