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

[Jonathan Arthur]

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