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fork() is called on platforms that do not support it #6

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agrimm opened this issue Apr 22, 2010 · 3 comments
Closed

fork() is called on platforms that do not support it #6

agrimm opened this issue Apr 22, 2010 · 3 comments

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@agrimm
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agrimm commented Apr 22, 2010

Because jruby is not recognised as being unable to support fork(), it (using master as of March 19 2010) produces the following error:

NotImplementedError: popen("-") is unimplemented

/Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/command.rb:245:in `call_command_fork'
/Users/agrimm/ruby/jruby/jruby-1.4.0/lib/ruby/gems/1.8/gems/bio-1.4.0.5000/lib/bio/command.rb:153: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'

When "|java" is added to the regular expression on line 150 in lib/bio/command.rb for non-fork supporting platforms, the error goes away. A similar error occurs with "Ruby Installer" for windows, which has an unrecognised platform of "i386-mingw32".
@ngoto
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ngoto commented Oct 6, 2010

I made a patch to solve the issue. It will soon be included in the main repository if no problems found.
http://github.com/ngoto/bioruby/commit/1344c27c90438d8c8840ee507d0ab43224f89054

@agrimm
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agrimm commented Oct 7, 2010

"It might mistake in minor platforms/architectures/interpreters." should have "It might make a mistake in ...".

I tried running with jruby the unit tests for a private project I'm working on. The tests had a lot of popen problems when it used a gem built from ngoto-master, and those problems were fixed by using a gem built from ngoto-incoming. So it looks like the changes work.

@ngoto
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ngoto commented Oct 8, 2010

Thank you. I close this issue.

http://github.com/bioruby/bioruby/commit/379f177edc0f95dee1ec0c2d2cf679c27918e41b

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@ngoto @agrimm