[Bioperl-l] problems with installing Bioperl on OSX

[Brian Osborne]

Madis,

For installation in "non-standard" locations you need to do something like
this (from the INSTALL file):

INSTALLING BIOPERL IN A PERSONAL OR PRIVATE MODULE AREA

 If you lack permission to install perl modules into the
 standard site_perl/ system area you can configure bioperl to
 install itself anywhere you choose. Ideally this would
 be a personal perl directory or standard place where you
 plan to put all your 'local' or personal perl modules.

 Note: you _must_ have write permission to this area.

 Simply pass a parameter to perl as it builds your system
 specific makefile.

 Example:

   perl Makefile.PL  LIB=/home/dag/My_Local_Perl_Modules
   make
   make test
   make install

 This tells perl to install bioperl in the desired place, e.g.:

  /home/dag/My_Perl_Modules/Bio/Seq.pm

 Then in your Bioperl script you would write:

  use lib "/home/dag/My_Local_Perl_Modules";
  use Bio::Seq;

 The man pages will probably be installed in $LIB/man. For more
 information on these sorts of custom installs see the documentation
 for ExtUtils::MakeMaker.

 See below for how to use modules that are not installed in the
 standard Perl5 location.


BIO





-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason Stajich
Sent: Friday, August 01, 2003 10:23 AM
To: Madis Metsis
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] problems with installing Bioperl on OSX

no idea - this is question for perl installation gurus.

What does
% perl -V

I assume you get the message when you try and do
% perl Makefile.PL

Are you sure that the version in your path is the version you want to run?


I've installed perl 5.8.0 in /usr/local/bin on OSX and have not had
problems.

-jason
On Fri, 1 Aug 2003, Madis Metsis wrote:

> Hi!
>
> I am installing Bioperl on a OSX machine and get this message:
> *****
> Error: Unable to locate installed Perl libraries or Perl source code.
>
> It is recommended that you install perl in a standard location before
> building extensions. Some precompiled versions of perl do not contain
> these header files, so you cannot build extensions. In such a case,
> please build and install your perl from a fresh perl distribution. It
> usually solves this kind of problem.
>
> (You get this message, because MakeMaker could not find
> "/System/Library/Perl/darwin/CORE/perl.h")
> ****
>
> Thats true, perl.h is not in right place, since both Apple preinstalled
and
> current Serverlogistics installer are not placing it in that place.
>
> How do I get around it. To install Perl AGAIN having 2 copies already on
> machine sounds....
> Is there a line in Makefile.pl that could be modified to "show" to
location
> of perl.h and the rest of perl.
>
> Thanks in advance for any kind of help
>
> Madis Metsis
>
> Center for Genomics and Bioinformatics
> Karolinska Institute
> Stockholm
> Sweden
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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