[BioRuby] FW: installing bio::graphics

[jan aerts (RI)]

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-----Original Message-----
From: jan aerts (RI)
Sent: Fri 15/02/2008 01:38
To: Robert Citek
Subject: RE: [BioRuby] installing bio::graphics
 
Hi Robert.

I'm testing things out here, and all seems to work... Could you tell me what version of rubygems you're using ("gem --version")? If it's not 1.0.1, you can upgrade using "sudo gem update --system".

Then can you try the following?
  ruby -rubygems -e "require 'bio'; require 'bio-graphics' ; puts 'hello' "

If this works, it means that rubygems were not loaded. You can fix that by setting the RUBYOPT environment variable. See http://docs.rubygems.org/read/chapter/3#page70 for more information.

Hope this helps.
jan.

-----Original Message-----
From: bioruby-bounces at lists.open-bio.org on behalf of Robert Citek
Sent: Thu 14/02/2008 17:00
To: bioruby at lists.open-bio.org
Subject: [BioRuby] installing bio::graphics
 
Hello all,

I'm trying to install the Bio::Graphics package for Ruby:

  http://bio-graphics.rubyforge.org/

The site has instructions for installing under Ubuntu:

    * gem install bio
    * sudo apt-get install libcairo-ruby

While I can get libcairo-ruby to install, I'm getting an error with using gem:

$ sudo apt-get install rubygems

$ gem install bio
Bulk updating Gem source index for: http://gems.rubyforge.org
ERROR:  While executing gem ... (Errno::EACCES)
    Permission denied - /var/lib/gems/1.8/cache/bio-1.2.1.gem

If I add a sudo, then things seem to work:

$ sudo gem install bio
Bulk updating Gem source index for: http://gems.rubyforge.org
Successfully installed bio-1.2.1

$ sudo gem install bio-graphics
Successfully installed bio-graphics-1.4
Installing ri documentation for bio-graphics-1.4...
Installing RDoc documentation for bio-graphics-1.4...

However, now when I try to run a trimmed down version of the example
on the page, I get an error message:

$ ruby -e "puts 'hello' "
hello

$ ruby -e "require 'bio' ; puts 'hello' "
hello

$ ruby -e "require 'bio-graphics' ; puts 'hello' "
-e:1:in `require': no such file to load -- bio-graphics (LoadError)
        from -e:1

$ ruby -e "require_gem 'bio-graphics'  ; puts 'hello' "
-e:1: undefined method `require_gem' for main:Object (NoMethodError)

$ ruby -e "gem 'bio-graphics' ; puts 'hello' "
-e:1: undefined method `gem' for main:Object (NoMethodError)

Did using gem to install bio and bio-graphics not work?  What am I overlooking?

Regards,
- Robert
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