[BioRuby] Installing & testing BioRuby on Windows

[Peter Cock]

2011/11/23 Naohisa Goto <ngoto at gen-info.osaka-u.ac.jp>:
> Hi,
>
> I've fixed all of the test failures/errors which are reproduced on my
> Windows machines.
>
> Now 0 failures 0 errors, with latest git version, on Windows 7
> Enterprise 32-bit with Ruby 1.9.3-p0 (mingw32).

Great. I ran the tests again on my machine, using commit
d2d66f833d0b20647e8d761d2a240b99b206eaa8 and things
have improved a lot - I'm only seeing some kind of permissions
problem calling batch files now:

Note my machine is Windows XP (32 bit), whereas you have
Windows 7 Enterprise 32 bit. This may be important.

I have the same version of Ruby (I think):

C:\repositories\bioruby>ruby -v
ruby 1.9.3p0 (2011-10-30) [i386-mingw32]

C:\repositories\bioruby>ruby Test\runner.rb
C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will
 be deprecated in the future, use String#encode instead.
Run options:

# Running tests:

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Finished tests in 25.234052s, 144.8043 tests/s, 832.0503 assertions/s.

  1) Error:
test_call_command(Bio::FuncTestCommandCallMisc1):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:243:in `popen'
    C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen'
    C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call
_command'

  2) Error:
test_call_command_open3(Bio::FuncTestCommandCallMisc1):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call
_command_open3'
    Test/runner.rb:36:in `<main>'

  3) Error:
test_call_command_popen(Bio::FuncTestCommandCallMisc1):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:243:in `popen'
    C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call
_command_popen'

  4) Error:
test_call_command(Bio::FuncTestCommandCallSimple):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:243:in `popen'
    C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen'
    C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call
_command'

  5) Error:
test_call_command_open3(Bio::FuncTestCommandCallSimple):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call
_command_open3'
    Test/runner.rb:36:in `<main>'

  6) Error:
test_call_command_popen(Bio::FuncTestCommandCallSimple):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:243:in `popen'
    C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call
_command_popen'

  7) Error:
test_call_command(Bio::FuncTestCommandCallWithSpace):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:243:in `popen'
    C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen'
    C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call
_command'

  8) Error:
test_call_command_open3(Bio::FuncTestCommandCallWithSpace):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call
_command_open3'
    Test/runner.rb:36:in `<main>'

  9) Error:
test_call_command_popen(Bio::FuncTestCommandCallWithSpace):
Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech
oarg2.bat
    C:/repositories/bioruby/lib/bio/command.rb:243:in `popen'
    C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen'
    C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call
_command_popen'

3654 tests, 20996 assertions, 0 failures, 9 errors, 0 skips

C:\repositories\bioruby>

Thanks,

Peter