[Bioperl-l] Installation problems: "unable to remap"
jarthur at med.usyd.edu.au
Sun Nov 20 17:38:48 EST 2005
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 (.......)"
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
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