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Bug#848236: src:gbrowse: Fails to build from source since bioperl upgrade has broken libbio-graphics-perl



Package: src:gbrowse
Severity: serious
Justification: FTBFS

Hi,

when trying to build gbrowse it fails to build from source:

...
CGI::param called in list context from /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm line 2348, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 412.
CGI::param called in list context from /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 271, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 412, <STDIN> line 1.
CGI::param called in list context from /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm line 271, this can lead to vulnerabilities. See the warning in "Fetching the value or values of a single named parameter" at /usr/share/perl5/CGI.pm line 412, <STDIN> line 1.
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 180) 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-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1842
STACK (eval) /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1570
STACK Bio::Graphics::Browser2::RenderPanels::run_local_requests /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:1524
STACK Bio::Graphics::Browser2::RenderPanels::request_panels /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm:195
STACK Bio::Graphics::Browser2::Render::render_deferred /build/gbrowse-2.54+dfsg/t/../lib/Bio/Graphics/Browser2/Render.pm:3589
STACK toplevel t/05.deferredrendering.t:102
-------------------------------------
...


The cause is most probably that libbio-graphics-perl does not work
together with bioperl 1.7.1 (see also #848105).  I'm now becoming aware
that with the naive upgrade to bioperl 1.7.1 we have triggered problems
that should have solved inside a transition via experimental.  My
proposed course of action is as follows:

  1. Revert the version bump of bioperl and upload the old version
     with an epoch (1:1.6.924-6).
  2. Upload 1.7.1-2 to experimental
  3. Solve all issues with BioPerl 1.7.x after Stretch release.

Does anybody have a better plan?

Kind regards

        Andreas.


-- System Information:
Debian Release: 8.6
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)


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