[Debian-med-packaging] Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)
Lincoln Stein
lincoln.stein at gmail.com
Mon Jan 16 20:23:37 UTC 2017
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 <gregoa at 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.
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