[Bioperl-l] Bioperl 1.6

Chris Fields cjfields at illinois.edu
Mon Jan 18 23:04:57 EST 2010


Hmm, the trouchelle repo is the only one that had a working DB_File for perl 5.10 (not sure but I think 5.8.9 was fine).  Probably worth contacting them about this to see if they can drop the (way out-of-date) 1.4 distribution.

chris

On May 18, 2008, at 9:22 PM, Guohong Hu wrote:

> Thank for you all. The problem is solved. The bioperl 1.4 version is from
> the Trouchelle repo, but 1.6 is in the Bioperl Regular Releases repo. When I
> added all the repo according to the bioperl wiki instruction, somehow 1.4
> became a prerequisite for 1.6. But Chris's question reminded me, so I
> removed Trouchelle repo, and the installation proceeded without errors. I
> suggested we put a note in the wiki link since it looks like an odd issue
> not just for me.
> 
> Best,
> Guohong
> 
> 
> 
> _________________________________________
> ·¢¼þÈË: Chris Fields [mailto:cjfields at illinois.edu] 
> ·¢ËÍʱ¼ä: 2010Äê1ÔÂ18ÈÕ 23:30
> ÊÕ¼þÈË: Guohong Hu
> ³­ËÍ: bioperl-l at lists.open-bio.org
> Ö÷Ìâ: 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
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 




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