[BioRuby] biographics/pango problem?

George Githinji georgkam at gmail.com
Tue Jul 1 13:42:30 EDT 2008 

Hi Jan and Frank,
I did a sudo gem list --local
 The ruby bindings for pango or gnome were missing. So i did

$ sudo gem install libpango1-ruby
ERROR:  could not find gem libpango1-ruby locally or in a repository

$ sudo gem install libgnome2-ruby
ERROR:  could not find gem libgnome2-ruby locally or in a repository



I then tried Frank's way but the packages could not compile.

Then i decided to try install ruby-gnome2

sudo apt-get install ruby-gnome2

The following extra packages will be installed:
  libart2-ruby libart2-ruby1.8 libatk1-ruby libatk1-ruby1.8 libgconf2-ruby
  libgconf2-ruby1.8 libgdk-pixbuf2-ruby libgdk-pixbuf2-ruby1.8
libglade2-ruby
  libglade2-ruby1.8 libglib2-ruby1.8 libgnome2-ruby libgnome2-ruby1.8
  libgnomecanvas2-ruby libgnomecanvas2-ruby1.8 libgnomeprint2-ruby
  libgnomeprint2-ruby1.8 libgnomeprintui2-ruby libgnomeprintui2-ruby1.8
  libgnomevfs2-ruby libgnomevfs2-ruby1.8 libgtk-mozembed-ruby
  libgtk-mozembed-ruby1.8 libgtk2-ruby libgtk2-ruby1.8 libgtkglext1
  libgtkglext1-ruby libgtkglext1-ruby1.8 libgtkhtml2-ruby
libgtkhtml2-ruby1.8
  libgtksourceview1-ruby libgtksourceview1-ruby1.8 libopengl-ruby
  libopengl-ruby1.8 libpanel-applet2-ruby libpanel-applet2-ruby1.8
  libpango1-ruby libpango1-ruby1.8 librsvg2-ruby librsvg2-ruby1.8
libvte-ruby
  libvte-ruby1.8
The following NEW packages will be installed:
  libart2-ruby libart2-ruby1.8 libatk1-ruby libatk1-ruby1.8 libgconf2-ruby
  libgconf2-ruby1.8 libgdk-pixbuf2-ruby libgdk-pixbuf2-ruby1.8
libglade2-ruby
  libglade2-ruby1.8 libglib2-ruby1.8 libgnome2-ruby libgnome2-ruby1.8
  libgnomecanvas2-ruby libgnomecanvas2-ruby1.8 libgnomeprint2-ruby
  libgnomeprint2-ruby1.8 libgnomeprintui2-ruby libgnomeprintui2-ruby1.8
  libgnomevfs2-ruby libgnomevfs2-ruby1.8 libgtk-mozembed-ruby
  libgtk-mozembed-ruby1.8 libgtk2-ruby libgtk2-ruby1.8 libgtkglext1
  libgtkglext1-ruby libgtkglext1-ruby1.8 libgtkhtml2-ruby
libgtkhtml2-ruby1.8
  libgtksourceview1-ruby libgtksourceview1-ruby1.8 libopengl-ruby
  libopengl-ruby1.8 libpanel-applet2-ruby libpanel-applet2-ruby1.8
  libpango1-ruby libpango1-ruby1.8 librsvg2-ruby librsvg2-ruby1.8
libvte-ruby
  libvte-ruby1.8 ruby-gnome2

It may look like an overkill but it worked!


Thank you so much for pointing the way.

George



On Tue, Jul 1, 2008 at 4:57 PM, Jan Aerts <jan.aerts at gmail.com> wrote:

> Regarding the trouble people are having to get the requirements set
> correctly (including myself: it took me ages to get it running on a
> Mac at my new job): does anyone have an idea what low-level drawing
> engines could be used instead of cairo? I'm pretty happy with cairo
> itself, but it's just the hassle of getting it running.
>
> If we find a better/simpler engine, we can always create a new git
> branch. I won't have much time to code on this myself, but please feel
> free to fork from git and start hacking away :-)
>
> Note: I've done SVG, and that's a no-go.
>
> jan.
>
> On Tue, Jul 1, 2008 at 2:26 PM, Frank Schwach <f.schwach at uea.ac.uk> wrote:
> > George,
> >
> > I also had lots of problems getting the dependencies for Bio::Graphics
> > up and running on my Centos5 machine but now it is working.
> > In the end I did this:
> >
> > Installed pango-devel (there is probably a package for Ubuntu)
> >
> > Installed ruby-gtk2 to get pango and glib2 ruby bindings:
> >
> http://sourceforge.net/project/showfiles.php?group_id=53614&package_id=48093
> >
> > Most recent version didn't compile on my system so I used
> > ruby-gtk2-0.16.0.tar.gz
> >
> > After unpacking I configured like this to get the bits that I needed:
> > $ ruby extconf.rb glib pango
> >
> > then make, make/install.
> >
> > Glib2.0 or higher is required and you have to make sure that GTK1 is not
> > installed on the system anymore (I first had both in parallel and that
> > didn't work).
> >
> > Maybe this helps solve your problem too. Good luck!
> >
> > Frank
> >
> >
> >
> > On Tue, 2008-07-01 at 15:49 +0300, George Githinji wrote:
> >> Hey,
> >> I recently migrated my application from windows(where it was running
> okl) to
> >> a linux box (because it is open source and has better  support)
> >> I am running Ubuntu 8.04 (hardy) with rails 1.2.1, ruby 1.8.6, bioruby
> 1.2.1
> >> and biographics 1.4
> >> I have also installed libcairo per the instructions on the bio-graphics
> >> library webpage.
> >> however i think i am having problems with pango.
> >>
> >> Is there a pango alternative? Anyway that i can resolve the error below?
> >>
> >> => Booting Mongrel (use 'script/server webrick' to force WEBrick)
> >> => Rails 2.1.0 application starting on http://0.0.0.0:3013
> >> => Call with -d to detach
> >> => Ctrl-C to shutdown server
> >> ** Starting Mongrel listening at 0.0.0.0:3013
> >> ** Starting Rails with development environment...
> >> /usr/local/lib/site_ruby/1.8/rubygems/custom_require.rb:27:in
> >> `gem_original_require': no such file to load -- pango
> (MissingSourceFile)
> >> Exiting
> >>         from
> /usr/local/lib/site_ruby/1.8/rubygems/custom_require.rb:27:in
> >> `require'
> >>         from
> >>
> /usr/lib/ruby/gems/1.8/gems/activesupport-2.1.0/lib/active_support/dependencies.rb:509:in
> >> `require'
> >>         from
> >>
> /usr/lib/ruby/gems/1.8/gems/activesupport-2.1.0/lib/active_support/dependencies.rb:354:in
> >> `new_constants_in'
> >>         from
> >>
> /usr/lib/ruby/gems/1.8/gems/activesupport-2.1.0/lib/active_support/dependencies.rb:509:in
> >> `require'
> >>         from
> >> /usr/lib/ruby/gems/1.8/gems/bio-graphics-1.4/lib/bio-graphics.rb:12
> >>         from
> /usr/local/lib/site_ruby/1.8/rubygems/custom_require.rb:32:in
> >> `gem_original_require'
> >>         from
> /usr/local/lib/site_ruby/1.8/rubygems/custom_require.rb:32:in
> >> `require'
> >>         from
> >>
> /usr/lib/ruby/gems/1.8/gems/activesupport-2.1.0/lib/active_support/dependencies.rb:509:in
> >> `require'
> >>          ... 29 levels...
> >>         from
> >> /usr/lib/ruby/gems/1.8/gems/rails-2.1.0/lib/commands/server.rb:39
> >>         from
> /usr/local/lib/site_ruby/1.8/rubygems/custom_require.rb:27:in
> >> `gem_original_require'
> >>         from
> /usr/local/lib/site_ruby/1.8/rubygems/custom_require.rb:27:in
> >> `require'
> >>         from script/server:3
> >>
> >
> >
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
>



-- 
---------------
Sincerely
George

Research Assistant
KEMRI-Wellcome Trust Program
Kilifi, Kenya

Skype: george_g2
Website: http://biorelated.wordpress.com/

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