[Debian-med-packaging] Bug#848105: Bio/Coordinate/Pair.pm removed from BioPerl in version 1.00070001

[Andreas Tille]

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 at debian.org / chris-lamb.co.uk
>        `-


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