Re: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: Fails to build from source since bioperl upgrade has broken libbio-graphics-perl)
On 16 December 2016 at 09:50, Andreas Tille <andreas@an3as.eu> wrote:
> 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.
>
> 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.
Bioperl is a massive collection of perl modules that grew unmaintainable.
The proposed solution (upstream) for this was that bioperl would be split
into smaller more manageble distributions. For example, there is now
bio-biblio, bio-eutilities, and bio-coordinates which were previously part
of bioperl itself. The core bioperl is now the bioperl-live distribution.
This may cause issues for other packages in Debian because in Debian they
are dependent on bioperl package instead of being dependent on a specific
perl module. Even more trouble because the new perl distributions are not
yet packaged in Debian at all. Another issue is that some of them are not
even officially released.
There is at least one very important fix on the new bioperl which fixes
the connection to the NCBI servers (although the fix is simple enough
that could be backported). Other reason in favour of upgrading is that
bioperl-live is tricky to install and the main dependency of the other
bioperl distributions. Any user wanting to install the other packages
could probably handle their installation from CPAN but would be nice if
Debian supplied bioperl-live as a foundation for that.
Carnë
Reply to: