[Debian-med-packaging] Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)
gregor herrmann
gregoa at debian.org
Mon Jan 16 21:19:15 UTC 2017
On Mon, 16 Jan 2017 20:23:37 +0000, Lincoln Stein wrote:
> Oh dear. What happens when you just "Build test" on the git checkout?
Voilà:
[..]
t/03.render.t ............. 1/150
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The requested glyph class, ``arrow'' is not available: Attempt to reload Bio/Graphics/Glyph/arrow.pm aborted.
Compilation failed in require at (eval 178) 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 /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
STACK: Bio::Graphics::Glyph::make_subglyph /usr/share/perl5/Bio/Graphics/Glyph.pm:310
STACK: Bio::Graphics::Glyph::new /usr/share/perl5/Bio/Graphics/Glyph.pm:270
STACK: Bio::Graphics::Glyph::Factory::make_glyph /usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:346
STACK: Bio::Graphics::Panel::_add_track /usr/share/perl5/Bio/Graphics/Panel.pm:414
STACK: Bio::Graphics::Panel::_do_add_track /usr/share/perl5/Bio/Graphics/Panel.pm:386
STACK: Bio::Graphics::Panel::add_track /usr/share/perl5/Bio/Graphics/Panel.pm:312
STACK: Bio::Graphics::Browser2::RenderPanels::render_scale_bar /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1080
STACK: Bio::Graphics::Browser2::Render::asynchronous_update_overview_scale_bar /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:2547
STACK: Bio::Graphics::Browser2::Action::ACTION_navigate /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm:144
STACK: Bio::Graphics::Browser2::Render::asynchronous_event /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:432
STACK: t/03.render.t:178
-----------------------------------------------------------
RenderPanels error: can't create /tmp/gbrowse_testing/cache/volvox/c6/1a/93/c61a932ed29ba5ba0d5fb4cb62224dd1/data: No such file or directory at /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/CachedTrack.pm line 158.
RenderPanels error:
------------- EXCEPTION: Bio::Root::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 178) 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 /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 /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::RenderPanels::request_panels /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:192
STACK: Bio::Graphics::Browser2::Render::render_deferred /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:3602
STACK: Bio::Graphics::Browser2::Render::background_track_render /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:529
STACK: Bio::Graphics::Browser2::Action::ACTION_navigate /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm:141
STACK: Bio::Graphics::Browser2::Render::asynchronous_event /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:432
STACK: t/03.render.t:178
-----------------------------------------------------------
t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 109/150 subtests
t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
t/04.remoteserver.t ....... 1/43 RenderPanels error:
------------- EXCEPTION: Bio::Root::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: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
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 /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::Render::Slave::render_tracks /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
STACK: Bio::Graphics::Browser2::Render::Slave::run_operation /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
STACK: Bio::Graphics::Browser2::Render::Slave::process_request /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
STACK: Bio::Graphics::Browser2::Render::Slave::process_connection /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
STACK: Bio::Graphics::Browser2::Render::Slave::request_loop /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
STACK: Bio::Graphics::Browser2::Render::Slave::run /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
STACK: t/04.remoteserver.t:81
-----------------------------------------------------------
t/04.remoteserver.t ....... 3/43 Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line 136.
RenderPanels error:
------------- EXCEPTION: Bio::Root::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: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
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 /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::Render::Slave::render_tracks /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
STACK: Bio::Graphics::Browser2::Render::Slave::run_operation /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
STACK: Bio::Graphics::Browser2::Render::Slave::process_request /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
STACK: Bio::Graphics::Browser2::Render::Slave::process_connection /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
STACK: Bio::Graphics::Browser2::Render::Slave::request_loop /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
STACK: Bio::Graphics::Browser2::Render::Slave::run /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
STACK: t/04.remoteserver.t:81
-----------------------------------------------------------
Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line 136.
RenderPanels error:
------------- EXCEPTION: Bio::Root::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: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
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 /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::Render::Slave::render_tracks /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
STACK: Bio::Graphics::Browser2::Render::Slave::run_operation /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
STACK: Bio::Graphics::Browser2::Render::Slave::process_request /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
STACK: Bio::Graphics::Browser2::Render::Slave::process_connection /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
STACK: Bio::Graphics::Browser2::Render::Slave::request_loop /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229
STACK: Bio::Graphics::Browser2::Render::Slave::run /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160
STACK: t/04.remoteserver.t:81
-----------------------------------------------------------
Use of uninitialized value in numeric gt (>) at t/04.remoteserver.t line 136.
t/04.remoteserver.t ....... Failed 6/43 subtests
t/05.deferredrendering.t .. 1/19 RenderPanels error:
------------- EXCEPTION: Bio::Root::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: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
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 /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::RenderPanels::request_panels /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:178
STACK: Bio::Graphics::Browser2::Render::render_deferred /tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:3602
STACK: t/05.deferredrendering.t:102
-----------------------------------------------------------
t/05.deferredrendering.t .. Failed 2/19 subtests
[..]
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=340, 24 wallclock secs ( 0.09 usr 0.00 sys + 9.23 cusr 1.13 csys = 10.45 CPU)
Result: FAIL
Failed 3/10 test programs. 6/340 subtests failed.
> Sounds like path issues.
Please note that the perl in Debian has already removed cwd() from
@INC. That's at least the first failure group ("Can't find $module in
@INC") -- which does not happen when I try the git checkout. Hm.
Weird.
The second smells similarly but I haven't found the exact place.
Cheers,
gregor
--
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