[Bioperl-l] updates, new code, invitation to contribute

[James Wasmuth]

> So what is happening when someone "fails" to install bioperl? Did that 
> person try to install all dependencies and then gave up over the 
> ensuing hassle? 



When I first installed BioPerl through CPAN it seemed that the whole of 
CPAN distribution was loading onto my computer. Okay, it wasn't but it 
took an age. I can see how people not too used to dealing with Perl 
modules could think something has gone wrong. Perhaps a "Don't Panic in 
large friendly letters" should appear as its being installed. Seriously 
though, new users just need to be told to be brave.

anyway my 2p worth

-james

p.s.

> There are a lot of bugs sitting in the bugzilla queue.

I'll start having a look at some over the weekend. I've been silent due 
to other commitments, but could do with the distraction









Hilmar Lapp wrote:

>
> On Tuesday, April 26, 2005, at 01:11  PM, Jason Stajich wrote:
>
>> Bio::Factory::FTLocationFactory
>>  Hierarchical parsing works even for joins of joins now.  This is 
>> using a regexp solution which seems to be suitably fast but has the 
>> problem of not working on perls < 5.6.1.
>>
>
> It won't be difficult to make the test conditional on the perl 
> version, but I wonder what happens if a perl 5.005 or lower loads the 
> module and needs to compile the expression. Haven't had a chance to 
> investigate yet.
>
>> [...]
>> Bug fixing help!
>> There are a lot of bugs sitting in the bugzilla queue.  I realize it 
>> may not seem easy for someone to jump in and work on, but that is how 
>> you learn the toolkit (it's how I learned to do things on this project).
>
>
> What would also help I think if people can write up small short test 
> cases that expose the bug.
>
>> [...]
>> I think it may be worth considering moving stuff that has lots of 
>> dependancies out of the main core code and into separate installable 
>> packages.  IO::String is not a large dependancy, but LWP starts to be 
>> add any of the XML modules, Graph, etc and it seems to be too large 
>> of a hurdle for many new folks.  Maybe anything which depends on code 
>> linked to an external C library would be a candidate.
>
>
> In a way I agree but what I'm not sure about is how separating out 
> modules with compiled dependencies will help if you want those modules 
> anyway. If you don't want them then failure to install those 
> dependencies should not be a cause to worry, and in fact one should 
> then not even bother to try to install them.
>
> So what is happening when someone "fails" to install bioperl? Did that 
> person try to install all dependencies and then gave up over the 
> ensuing hassle? Maybe we need to better document which dependencies 
> are worth installing and which aren't unless you are certain you'll 
> use a particular set of modules or functionality.
>
> Maybe it's the Bundle that's trying to do too good of a job by 
> including virtually all dependencies? Maybe there should be different 
> bundles for different intended uses?
>
> How would separating out modules with compiled dependencies help an 
> RPM maintainer if she wants to build an RPM for the entire bioperl 
> anyway (in either one or a set of RPMs)?
>
> Installing bioperl is indeed a PITA, I've done it too many times. The 
> main pain, however, in my experience comes from LWP, GD, and sometimes 
> expat. None of these are needed for much of the core functionality, 
> but based on list traffic many users out there do want GBrowse and/or 
> Bio::DB::* modules, for which you'll have to have them.
>
>     -hilmar


-- 
"Until man duplicates a blade of grass, nature can laugh at his so-called scientific knowledge...."
            --Thomas Edison 

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