[ensembl-dev] Newbie question: BlastView config for Ubuntu "Lucid" woes

Nick Langridge nickl at ebi.ac.uk
Tue Jan 10 13:06:31 GMT 2012


Hi Andy/Bob,

I tried applying the patch suggested in the bug report, but we still had 
problems (specifically Ensembl would fail to connect to the DAS 
registry). Maybe there is a better fix (?), but I didn't spend too long 
messing with it as it was easy for us to change the libwww version.

Cheers,
Nick



On 10/01/2012 12:58, Andy Jenkinson wrote:
> Hi Bob,
>
> If I remember correctly, the incompatibility is to do with a missing "parse_head" method in LWP::Protocol, as it was moved elsewhere or re-engineered in later versions of libwww. I think that is what causes the LWP::Parallel tests to fail. Again from memory, the method itself did not actually do anything substantial under normal circumstances, so it may be possible to fix the incompatibility. For example you could create an empty method in the symbol table (which as hacks go is possibly the cleanest since it need not require modifying either library), or modify LWP::Parallel to not call it. However I never tested either solution myself.
>
> See here for the original bug rep and a potential solution:
> https://rt.cpan.org/Public/Bug/Display.html?id=40261
>
> Let me know if my memory is inaccurate or you need further help.
>
> Cheers,
> Andy
>
> On 10 Jan 2012, at 12:42, Nick Langridge wrote:
>
>    
>> Hi Bob,
>>
>> I recently hit the same issue and in the end I reverted to an older version of libwww (http://backpan.perl.org/authors/id/G/GA/GAAS/libwww-perl-5.814.tar.gz).
>>
>>      
>>> I'm loathe to remove my distribution's version of libwww as it will break other functionality
>>>        
>> Could you install an older vesion to a separate lib dir and use it only for Ensembl?
>>
>> Cheers,
>> Nick
>>
>> On 10/01/2012 12:28, Martin Steele wrote:
>>      
>>> Hi All,
>>>
>>> This is my first attempt at installing and configuring an Ensembl/BLAST/BlastView resource from scratch, and I've come unstuck when running the blast_database.pl script. I'd be grateful for any (gentle) pointers/solutions. The script fails with:
>>>
>>> Base class package "LWP::Parallel::UserAgent" is empty.
>>>      (Perhaps you need to 'use' the module which defines that package first,
>>>      or make that module available in @INC<snip>
>>>
>>> I've tried to install the LWP::Parallel::UserAgent module from CPAN, but it fails its tests and hence doesn't install. The problem can be traced to an incompatibility between the newer version of libwww-perl package that comes with the Ubuntu "Lucid" (10.04.3) platform that I'm using. The distro has a libwww version of 6.03, whereas the last version with a working UserAgent module seems to have been 5.814. I've tried a fix and a patch recommended at https://rt.cpan.org/Public/Bug/Display.html?id=40261, but to no avail.
>>>
>>> So, what do people do in such a situation? I'm loathe to remove my distribution's version of libwww as it will break other functionality, so what do others in the community do here? Seeing that the UserAgent code appears to have been dormant since 2004, surely this must be a reasonably common problem (though Google doesn't seem to suggest this).
>>>
>>> Thanks for any help,
>>> Bob
>>>
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>>>
>>>
>>>        
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>    




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