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 <gre...@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.
