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

Wed Jan 18 01:11:47 UTC 2017

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 at 6:27 PM gregor herrmann <gregoa at 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 data files due to an assumption
> about
>
> > the current working directory. When he fixed this, there were just a
>
> > handful of tests still failing.
>
>
>
> Right, that's when I built from a clone of the debian package git
>
> repo. With your github repo, this was not necessary for reasons I
>
> haven't yet understood.
>
>
>
> > Gregor, is there a patch file that I can
>
> > apply to get up to the same point you got to?
>
>
>
> Oh, scratch what I wrote above, now I get the same with the debian
>
> repo, so no more "Can't find foo in @INC". Good, at least the
>
> failures are consistent now (for whatever reason, maybe the 5.24.1
>
> upload to unstable changed something), and no patch for that part
>
> needed.
>
>
>
> So now we are still at:
>
>
>
>
>
> t/03.render.t .............
>
> 1..150
>
> ok 1
>
> ok 2
>
> ok 3
>
> ok 4
>
> ok 5
>
> ok 6
>
> ok 7
>
> ok 8
>
> ok 9
>
> ok 10
>
> ok 11
>
> ok 12
>
> ok 13
>
> ok 14
>
> ok 15
>
> ok 16
>
> ok 17
>
> ok 18
>
> ok 19
>
> ok 20
>
> ok 21
>
> ok 22
>
> ok 23
>
> ok 24
>
> ok 25
>
> ok 26
>
> ok 27
>
> ok 28
>
> ok 29
>
> ok 30
>
> ok 31
>
> ok 32
>
> ok 33
>
> ok 34
>
> ok 35
>
> ok 36
>
> ok 37
>
> ok 38
>
> ok 39
>
> ok 40
>
> ok 41
>
> Dubious, test returned 255 (wstat 65280, 0xff00)
>
> Failed 109/150 subtests
>
> Sometimes this test gets 'stuck'. If this happens, kill the test and Build
> test again.
>
> RenderPanels error:
>
> ------------- EXCEPTION -------------
>
> MSG: The requested glyph class, ``span'' is not available: Attempt to
> reload Bio/Graphics/Glyph/span.pm aborted.
>
> Compilation failed in require at (eval 138) line 2, <> line 132.
>
>
>
> STACK Bio::Graphics::Glyph::Factory::make_glyph
> /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
>
> STACK Bio::Graphics::Glyph::add_feature
> /usr/share/perl5/Bio/Graphics/Glyph.pm:424
>
> STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
>
> STACK (eval)
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1597
>
> STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1551
>
> STACK Bio::Graphics::Browser2::Render::Slave::render_tracks
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
>
> STACK Bio::Graphics::Browser2::Render::Slave::run_operation
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_request
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_connection
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
>
> STACK Bio::Graphics::Browser2::Render::Slave::request_loop
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
>
> STACK Bio::Graphics::Browser2::Render::Slave::run
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
>
> STACK toplevel t/04.remoteserver.t:81
>
> -------------------------------------
>
>
>
> Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line
> 136.
>
> RenderPanels error:
>
> ------------- EXCEPTION -------------
>
> MSG: The requested glyph class, ``span'' is not available: Attempt to
> reload Bio/Graphics/Glyph/span.pm aborted.
>
> Compilation failed in require at (eval 138) line 2, <> line 132.
>
>
>
> STACK Bio::Graphics::Glyph::Factory::make_glyph
> /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
>
> STACK Bio::Graphics::Glyph::add_feature
> /usr/share/perl5/Bio/Graphics/Glyph.pm:424
>
> STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
>
> STACK (eval)
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1597
>
> STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1551
>
> STACK Bio::Graphics::Browser2::Render::Slave::render_tracks
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
>
> STACK Bio::Graphics::Browser2::Render::Slave::run_operation
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_request
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_connection
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
>
> STACK Bio::Graphics::Browser2::Render::Slave::request_loop
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
>
> STACK Bio::Graphics::Browser2::Render::Slave::run
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
>
> STACK toplevel t/04.remoteserver.t:81
>
> -------------------------------------
>
>
>
> Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line
> 136.
>
> RenderPanels error:
>
> ------------- EXCEPTION -------------
>
> MSG: The requested glyph class, ``span'' is not available: Attempt to
> reload Bio/Graphics/Glyph/span.pm aborted.
>
> Compilation failed in require at (eval 138) line 2, <> line 132.
>
>
>
> STACK Bio::Graphics::Glyph::Factory::make_glyph
> /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
>
> STACK Bio::Graphics::Glyph::add_feature
> /usr/share/perl5/Bio/Graphics/Glyph.pm:424
>
> STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
>
> STACK (eval)
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1597
>
> STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1551
>
> STACK Bio::Graphics::Browser2::Render::Slave::render_tracks
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
>
> STACK Bio::Graphics::Browser2::Render::Slave::run_operation
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_request
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
>
> STACK Bio::Graphics::Browser2::Render::Slave::process_connection
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
>
> STACK Bio::Graphics::Browser2::Render::Slave::request_loop
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
>
> STACK Bio::Graphics::Browser2::Render::Slave::run
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
>
> STACK toplevel t/04.remoteserver.t:81
>
> -------------------------------------
>
>
>
> Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line
> 136.
>
> t/04.remoteserver.t .......
>
> 1..43
>
> ok 1
>
> ok 2
>
> ok 3
>
> ok 4
>
> ok 5
>
> ok 6
>
> ok 7
>
> ok 8
>
> ok 9
>
> ok 10
>
> not ok 11
>
> # Failed test 11 in t/04.remoteserver.t at line 136 fail #2
>
> ok 12
>
> ok 13
>
> ok 14
>
> ok 15
>
> ok 16
>
> ok 17
>
> ok 18
>
> ok 19
>
> ok 20
>
> ok 21
>
> ok 22
>
> not ok 23
>
> # Failed test 23 in t/04.remoteserver.t at line 136 fail #5
>
> ok 24
>
> ok 25
>
> ok 26
>
> ok 27
>
> ok 28
>
> ok 29
>
> ok 30
>
> ok 31
>
> ok 32
>
> ok 33
>
> ok 34
>
> not ok 35
>
> # Failed test 35 in t/04.remoteserver.t at line 136 fail #8
>
> ok 36
>
> ok 37
>
> ok 38
>
> not ok 39
>
> # Test 39 got: '2' (t/04.remoteserver.t at line 149)
>
> #    Expected: '4'
>
> ok 40
>
> ok 41
>
> Failed 6/43 subtests
>
> RenderPanels error:
>
> ------------- EXCEPTION -------------
>
> MSG: The requested glyph class, ``span'' is not available: Attempt to
> reload Bio/Graphics/Glyph/span.pm aborted.
>
> Compilation failed in require at (eval 181) line 2, <> line 45.
>
>
>
> STACK Bio::Graphics::Glyph::Factory::make_glyph
> /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
>
> STACK Bio::Graphics::Glyph::add_feature
> /usr/share/perl5/Bio/Graphics/Glyph.pm:424
>
> STACK Bio::Graphics::Browser2::RenderPanels::add_features_to_track
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1869
>
> STACK (eval)
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1597
>
> STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1551
>
> STACK Bio::Graphics::Browser2::RenderPanels::request_panels
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:185
>
> STACK Bio::Graphics::Browser2::Render::render_deferred
> /build/gbrowse-2.56+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm:3608
>
> STACK toplevel t/05.deferredrendering.t:102
>
> -------------------------------------
>
>
>
> t/05.deferredrendering.t ..
>
> 1..19
>
> ok 1
>
> ok 2
>
> ok 3
>
> ok 4
>
> not ok 5
>
> # Test 5 got: 'ERROR' (t/05.deferredrendering.t at line 124)
>
> #   Expected: 'AVAILABLE'
>
> ok 6
>
> ok 7
>
> ok 8
>
> ok 9
>
> ok 10
>
> ok 11
>
> ok 12
>
> ok 13
>
> not ok 14
>
> # Test 14 got: 'ERROR AVAILABLE AVAILABLE AVAILABLE AVAILABLE'
> (t/05.deferredrendering.t at line 130)
>
> #    Expected: 'AVAILABLE AVAILABLE AVAILABLE AVAILABLE AVAILABLE'
>
> ok 15
>
> ok 16
>
> ok 17
>
> ok 18
>
> ok 19
>
> Failed 2/19 subtests
>
> t/06.featuresearch.t ......
>
> [..]
>
> Test Summary Report
>
> -------------------
>
> t/03.render.t           (Wstat: 65280 Tests: 41 Failed: 0)
>
>   Non-zero exit status: 255
>
>   Parse errors: Bad plan.  You planned 150 tests but ran 41.
>
> t/04.remoteserver.t     (Wstat: 0 Tests: 41 Failed: 4)
>
>   Failed tests:  11, 23, 35, 39
>
>   Parse errors: Bad plan.  You planned 43 tests but ran 41.
>
> t/05.deferredrendering.t (Wstat: 0 Tests: 19 Failed: 2)
>
>   Failed tests:  5, 14
>
> Files=10, Tests=337, 24 wallclock secs ( 0.08 usr  0.02 sys +  9.06 cusr
> 0.96 csys = 10.12 CPU)
>
> Result: FAIL
>
> Failed 3/10 test programs. 6/337 subtests failed.
>
>
>
>
>
> Wild guess: Is this some incompatibility with Bio::Graphics?
>
> We have 2.40, if this helps.
>
>
>
>
>
> Cheers,
>
> gregor
>
>
>
> --
>
>  .''`.  https://info.comodo.priv.at/ - Debian Developer
> https://www.debian.org
>
>  : :' : OpenPGP fingerprint D1E1 316E 93A7 60A8 104D  85FA BB3A 6801 8649
> AA06
>
>  `. `'  Member of VIBE!AT & SPI, fellow of the Free Software Foundation
> Europe
>
>    `-   NP: Pink Floyd: Young Lust
>
> --
Written on my cell phone. Anything that seems odd is the fault of
auto-correct.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20170118/3f8b4755/attachment-0001.html>