agrimm

Note: This is based on the following zombie-chaser commit:

commit 20173f84a936fb41109c765d8ea080fb0793b403
Author: Andrew Grimm <[email protected]>
Date: Sun Apr 4 17:34:52 2010 +1000

    Failed attempt at collision avoidance.

agrimm

Note: This is based on the following zombie-chaser commit:

commit 20173f84a936fb41109c765d8ea080fb0793b403
Author: Andrew Grimm <[email protected]>
Date: Sun Apr 4 17:34:52 2010 +1000

    Failed attempt at collision avoidance.

This was from continuously running two copies of test/integration.rb at the same time

agrimm

commit 2a1e2a6c7d2b7036a36c291cc220cbc486815aa8
Author: Andrew Grimm <[email protected]>
Date:   Sun Apr 11 19:19:27 2010 +1000

    Move library files and ui files into a lib subdirectory, and other changes to file loading.

Andrew-Grimms-MacBook-Pro:zombie-chaser agrimm$ jruby -Ilib -I../bioruby-blessed/lib/ bin/zombie-chaser --test ../bioruby-blessed/test/unit/bio/sequence/test_na.rb Bio::Sequence::NA
Gosu not installed. Please use the --console option, or install gosu
Loaded suite bin/zombie-chaser
Started

agrimm

Andrew-Grimms-MacBook-Pro:zombie-chaser agrimm$ jruby --1.9 -Ilib bin/zombie-chaser 
/Users/agrimm/ruby/zombie-chaser/lib/zombie-chaser/zombie_test_chaser.rb:3:in `require': no such file to load -- test/unit/collector/objectspace (LoadError)
	from /Users/agrimm/ruby/zombie-chaser/lib/zombie-chaser/zombie_test_chaser.rb:3
	from /Users/agrimm/ruby/zombie-chaser/lib/zombie-chaser/zombie_test_chaser.rb:3:in `require'
	from bin/zombie-chaser:3

agrimm

 55) Error:
TypeError: can't convert Array into String
    /Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/command.rb:188:in `call_command_popen'
    /Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/command.rb:147:in `call_command'
    /Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/appl/clustalw.rb:209:in `exec_local'
    /Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/appl/clustalw.rb:177:in `query_by_filename'
    /Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/appl/clustalw.rb:151:in `query_string'
    /Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/appl/clustalw.rb:127:in `query_align'
    /Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/appl/clustalw.rb:110:in `query'
    /Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/alignment.r

agrimm

# FIXME intended structure: 
# # A class that generates a variety of receivers, methods, parameters and blocks
# # A class representing a single action
# # Module for logging
# # A monkey-patched method that'd enable an object id and implementation-independent representation of an object

# FIXME make this configurable
srand(42)

# FIXME make a better way of creating random objects

agrimm

Andrew-Grimms-MacBook-Pro:github agrimm$ rvm use system
Now using system ruby.
Andrew-Grimms-MacBook-Pro:github agrimm$ ruby --version
ruby 1.8.7 (2009-06-12 patchlevel 174) [universal-darwin10.0]
Andrew-Grimms-MacBook-Pro:github agrimm$ irb
>> C = Class.new
=> C
>> C.freeze.clone.to_s # Fails
TypeError: can't modify frozen object
	from (irb):2:in `to_s'

agrimm

# This version was updated 2010-12-05 Sydney time
agrimm@agrimm-virtual-machine:~$ rvm --version

rvm 1.1.2 by Wayne E. Seguin ([email protected]) [http://rvm.beginrescueend.com/]

agrimm@agrimm-virtual-machine:~$ rvm list

rvm rubies

   ruby-1.9.2-head [ x86_64 ]

agrimm

agrimm@agrimm-virtual-machine:~/virtual/small_eigen_collider$ rvm install ruby-head-r29837 --patch refinements.diff
/home/agrimm/.rvm/rubies/ruby-head, this may take a while depending on your cpu(s)...

ruby-head - #fetching 
Updating ruby from http://svn.ruby-lang.org/repos/ruby/trunk
Checking out revision -r 29837 from http://svn.ruby-lang.org/repos/ruby/trunk
Copying from repo to src path...
Applying patch 'refinements.diff' (located at /home/agrimm/virtual/small_eigen_collider/refinements.diff)
Running autoconf
ruby-head - #configuring 

agrimm

agrimm@agrimm-virtual-machine:~/virtual/small_eigen_collider$ ruby --version
jruby 1.6.0.dev (ruby 1.8.7 patchlevel 249) (2010-12-10 fatal: unrecognized argument: --format=format:%h) (OpenJDK 64-Bit Server VM 1.6.0_18) [linux-amd64-java]
agrimm@agrimm-virtual-machine:~/virtual/small_eigen_collider$ irb
jruby-head > Dir.allocate.inspect
Java::JavaLang::NullPointerException: 
	from org.jruby.RubyDir.inspect(RubyDir.java:498)
	from org.jruby.RubyDir$i_method_0_0$RUBYINVOKER$inspect.call(org/jruby/RubyDir$i_method_0_0$RUBYINVOKER$inspect.gen:65535)
	from org.jruby.runtime.callsite.CachingCallSite.cacheAndCall(CachingCallSite.java:262)
	from org.jruby.runtime.callsite.CachingCallSite.call(CachingCallSite.java:105)
	from org.jruby.ast.CallNoArgNode.interpret(CallNoArgNode.java:61)