Forum: JRuby jrubyc problem

Hallo,
I installed Bioruby with

jruby setup.rb.

then I run this script with jruby
--------------
#!/usr/bin/env jruby

require 'bio'

# creating a Bio::Sequence::NA object containing ambiguous alphabets
ambiguous_seq = Bio::Sequence::NA.new("atgcyrwskmbdhvn")

# show the contents and class of the DNA sequence object
p ambiguous_seq              # => "atgcyrwskmbdhvn"
p ambiguous_seq.class        # => Bio::Sequence::NA

# convert the sequence to a Regexp object
p ambiguous_seq.to_re        # =>
/atgc[tc][ag][at][gc][tg][ac][tgc][atg][atc][agc][atgc]/
p ambiguous_seq.to_re.class  # => Regexp

# example to match an ambiguous sequence to the rigid sequence
att_or_atc = Bio::Sequence::NA.new("aty").to_re
puts "match" if att_or_atc.match(Bio::Sequence::NA.new("att"))
if Bio::Sequence::NA.new("atc") =~ att_or_atc
 puts "also match"
end
--------------

without any problems.

After this I run it with Java and I have got following problem:

jrubyc s01.rb an then java -cp /home/mitlox/jruby-1.4.0/lib/jruby.jar:.
s01
Exception in thread "main" s01.rb:3:in `require': no such file to load
-- bio (LoadError)
       from s01.rb:3
       ...internal jruby stack elided...
       from Kernel.require(s01.rb:3)
       from (unknown).(unknown)(:1)

What did I wrong?

Best regards,

On Fri, Feb 5, 2010 at 23:55, Fla As <lists@ruby-forum.com> wrote:
>
> p ambiguous_seq.to_re.class  # => Regexp
>
>
>
>
>

I've just installed bioruby as gem and it works adding require
'rubygems' at top. Both, plain .rb and compiled to .class

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gem compiles Bioruby to class if yes how can I get a jar file of 
Bioruby?



Jesús García Sáez wrote:
> On Fri, Feb 5, 2010 at 23:55, Fla As <lists@ruby-forum.com> wrote:
>>
>> p ambiguous_seq.to_re.class �# => Regexp
>>
>>
>>
>>
>>
> 
> I've just installed bioruby as gem and it works adding require
> 'rubygems' at top. Both, plain .rb and compiled to .class
> 
> ---------------------------------------------------------------------
> To unsubscribe from this list, please visit:
> 
>     http://xircles.codehaus.org/manage_email

Do:

jar -cf bioruby.jar bioruby.class

Then you can include bioruby.jar (which holds any other classes as
well) in your jruby project

To update the jar file

jar -uf bioruby.jar bioruby.class otherthings.class ..


On Tue, Feb 9, 2010 at 1:31 PM, Fla As <lists@ruby-forum.com> wrote:
>>>
>>     http://xircles.codehaus.org/manage_email
>
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I did:
gem install bio
but in /jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0/lib/bio/ are only 
rb files and not class files.

Where can I find bioruby.class and does this class file contain the 
complete bioruby?

Maarten Mortier wrote:
> Do:
> 
> jar -cf bioruby.jar bioruby.class
> 
> Then you can include bioruby.jar (which holds any other classes as
> well) in your jruby project
> 
> To update the jar file
> 
> jar -uf bioruby.jar bioruby.class otherthings.class ..

On Mon, Mar 1, 2010 at 6:55 AM, Fla As <lists@ruby-forum.com> wrote:
> I did:
> gem install bio
> but in /jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0/lib/bio/ are only
> rb files and not class files.
>
> Where can I find bioruby.class and does this class file contain the
> complete bioruby?

Do you need it in .class form? Generally Ruby applications ship in 
source form.

Perhaps you can tell us what you're trying to accomplish?

- Charlie

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Maybe class files could be faster than rb files and therefore I have 
tried to use class files.

Charles Nutter wrote:
> On Mon, Mar 1, 2010 at 6:55 AM, Fla As <lists@ruby-forum.com> wrote:

> 
> Perhaps you can tell us what you're trying to accomplish?
> 
> - Charlie

In JRuby, whether you run from .class files or .rb files, your
application code will eventually run as JVM bytecode. There's no need
to compile to .class files to get better performance from JRuby.

On Wed, Mar 3, 2010 at 6:40 AM, Fla As <lists@ruby-forum.com> wrote:
> Maybe class files could be faster than rb files and therefore I have
> tried to use class files.

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