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
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From 21d8d702fed4907b8a234fc92f5aab888d6dbb9c Mon Sep 17 00:00:00 2001 From: gregor herrmann <gre...@debian.org> Date: Mon, 16 Jan 2017 20:20:16 +0100 Subject: [PATCH 1/2] Drop patch fix_perl_deprecation. The issue is fixed in the new upstream release. --- debian/patches/fix_perl_deprecation | 18 ------------------ debian/patches/series | 1 - 2 files changed, 19 deletions(-) delete mode 100644 debian/patches/fix_perl_deprecation diff --git a/debian/patches/fix_perl_deprecation b/debian/patches/fix_perl_deprecation deleted file mode 100644 index 42c1f31..0000000 --- a/debian/patches/fix_perl_deprecation +++ /dev/null @@ -1,18 +0,0 @@ -Subject: perl deprecated left brakets in regexp without escape -Description: warning switched to error in perl, need to escape - brakets in perl regexp if braket is a string pattern -Author: Olivier Sallou <osal...@debian.org> -Last-Updated: 2016-12-14 -Bug-Debian: https://bugs.debian.org/826458 -Forwarded: no ---- a/lib/Bio/Graphics/Browser2/DataSource.pm -+++ b/lib/Bio/Graphics/Browser2/DataSource.pm -@@ -960,7 +960,7 @@ sub db_settings { - - # Do environment substitutions in the args. Assume that the environment is safe. - foreach (@argv) { -- s/\$ENV\{(\w+)\}/$ENV{$1}||''/ge; -+ s/\$ENV\{(\w+)\}/$ENV\{$1\}||''/ge; - s/\$HTDOCS/Bio::Graphics::Browser2->htdocs_base/ge; - s/\$DB/Bio::Graphics::Browser2->db_base/ge; - s/\$CONF/Bio::Graphics::Browser2->config_base/ge; diff --git a/debian/patches/series b/debian/patches/series index 2651d71..1806e95 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -4,4 +4,3 @@ manpages.patch fix_pop_url skip_check_installed_test.patch source_init_functions -fix_perl_deprecation -- 2.11.0
From a3542550a97f6967bbe2caf12dc6c845ceb26a24 Mon Sep 17 00:00:00 2001 From: gregor herrmann <gre...@debian.org> Date: Mon, 16 Jan 2017 20:30:38 +0100 Subject: [PATCH 2/2] debian/rules: update name of a config file in chmod call. --- debian/rules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/rules b/debian/rules index 5fba88f..a4ef83e 100755 --- a/debian/rules +++ b/debian/rules @@ -37,7 +37,7 @@ override_dh_auto_install: rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/prototype.js rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/scriptaculous.js chmod 644 debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm - chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled + chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf #Remove database (kept as separate package) rm -rf debian/gbrowse/var/lib/gbrowse/databases/* #Rename pl scripts in bin -- 2.11.0
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