[Bioperl-l] Installation problems: "unable to remap"

[Jason Stajich]

Did you actually install Bioperl?  It isn't part of Bundle::BioPerl.

-jason
On Nov 20, 2005, at 5:38 PM, Jonathan Arthur wrote:

> Hello all,
>
> Thanks Paul and Brian for your help.This has helped me make some  
> progress, but I am still having installation problems. Now, using  
> cpan, when I type: install Bundle::BioPerl all I get is a long list  
> of models marked as "up to date" e.g.
>
> CPAN: Storable loaded ok
> Going to read /home/jonathan/.cpan/Metadata
>  Database was generated on Thu, 10 Nov 2005 07:02:24 GMT
> MIME::Base64 is up to date.
> Digest::Md5 is up to date.
> URI is up to date.
> ...
> Graph::Directed is up to date.
>
> and that's it. No error messages, no failed tests, nothing. However:
>
> perl -e "use Bio::Perl" gives
>
> "Can't locate Bio/Perl.pm in @INC (.......)"
>
> Any ideas?
>
> Thanks again for your help.
>
> Jonathan
>
> Paul G Cantalupo wrote:
>
>> Jonathan,
>>
>> The problem is cygwin Perl. See the following:
>>
>> 1) http://sources.redhat.com/ml/cygwin-announce/2005-07/msg00031.html
>> 2) The 'rebase' README file in /usr/share/doc/Cygwin/
>>
>> Paul
>>
>> Paul Cantalupo
>> Research Specialist/Systems Programmer
>> 559 Crawford Hall
>> Department of Biological Sciences
>> University of Pittsburgh
>> Pittsburgh, PA 15260
>> Work: 412-624-4687
>> Fax: 412-624-4759
>>
>> Ask me about Toastmasters: www.toastmasters.org
>> Midday Club Treasurer
>>
>> On Fri, 18 Nov 2005, Jonathan Arthur wrote:
>>
>>> Hello all,
>>>
>>> I am having difficulty installing BioPerl. I am running Windows  
>>> XP Professional with cygwin. I am using the CPAN installer to  
>>> attempt to install the Bundle::BioPerl modules.
>>>
>>> The installation appears to go relatively smoothly and end  
>>> normally. It does note at the end that there were installation  
>>> problems with File::Spec, GD::SVG, and Data::Stag. Nonetheless,  
>>> when I try to "use Bio::Perl"  Perl cannot find the module and  
>>> exploring /usr/lib confirms the modules are not present.
>>>
>>> I then tried installing the problem modules above on the  
>>> assumption that the final installation of Bio::Perl was dependent  
>>> on these modules being successfully installed. The creation of  
>>> the makefile for GD::SVG dies with:
>>>
>>> C:\cygwin\bin\perl.exe (800): *** unable to remap c:\cygwin\bin 
>>> \cygfreetype-6.dll to same address as parent(0xE100000) != 0xEA0000
>>>
>>> Data::Stag installation experiences a similar error (with  
>>> different .dll) when trying to install the Tk dependency.
>>>
>>> File::Spec installation appears to install fine (bar some failed  
>>> tests because it can't load File::Spec::VMS) and it is present  
>>> in /usr/lib/perl5 so it is not clear what the cpan installation  
>>> is complaining about in regard to this module.
>>>
>>> Could anyone assist with these installation problems?
>>>
>>> Regards,
>>>
>>> Jonathan
>>>
>>> -- 
>>> Dr Jonathan Arthur
>>> Sesqui Lecturer in Bioinformatics
>>> Central Clinical School, Faculty of Medicine and SUBIT
>>> Medical Foundation Building, K25
>>> University of Sydney
>>> Ph: +61 2 9036 3132
>>> Email: jarthur at med.usyd.edu.au
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>
>
> -- 
> Dr Jonathan Arthur
> Sesqui Lecturer in Bioinformatics
> Central Clinical School, Faculty of Medicine and SUBIT
> Medical Foundation Building, K25
> University of Sydney
> Ph: +61 2 9036 3132
> Email: jarthur at med.usyd.edu.au
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12