[Bioperl-l] Installation problems: "unable to remap"
jason.stajich at duke.edu
Sun Nov 20 21:37:12 EST 2005
Did you actually install Bioperl? It isn't part of Bundle::BioPerl.
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.
> Paul G Cantalupo wrote:
>> 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 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?
>>> 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
> 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
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