Oh dear. What happens when you just "Build test" on the git checkout? Sounds like path issues. I can try applying the Deb patches and try to reproduce. Unfortunately I am a Deb packaging newbie.
Lincoln On Mon, Jan 16, 2017 at 3:01 PM gregor herrmann <gre...@debian.org> wrote: > On Mon, 16 Jan 2017 16:45:52 +0100, Andreas Tille wrote: > > > > > > If you want to use the same list of tests to skip during build, you > > > > can do something like > > > > > https://sources.debian.net/src/libipc-sharelite-perl/0.17-4/debian/rules > > > Ahhh, OK. I wrongly assumed that would be some magic since in the > > > bioperl case it worked without this extra means. > > > > The magic there worked because it was only needed for autopkgtest and > > not at build time :) > > > > > > I migt be able to try a build later today. > > > > > > After safely landing in Berlin (from Debian Med sprint in Bukarest) I > > > tried with your hints and the only remaining issue seems to be: > > > > > > t/00.compile.t (Wstat: 3840 Tests: 90 Failed: 15) > > > Failed tests: 1, 3, 5, 7, 10, 15, 17-18, 29, 31, 33, 35 > > > 41, 45, 47 > > > Non-zero exit status: 15 > > > > Lucky you :) > > When I try to build the package from git, I get: > > > > Test Summary Report > > ------------------- > > t/00.compile.t (Wstat: 3840 Tests: 90 Failed: 15) > > Failed tests: 1, 3, 5, 7, 10, 15, 17-18, 29, 31, 33, 35 > > 41, 45, 47 > > Non-zero exit status: 15 > > t/02.rearchitecture.t (Wstat: 65280 Tests: 0 Failed: 0) > > Non-zero exit status: 255 > > Parse errors: Bad plan. You planned 90 tests but ran 0. > > t/03.render.t (Wstat: 65280 Tests: 0 Failed: 0) > > Non-zero exit status: 255 > > Parse errors: Bad plan. You planned 150 tests but ran 0. > > t/04.remoteserver.t (Wstat: 65280 Tests: 0 Failed: 0) > > Non-zero exit status: 255 > > Parse errors: Bad plan. You planned 43 tests but ran 0. > > t/05.deferredrendering.t (Wstat: 65280 Tests: 0 Failed: 0) > > Non-zero exit status: 255 > > Parse errors: Bad plan. You planned 19 tests but ran 0. > > t/06.featuresearch.t (Wstat: 65280 Tests: 0 Failed: 0) > > Non-zero exit status: 255 > > Parse errors: Bad plan. You planned 26 tests but ran 0. > > t/07.karyotype.t (Wstat: 65280 Tests: 0 Failed: 0) > > Non-zero exit status: 255 > > Parse errors: Bad plan. You planned 3 tests but ran 0. > > Files=10, Tests=103, 5 wallclock secs ( 0.03 usr 0.03 sys + 4.19 cusr > 0.36 csys = 4.61 CPU) > > Result: FAIL > > Failed 7/10 test programs. 15/103 subtests failed. > > > > > > Ah, found it: > > > > # Failed test 'cgi-bin/das compiled ok' > > # at t/00.compile.t line 47. > > # stdout: > > # stderr: Backslash found where operator expected at > /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line > 963, near "$ENV\" > > # (Missing operator before \?) > > # Backslash found where operator expected at > /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line > 963, near "$1\" > > # (Missing operator before \?) > > # Variable "$semantic_label" is not imported at > /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line > 984, <DATA> line 192. > > # (Did you mean &semantic_label instead?) > > # syntax error at > /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line > 963, near "$ENV\" > > # syntax error at > /build/gbrowse-2.56+dfsg/blib/lib/Bio/Graphics/Browser2/DataSource.pm line > 963, near "''}" > > > > This seems to come from debian/patches/fix_perl_deprecation. > > > > *a bit later* > > > > Yes, this patch is wrong now and can be dropped, as the original > > issue was fixed in the 2.56 release. (Attached) > > > > This brings me to: > > > > 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 > > > > So t/00.compile.t just works. But I still have other issues. > > > > Seems they all fail with something like > > "Can't locate testdata/conf/../../../conf/plugins/Aligner.pm in @INC ..." > > which is quite weird path ... -- But it's fine, so we probably have a > > ". removed from @INC" problem here somewhere. > > > > I guess that's it: > > > > lib/Bio/Graphics/Browser2/PluginSet.pm > > > > my $class = "Bio\:\:Graphics\:\:Browser2\:\:Plugin\:\:$plugin"; > > for my $search_path (@search_path) { > > my $plugin_with_path = "$search_path/$plugin.pm"; > > if (eval {require $plugin_with_path}) { > > > > Ok, changing this to "./$plugin_with_path" gets rid of this error but > > later we still get something similar: > > > > # prove --blib --verbose t/05.deferredrendering.t > > t/05.deferredrendering.t .. > > 1..19 > > ok 1 > > ok 2 > > ok 3 > > 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 > > ------------------------------------- > > > > 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 > > > > Test Summary Report > > ------------------- > > t/05.deferredrendering.t (Wstat: 0 Tests: 19 Failed: 2) > > Failed tests: 5, 14 > > Files=1, Tests=19, 10 wallclock secs ( 0.04 usr 0.00 sys + 0.95 cusr > 0.16 csys = 1.15 CPU) > > Result: FAIL > > > > > > And I'm not sure where this comes from, category "cwd removed from > > @INC). I think this is a question for Lincoln (added back in cc). > > > > > I wonder how these numbers relate to the tests inside the test file and > > > what might be the recommended procedure: Patching single tests (those > > > 1, 3, 5, ...) or the wimpy way to exclude the whole file. May be there > > > is some hint how these tests might pass but I personally have no idea. > > > > Depends if you see them during the build or in autopkgtests. During > > build the test should succeed (which it does now); during autopkgtest > > they might fail because they need something from the source tree > > which is not present in the temporary test directory (and from a > > quick look at t/00.compile.t this assumption is quite realistic). In > > that case you can either try to patch t/00.compile.t (to tell it > > about the right paths) or simply ignore the test as (at least that's > > my impression), since the syntax happens in autopkgtest-pkg-perl's > > syntax.t anyway. > > > > Let's see. > > > > Ok, one change in d/rules to build the package (attached). And then I > > can't test the autopkgtest run because it somehow explodes. *sigh* > > > > Ok, -d helps: > > > > pmerror:/tmp/apt-dpkg-install-i5hiWj/102-gbrowse.deb:42.1125:trying to > overwrite > '/usr/share/man/man3/Bio::DB::SeqFeature::Store::LoadHelper.3pm.gz', which > is also in package libbio-perl-perl 1.7.1-2 > > > > > > > > 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: Michael Penn: Trampoline > > -- Written on my cell phone. Anything that seems odd is the fault of auto-correct.
