[Bioperl-l] Need help installing Bioperl on Windows

Scott Cain cain.cshl at gmail.com
Thu Oct 23 17:21:29 EDT 2008


Ah, I forgot to ask: are you using perl 5.10?  I've found that to be
completely broken for ActiveState's perl (other perl 5.10 builds seem
to be fine).  I would suggest you use perl 5.8.

Scott


On Thu, Oct 23, 2008 at 5:17 PM, Corbo, Joseph
<jcorbo at pathology.wustl.edu> wrote:
> Unfortunately, I tried the installation again after adding the tcool
> repository as Scott suggested, and I got exactly the same error message.
> Anybody have another idea?  Thanks, Joe
>
>
> -----Original Message-----
> From: Scott Cain [mailto:cain.cshl at gmail.com]
> Sent: Thursday, October 23, 2008 3:55 PM
> To: Corbo, Joseph
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Need help installing Bioperl on Windows
>
> Hi Joe,
>
> I just ran into the same problem when installing GBrowse on Windows.
> You need to add yet another repository: tcool
> http://ppm.tcool.org/archives/  which provides DB_File.
>
> Scott
>
>
> On Thu, Oct 23, 2008 at 4:47 PM, Corbo, Joseph
> <jcorbo at pathology.wustl.edu> wrote:
>> Greetings.  I am trying to install Bioperl on my Windows XP machine
> and
>> am having a problem I would greatly appreciate some help with.  I am
>> following the directions for installing Bioperl as given on the
> Bioperl
>> website page "Installing Bioperl on Windows" under the section
>> "Installation using the Perl Package Manager".  I added the three new
>> repositories (http://bioperl.org/DIST/ etc.) as they instruct.  Then
>> when I try to install Bioperl either using the GUI installation or the
>> command line sequence "ppm-shell, search bioperl, install [number]" I
>> get the following error message which I don't know how to fix:
>>
>>
>>
>> WARNING: Can't find any package that provides DB_File:: for
>> Bundle-BioPerl-Core
>>
>>
>>
>> bioperl depends on Bundle-BioPerl-Core
>>
>> bioperl depends on SVG
>>
>> bioperl depends on GD-SVG
>>
>> bioperl depends on Spreadsheet-ParseExcel
>>
>> bioperl depends on XML-SAX
>>
>> bioperl depends on AcePerl
>>
>> bioperl depends on XML-SAX-ExpatXS
>>
>> bioperl depends on SOAP-Lite
>>
>> bioperl depends on SVG-Graph
>>
>> bioperl depends on Bio-ASN1-EntrezGene
>>
>> bioperl depends on XML-XPath
>>
>> bioperl depends on Convert-Binary-C
>>
>> bioperl depends on XML-Twig
>>
>> bioperl depends on Set-Scalar
>>
>> bioperl depends on Text-Shellwords
>>
>> bioperl depends on Data-Stag
>>
>> bioperl depends on libxml-perl
>>
>> bioperl depends on XML-Writer
>>
>> bioperl depends on Graph
>>
>> bioperl depends on Class-AutoClass
>>
>> bioperl depends on Clone
>>
>> bioperl depends on XML-DOM-XPath
>>
>> bioperl depends on IO-stringy
>>
>> bioperl depends on OLE-Storage_Lite
>>
>> bioperl depends on XML-NamespaceSupport
>>
>> bioperl depends on Cache-Cache
>>
>> bioperl depends on MIME-Lite
>>
>> bioperl depends on Math-Derivative
>>
>> bioperl depends on Math-Spline
>>
>> bioperl depends on Statistics-Descriptive
>>
>> bioperl depends on Tree-DAG_Node
>>
>> bioperl depends on Heap
>>
>> bioperl depends on Test-Deep
>>
>> bioperl depends on XML-DOM
>>
>> bioperl depends on XML-XPathEngine
>>
>> bioperl depends on Error
>>
>> bioperl depends on Email-Date-Format
>>
>> bioperl depends on MIME-Types
>>
>> bioperl depends on MailTools
>>
>> bioperl depends on Test-Tester
>>
>> bioperl depends on Test-NoWarnings
>>
>> bioperl depends on XML-RegExp
>>
>> bioperl depends on Test-Pod
>>
>> bioperl depends on TimeDate
>>
>>
>>
>>
>>
>> Any thoughts on how to fix this?  Thanks, Joe Corbo
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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