gistfile1.txt

###################
# One kind of error
###################

192-168-1-2:alignment_threading_replication agrimm$ rake
(in /Users/agrimm/ruby/alignment_threading_replication)
Loaded suite test/test_multithreaded_alignment
Started


ERROR: Multiple sequences found with same name (found 0 at least twice)!

F.
Finished in 9.235455 seconds.

  1) Failure:
test_alignment_works_in_multiple_threads(TestAlignment) [test/test_multithreaded_alignment.rb:34]:
Can't handle multiple threaded scenario.
Exception raised:
Class: <NoMethodError>
Message: <"undefined method `close' for nil:NilClass">
---Backtrace---
/Library/Ruby/Gems/1.8/gems/bio-1.4.0/lib/bio/appl/clustalw.rb:149:in `query_string'
test/test_multithreaded_alignment.rb:50:in `join'
test/test_multithreaded_alignment.rb:50:in `test_alignment_works_in_multiple_threads'
test/test_multithreaded_alignment.rb:50:in `each'
test/test_multithreaded_alignment.rb:50:in `test_alignment_works_in_multiple_threads'
test/test_multithreaded_alignment.rb:34:in `test_alignment_works_in_multiple_threads'
---------------

2 tests, 2 assertions, 1 failures, 0 errors
rake aborted!
Command failed with status (1): [/System/Library/Frameworks/Ruby.framework/...]
/Users/agrimm/ruby/alignment_threading_replication/rakefile:4
(See full trace by running task with --trace)
192-168-1-2:alignment_threading_replication agrimm$ rake
(in /Users/agrimm/ruby/alignment_threading_replication)
Loaded suite test/test_multithreaded_alignment
Started


ERROR: Multiple sequences found with same name (found 0 at least twice)!



ERROR: Multiple sequences found with same name (found 0 at least twice)!



ERROR: Multiple sequences found with same name (found 0 at least twice)!



ERROR: Multiple sequences found with same name (found 0 at least twice)!



ERROR: Multiple sequences found with same name (found 0 at least twice)!



ERROR: Multiple sequences found with same name (found 0 at least twice)!

F.
Finished in 9.982433 seconds.

  1) Failure:
test_alignment_works_in_multiple_threads(TestAlignment) [test/test_multithreaded_alignment.rb:34]:
Can't handle multiple threaded scenario.
Exception raised:
Class: <Errno::ENOENT>
Message: <"No such file or directory - /var/folders/SZ/SZere5L+EMORF-dGje2dyU+++TI/-Tmp-/clustalout20100126-4542-1bv4po0-0">
---Backtrace---
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/tempfile.rb:170:in `unlink'
test/test_multithreaded_alignment.rb:50:in `join'
test/test_multithreaded_alignment.rb:50:in `test_alignment_works_in_multiple_threads'
test/test_multithreaded_alignment.rb:50:in `each'
test/test_multithreaded_alignment.rb:50:in `test_alignment_works_in_multiple_threads'
test/test_multithreaded_alignment.rb:34:in `test_alignment_works_in_multiple_threads'
---------------

2 tests, 2 assertions, 1 failures, 0 errors
rake aborted!
Command failed with status (1): [/System/Library/Frameworks/Ruby.framework/...]
/Users/agrimm/ruby/alignment_threading_replication/rakefile:4
(See full trace by running task with --trace)

#######################
# Another kind of error
#######################

192-168-1-2:alignment_threading_replication agrimm$ rake
(in /Users/agrimm/ruby/alignment_threading_replication)
Loaded suite test/test_multithreaded_alignment
Started
F.
Finished in 9.401497 seconds.

  1) Failure:
test_alignment_works_in_multiple_threads(TestAlignment) [test/test_multithreaded_alignment.rb:34]:
Can't handle multiple threaded scenario.
Exception raised:
Class: <Errno::ENOENT>
Message: <"No such file or directory - /var/folders/SZ/SZere5L+EMORF-dGje2dyU+++TI/-Tmp-/clustalout20100126-16158-18o4hcl-0.lock">
---Backtrace---
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/tempfile.rb:72:in `rmdir'
test/test_multithreaded_alignment.rb:50:in `join'
test/test_multithreaded_alignment.rb:50:in `test_alignment_works_in_multiple_threads'
test/test_multithreaded_alignment.rb:50:in `each'
test/test_multithreaded_alignment.rb:50:in `test_alignment_works_in_multiple_threads'
test/test_multithreaded_alignment.rb:34:in `test_alignment_works_in_multiple_threads'
---------------

2 tests, 2 assertions, 1 failures, 0 errors
rake aborted!
Command failed with status (1): [/System/Library/Frameworks/Ruby.framework/...]
/Users/agrimm/ruby/alignment_threading_replication/rakefile:4
(See full trace by running task with --trace)