Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-16 Thread Andreas Tille 
Hi Lincoln,

On Mon, Jan 16, 2017 at 06:14:34PM -0500, Lincoln Stein wrote:
> I need a little help to reproduce Gregor's failed tests, given that I'm a
> complete newbie wrt the Debian packaging system. I have cloned gbrowse
> 2.56+dfsg-1 from the Debian Med repository, but I don't know what command
> line to use to attempt the build. What is the next step? I'm guessing it is
> some form of dpkg-buildpackage, but the number of options is pretty
> overwhelming!

If you have installed the devscripts package you can try

debuild

which is a wrapper around dpkg-buildpackage and in principle needs no
options to reproduce the issue.  Debuild will inform you about missing
Build-Dependencies you need to install - simply use apt-get install what
is listed if anything is missing.  When doing so 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: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 90 tests but ran 0.
t/03.render.t   (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 150 tests but ran 0.
t/04.remoteserver.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 43 tests but ran 0.
t/05.deferredrendering.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 19 tests but ran 0.
t/06.featuresearch.t(Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 26 tests but ran 0.
t/07.karyotype.t(Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 3 tests but ran 0.
Files=10, Tests=103,  5 wallclock secs ( 0.05 usr  0.01 sys +  4.19 cusr  0.30 
csys =  4.55 CPU)
Result: FAIL
Failed 7/10 test programs. 15/103 subtests failed.
dh_auto_test: perl Build test --verbose 1 TEST_FILES=t/02.rearchitecture.t 
t/05.deferredrendering.t t/00.compile.t t/01.yeast.t t/07.balancer.t 
t/08.calign.t returned exit code 255


Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-16 Thread Lincoln Stein 
Hi,

I need a little help to reproduce Gregor's failed tests, given that I'm a
complete newbie wrt the Debian packaging system. I have cloned gbrowse
2.56+dfsg-1 from the Debian Med repository, but I don't know what command
line to use to attempt the build. What is the next step? I'm guessing it is
some form of dpkg-buildpackage, but the number of options is pretty
overwhelming!



Lincoln

On Mon, Jan 16, 2017 at 3:01 PM, gregor herrmann  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,  line 192.
> #   (Did you mean _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

Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-16 Thread gregor herrmann 
On Mon, 16 Jan 2017 21:38:14 +0100, Andreas Tille wrote:

> thanks a lot for you detailed analysis.  BTW, you should be able to `git
> push` into Debian Med repository - no need to do the attachment detour
> if this might be more convenient for you.

Ack, will do so next time.
 
> Hmmm, may be I misunderstand but the failed tests are preventing
> the build from succeeding and besides
> 
>   0001-Drop-patch-fix_perl_deprecation.patch
>   0002-debian-rules-update-name-of-a-config-file-in-chmod-c.patch
> 
> which I `git am`ed I did not found anything in your mail.

Right, the three tests are still failing, and I didn't provide a
patch because I haven't found a solution :)

(For the autopkgtest trial run, I first built the package with
DEB_BUILD_OPTIONS=nocheck.) 

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: Bettina Wegner: Drei Schwester


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Re: Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-16 Thread gregor herrmann 
On Mon, 16 Jan 2017 20:23:37 +, Lincoln Stein wrote:

> Oh dear. What happens when you just "Build test" on the git checkout?

Voilà:

[..]
t/03.render.t . 1/150 
- EXCEPTION: Bio::Root::Exception -
MSG: The requested glyph class, ``arrow'' is not available: Attempt to reload 
Bio/Graphics/Glyph/arrow.pm aborted.
Compilation failed in require at (eval 178) line 2.

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
STACK: Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:342
STACK: Bio::Graphics::Glyph::make_subglyph 
/usr/share/perl5/Bio/Graphics/Glyph.pm:310
STACK: Bio::Graphics::Glyph::new /usr/share/perl5/Bio/Graphics/Glyph.pm:270
STACK: Bio::Graphics::Glyph::Factory::make_glyph 
/usr/share/perl5/Bio/Graphics/Glyph/Factory.pm:346
STACK: Bio::Graphics::Panel::_add_track 
/usr/share/perl5/Bio/Graphics/Panel.pm:414
STACK: Bio::Graphics::Panel::_do_add_track 
/usr/share/perl5/Bio/Graphics/Panel.pm:386
STACK: Bio::Graphics::Panel::add_track 
/usr/share/perl5/Bio/Graphics/Panel.pm:312
STACK: Bio::Graphics::Browser2::RenderPanels::render_scale_bar 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1080
STACK: Bio::Graphics::Browser2::Render::asynchronous_update_overview_scale_bar 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:2547
STACK: Bio::Graphics::Browser2::Action::ACTION_navigate 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm:144
STACK: Bio::Graphics::Browser2::Render::asynchronous_event 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:432
STACK: t/03.render.t:178
---
RenderPanels error: can't create 
/tmp/gbrowse_testing/cache/volvox/c6/1a/93/c61a932ed29ba5ba0d5fb4cb62224dd1/data:
 No such file or directory at 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/CachedTrack.pm line 158.
RenderPanels error: 
- EXCEPTION: Bio::Root::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 178) line 2.

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
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 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::RenderPanels::request_panels 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:192
STACK: Bio::Graphics::Browser2::Render::render_deferred 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:3602
STACK: Bio::Graphics::Browser2::Render::background_track_render 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:529
STACK: Bio::Graphics::Browser2::Action::ACTION_navigate 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Action.pm:141
STACK: Bio::Graphics::Browser2::Render::asynchronous_event 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render.pm:432
STACK: t/03.render.t:178
---
t/03.render.t . Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 109/150 subtests 
t/04.remoteserver.t ... Sometimes this test gets 'stuck'. If this happens, 
kill the test and Build test again.
t/04.remoteserver.t ... 1/43 RenderPanels error: 
- EXCEPTION: Bio::Root::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: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:447
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 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1862
STACK: Bio::Graphics::Browser2::RenderPanels::run_local_requests 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1590
STACK: Bio::Graphics::Browser2::Render::Slave::render_tracks 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:471
STACK: Bio::Graphics::Browser2::Render::Slave::run_operation 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:325
STACK: Bio::Graphics::Browser2::Render::Slave::process_request 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:316
STACK: Bio::Graphics::Browser2::Render::Slave::process_connection 
/tmp/GBrowse/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240
STACK:

Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-16 Thread Lincoln Stein 
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  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,  line 192.
>
> #   (Did you mean _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:
>
>
>
> #

Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-16 Thread Andreas Tille 
Hi Gregor,

thanks a lot for you detailed analysis.  BTW, you should be able to `git
push` into Debian Med repository - no need to do the attachment detour
if this might be more convenient for you.

On Mon, Jan 16, 2017 at 09:01:11PM +0100, gregor herrmann wrote:
> On Mon, 16 Jan 2017 16:45:52 +0100, Andreas Tille wrote:
> > 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 :)

Ahhh ...
  
> > 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 :)

Hmmm, may be I was not looking properly - now I can reproduce all you
wrote.

> 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,  line 192.
> #   (Did you mean _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

Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-16 Thread gregor herrmann 
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, 
 line 192.
#   (Did you mean _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)

Re: ncbi-blast+ 2.6.0

2017-01-16 Thread olivier sallou 
Le lun. 16 janv. 2017 à 17:54, Aaron M. Ucko  a écrit :

> Great, thanks!
>
upload in progress, wiki at Paris CDG is better than in Bucarest  :-)

Olivier

>
> -- Aaron
>
> olivier sallou  writes:
>
> > Hi,
> > Package is almost ready, i should upload tomorrow.wifi was too slow at
> > airport to get deps and upload ;-)
> >
> > Olivier
> >
> > Le lun. 16 janv. 2017 17:23, Aaron M. Ucko  a écrit :
> >
> >> Hi, Olivier.
> >>
> >> BLAST+ 2.6.0 came out last week; will you have time to update the Debian
> >> package, or should I?
> >>
> >> Meanwhile, I do plan to package last week's release of
> ncbi-entrez-direct,
> >> but have been holding off because it's relatively minor and I'm working
> on
> >> eliminating the need to declare conflicts.  (The pairs of conflicting
> >> executables have such radically different usage that it should be
> possible
> >> to divert other packages' versions and substitute a script that figures
> >> out which executable the user meant to run.)
> >>
> >> --
> >> Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
> >> http://www.mit.edu/~amu/ |
> >> http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
>

Re: Name space conflicts

2017-01-16 Thread Andreas Tille 
Hi Aaron,

On Mon, Jan 16, 2017 at 12:03:56PM -0500, Aaron M. Ucko wrote:
> > Alternatively you might have a look into the solution I usually apply to
> > put original binary names in /usr/lib/debian-med/bin.  Feel free to
> > check the examples in plink and snap.
> 
> Thanks for the suggestion, but one of the conflicts (over /usr/bin/efetch)
> is with acedb-other, which is also from debian-med.  I've prepared local
> drafts of argument-analyzing scripts and just need to test and upload
> them.  I have both today and Friday off from work, so should be able to
> find time to take care of that this week.

A - hmmm, at least no different maintainer to fight for a solution
with. :-)

Admittedly efetch is not a sensible name in both cases but I assume you
will be able to deal with this. :-) 

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: Name space conflicts

2017-01-16 Thread Aaron M. Ucko 
Andreas Tille  writes:

> Alternatively you might have a look into the solution I usually apply to
> put original binary names in /usr/lib/debian-med/bin.  Feel free to
> check the examples in plink and snap.

Thanks for the suggestion, but one of the conflicts (over /usr/bin/efetch)
is with acedb-other, which is also from debian-med.  I've prepared local
drafts of argument-analyzing scripts and just need to test and upload
them.  I have both today and Friday off from work, so should be able to
find time to take care of that this week.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu

Name space conflicts (Was: ncbi-blast+ 2.6.0)

2017-01-16 Thread Andreas Tille 
Hi Aaron,

On Mon, Jan 16, 2017 at 11:23:18AM -0500, Aaron M. Ucko wrote:
> BLAST+ 2.6.0 came out last week; will you have time to update the Debian
> package, or should I?

Olivier has answered this in his response.
 
> Meanwhile, I do plan to package last week's release of ncbi-entrez-direct,
> but have been holding off because it's relatively minor and I'm working on
> eliminating the need to declare conflicts.  (The pairs of conflicting
> executables have such radically different usage that it should be possible
> to divert other packages' versions and substitute a script that figures
> out which executable the user meant to run.)

Alternatively you might have a look into the solution I usually apply to
put original binary names in /usr/lib/debian-med/bin.  Feel free to
check the examples in plink and snap.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-16 Thread gregor herrmann 
On Mon, 16 Jan 2017 05:55:20 +0100, Andreas Tille wrote:

> Since I learned from Perl team (in CC) that I can exclude tests via
> 
>debian/tests/pkg-perl/smoke-skip
> 
> I tried to use this feature.  Unfortunately this does not work as
> expected - at least in the build process.  

That's not unexpected since debian/tests/pkg-perl/smoke-skip is an
(optional) configuration file for the autopkgtest-pkg-perl framework
and is not related to building the package.

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


As for the
https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/tests/pkg-perl/smoke-skip
 
file:
It looks like you forgot the "t/" directory prefix for the test
file names.


> Could anybody with better
> Perl skills than me please have a look at the failed build time tests?

I migt be able to try a build later today.
 

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
   `-   BOFH excuse #238:  You did wha... oh _dear_

Re: pbcommand new upstream

2017-01-16 Thread Afif Elghraoui 
Hi, Sascha,

على الإثنين 16 كانون الثاني 2017 ‫01:37، كتب Sascha Steinbiss:
> 
> BTW, I've seen that you updated and uploaded kineticstools -- I just
> finished getting its autopkgtests to work again when I had to leave the
> sprint ;)
> Thanks for taking care of this!

Sure (and thank you and Andreas for working on it). I mostly wanted to
fix the issue with the package version and make sure some other
touch-ups made it into the upload.

Thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: pbcommand new upstream

2017-01-16 Thread Sascha Steinbiss 
Hi Afif,

>> OK, thanks for the confirmation. I’ll update to the latest version of 
>> pbcommand then.
> 
> Many thanks for updating pbcommand--but don't forget to push the final
> changes and tag. :)

[x] Done.

BTW, I've seen that you updated and uploaded kineticstools -- I just
finished getting its autopkgtests to work again when I had to leave the
sprint ;)
Thanks for taking care of this!

Best regards
Sascha



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