[Bioperl-l] Bioperl 1.6

Mark A. Jensen maj at fortinbras.us
Mon Jan 18 11:33:12 EST 2010


this issue's come up before, see this thread
http://lists.open-bio.org/pipermail/bioperl-l/2009-October/031400.html
MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Guohong Hu" <ghhu at sibs.ac.cn>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Monday, January 18, 2010 10:30 AM
Subject: Re: [Bioperl-l] Bioperl 1.6


> 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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>
>
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