[Bioperl-l] Bioperl 1.6

Chris Fields cjfields at illinois.edu
Mon Jan 18 10:30:20 EST 2010


Guohong, 

1.6.1 PPM doesn't (at least, shouldn't) require BioPerl 1.4 to be installed first.  Make sure the repos are set according to the Windows installation instructions on the BioPerl wiki:

http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows

IIRC the actual order of the PPM repository can be critical (PPM pulls based on highest version, first repo, but sometimes it gets confused).  Just curious but where is the v 1.4 PPM located?  If it is local to our PPM repo I can physically remove it to prevent this from happening.

chris

On Jan 17, 2010, at 8:34 PM, Guohong Hu wrote:

> Hi there,
> 
> 
> 
> I was trying to install BioPerl in windows using ppm, by following the
> instruction in
> "http://bioperl.open-bio.org/wiki/Installing_Bioperl_on_Windows". I set up
> the repositories, and did the search of Bioperl packages. The latest version
> available is BioPerl 1.6.1 on http://bioperl.org/DIST. When I tried to
> install it, a number of prerequisite modules were being installed too, which
> include Bioperl 1.4. Then an error message showed up during installation:
> 
> 
> 
> "ERROR: File conflict for 'C:/Perl/html/bin/bp_aacomp.html'.The package
> BioPerl has already installed a file that package bioperl wants to install."
> 
> 
> 
> It looks to me that BioPerl 1.6.1 had installed a file that bioperl 1.4
> wanted to install again. I don't know why bioperl 1.4 was one of the
> prerequisites for 1.6.1. If I just install 1.4, it will be installed without
> errors. But I need a newer version, because some modules (like
> 
> Bio::Tools::HMM) is not included in 1.4.
> 
> 
> 
> I saw on internet that somebody had the same problem when he was trying to
> install BioPerl 1.5, but I didn't find the solution.
> 
> 
> 
> Anybody has a clue on that? Thank you for your time.
> 
> 
> 
> GH
> 
> 
> 
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