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
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