Frequently Asked Questions

Problems with Ruby

RubyInline

Several people have reported problems with Ruby's requirement on RubyInline.

Biopieces uses an external gem (or module) called RubyInline to allow embedded C code that speed certain things up dramatically, so RubyInline is great.

RubyInline should not be confused with the inline gem which is an entirely different gem that for stupid reasons have been allowed on RubyForge even if RubyInline has been invoked by require inline years before the confusing inline gem.

If running bp_test suggests that RubyInline is not installed, you should install it using the command:

sudo gem install RubyInline

Now, if you get the following error:

sudo gem install RubyInline
ERROR:  Error installing RubyInline:
    ZenTest requires RubyGems version ~> 1.8. Try 'gem update --system' to update

This indicates that your version of gem is too old. This has been observed on Debian, and Ubuntu.

One solution is to download, compile, and install your own version of Ruby along with the required gems gnuplot, narray, and RubyInline. This is exactly what the ruby_installer.sh script in the download section does.

Comment by project member martinah...@gmail.com, Mar 2, 2012

I am positively pissed about the state of Ruby in Ubuntu. Unless you have applications requiring the system's Ruby I suggest that you remove everything and download, compile and install Ruby from scratch:

cd /usr/local/src
sudo wget http://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.3-p125.tar.gz
sudo tar -zxvf ruby-1.9.3-p125.tar.gz
cd ruby-1.9.3-p125
sudo ./configure
sudo ./make
sudo ./make install
sudo gem install gnuplot
sudo gem install narray
sudo gem install RubyInline

END-OF-STORY!

Comment by project member martinah...@gmail.com, Apr 24, 2012

Remember that gem 1.8 has nothing to do with ruby 1.8 - it is a coincidence that the version numbers are the same.

► Sign in to add a comment