[Bioperl-l] Bioperl 1.5.2 RC5 install onWinXPActivePerl 5.8.8.819

Chris Fields cjfields at uiuc.edu
Thu Nov 30 17:16:02 EST 2006


On Nov 30, 2006, at 3:41 PM, Nathan S. Haigh wrote:

> ...
>>
>> Okay, revise that.  I get the message you mentioned, but  
>> installation only
>> fails after tests are run.  The single failed test (rnamotif.t) is  
>> due to
>> DB_File not being installed, which Sendu has corrected in CVS and  
>> (I think)
>> the 1.5.2 branch.  However, I can't get DB_File to install via  
>> CPAN (I have
>> VC++ Express Edition installed).  I think XML::SAX and a few  
>> others fail as
>> well.
>>
>> Chris
>>
>>
>>
>
> Yes that's correct, I get the message but things then seem to  
> proceed normally (not that I know what normal is!).
> I had to install DB_File via PPM and install XML::SAX explicitly in  
> CPAN. That then seems to have cleared things up and the tests pass  
> and bioperl core is installed. However, there are other optional  
> dependencies that didn't install successfully - I suppose I should  
> investigate those tomorrow.
>
> Nath

The DB_File failure is due to compilation problems.  BTW, I can get  
XML::SAX to install, so that shouldn't be an issue.

I know that setting up the PPM is a pain, but I have to say it is  
much faster, and all required PPMs are available.  Which makes me  
curious: why bother with trying out a CPAN installation process at  
this point, especially when you have to use PPM to install some of  
the prereqs properly anyway?

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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