[BioRuby] Installing & testing BioRuby on Windows

[Naohisa Goto]

Hi Peter,

I think the failure may be due to the setting of permission for the file
or the folder.

Please look at the permisson for the file
C:\repositories\bioruby\Test\data\command\echoarg2.bat

By using explorer, right click the file and see "Property" -- "Security"
and see details. Please confirm if the ACL "Traverse Folder/Execute File"
is allowed and is not denyed.
http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/acl_special_permissions.mspx?mfr=true

The file permission can also be viewed by using cacls command 
on Windows.  Please show the output of the command.
C:\> cacls C:\repositories\bioruby\Test\data\command\echoarg2.bat

If the special ACL "FILE_EXECUTE" is shown as "DENY", its execution is
denyed and thus the tests failed.


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

> 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