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

[James D. White]

>
>
>Message: 13
>Date: Mon, 21 Nov 2005 09:38:48 +1100
>From: Jonathan Arthur <jarthur at med.usyd.edu.au>
>Subject: Re: [Bioperl-l] Installation problems: "unable to remap"
>To: bioperl-l at bioperl.org
>Message-ID: <4380FAF8.2000308 at med.usyd.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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.
>  
>
Bundle::BioPerl does not install Bioperl itself, only the prerequisites 
for Bioperl.
You are now ready to install Bioperl.

>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 ------------------------------
>