Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: Fails to build from source since bioperl upgrade has broken libbio-graphics-perl)
Hi,
this is a very *urgent* call to all BioPerl users to raise their
opinion. To verify what else might be broken by the new BioPerl I
tested its rdepends. I stumbled upon bioperl-run which is making
heavy use of
/usr/share/perl5/Bio/Tools/Run/WrapperBase.pm
which is also removed from latest BioPerl. So bioperl-run is broken as
well and even if we would manage to solve the issue with gbrowse I'm
afraid we are opening a can of worms when keeping bioperl 1.7.1. So
this is a serious and urgent call either for help or to confirm my plan
I mentioned below to revert bioperl to the old and tested version.
If I do not hear anything I'll do the revert on Saturday or latest
Sunday.
Kind regards
Andreas.
On Thu, Dec 15, 2016 at 02:45:06PM +0100, Andreas Tille wrote:
> 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)
>
>
--
http://fam-tille.de
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