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

[gregor herrmann]

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

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