[Bioperl-l] Problem with bioperl installation

[John Slimick]

Hello All:

I tried working with the Swedish site, but I got
confused by all the files there that I returned to
the CPAN installation.

The final lines of a failed install:

   txml-mode ok
   All tests successful, 1 test and 1 subtest dropped

   Files =
   /usr/bin/make -- OK
   Running make install

   mkdir /usr/bin/perl: File exists at
    /usr/local/lib/perl5/5.8.7/ExtUtils/Install.pm  line 112

   make *** [pure_site_install] Error 17

   /usr/bin/make isntall -- Not OK

and back to the prompt.

Earlier in the tests, one was failed with the message

   Can't locate HTTP/Headers.pm in @INC(.....)

Thanks in advance.

john slimick
slimick at pitt.edu

==============================================================

On Sun, 20 Nov 2005, Barry Moore wrote:

> John,
>
> I doesn't sound like your installation succeeded.  Did you get errors
> with make install?  Do you know where locate perl modules are installed
> on yours system (/usr/lib/perl5/site_perl/5.8.5/ on my system)?  If so
> is there a Bio directory there?  Can you give us more details on your
> install process?
>
> Barry
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of John Slimick
> Sent: Thursday, November 17, 2005 1:43 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Problem with bioperl installation
>
>
> Help!
>
> I have tried to install Bioperl for use in
> one of my classes, but I have found a roadblock.
> I have installed current Bioperl by using
> the CPAN route and also using the "make"
> approach. This is on a RH 9.0 system.
> I get the same error on either installation.
>
> Here is the file I wished to test (from the Bioperl
> document):
>
> =======================================================
> #!/usr/bin/perl -w
> use strict;
>
> use Bio::Perl;
>
> $seq_object = get_sequence('swiss',"ROA_HUMAN");
>
> write_sequence(">roa1.fasta",'fasta',$seq_object);
> ==========================================================
>
> I get the following message:
>
>    Can't locate Bio/Perl.pm in @INC( @INC contains ,,long file list)
>
> When I do:
>
>    $ find / -name Perl.pm -print
>
> as _root_ all I get is a single hit
> of
>
>    .../READLINE/Perl.pm
>
> Any thoughts?
>
> Thanks in advance.
>
> john slimick
> slimick at pitt.edu
>
>
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