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
> `. `'` la...@debian.org / chris-lamb.co.uk
> `-
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