[BioRuby] Installing & testing BioRuby on Windows

Mon Nov 7 11:38:28 UTC 2011

On Mon, Nov 7, 2011 at 11:26 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi all,
>
> Again I thought it would be useful to write down what I did to get
> BioRuby running on my Windows XP 32 bit machine (which will
> be a buildslave).
> ...
> After that there were 4 failures and 7 errors, which I will cover in the
> next email.

Full details at end of email, here is my attempt to summarise and guess
what is wrong:

Errors (1), (2) and (3) are permission failures in testing calling commands.
My guess is this is something about the batch file being used,

C:\repositories\bioruby>test/data/command/echoarg2.bat Hello
test: missing argument after `Hello'

C:\repositories\bioruby>test/data/command/echoarg2.bat Hello World
test: Hello: binary operator expected

Errors (4) and (5) may be transient network problems with efetch?

Errors (6), (7) and (8) are all from Bio::TestAbif about
NoMethodError: undefined method `match' for nil:NilClass

Errors (9) and (10) look like a path name escape test being too
strict and/or unaware of cross platform path separators.

Error (11) looks like it could be an error removing a file - note you
can't do this on Windows if there is an open handle to the file

If any of these are specific to my Windows setup, with some guidance we
can try to work out what is different.

Peter

---------------------------------------------------------

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 145.575330s, 25.4439 tests/s, 147.2434 assertions/s.

  1) Error:
test_call_command(Bio::FuncTestCommandCall):
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:40:in `test_call
_command'

  2) Error:
test_call_command_open3(Bio::FuncTestCommandCall):
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:71:in `test_call
_command_open3'
    test/runner.rb:27:in `<main>'

  3) Error:
test_call_command_popen(Bio::FuncTestCommandCall):
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:48:in `test_call
_command_popen'

  4) Failure:
test_efetch_multiple_xml(Bio::FuncTestPubmed) [C:/repositories/bioruby/test/func
tional/bio/io/test_pubmed.rb:108]:
Failed assertion, no message given.

  5) Failure:
test_efetch_multiple(Bio::FuncTestPubmedClassMethod) [C:/repositories/bioruby/te
st/functional/bio/io/test_pubmed.rb:91]:
<3> expected but was
<47>.

  6) Error:
test_complement(Bio::TestAbif):
NoMethodError: undefined method `match' for nil:NilClass
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e
ntry_data'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block
in get_directory_entries'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times'

    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di
rectory_entries'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia
lize'
    C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42
:in `new'
    C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42
:in `setup'

  7) Error:
test_seq(Bio::TestAbif):
NoMethodError: undefined method `match' for nil:NilClass
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e
ntry_data'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block
in get_directory_entries'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times'

    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di
rectory_entries'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia
lize'
    C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42
:in `new'
    C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42
:in `setup'

  8) Error:
test_to_biosequence(Bio::TestAbif):
NoMethodError: undefined method `match' for nil:NilClass
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e
ntry_data'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block
in get_directory_entries'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times'

    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di
rectory_entries'
    C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia
lize'
    C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42
:in `new'
    C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42
:in `setup'

  9) Failure:
test_escape_shell(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/test_
command.rb:59]:
<"bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was
<"\"bio'\"\"r u\"\"b\\y123 at 456:789\"">.

 10) Failure:
test_make_command_line(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/
test_command.rb:76]:
<"ruby test.rb atgcatgc bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was
<"ruby test.rb atgcatgc \"bio'\"\"r u\"\"b\\y123 at 456:789\"">.

 11) Error:
test_simple_xml(Bio::TestPhyloXMLWriter):
Errno::EACCES: Permission denied - C:/Temp/PhyloXML20111107-1116-m0djng/example_
tree1.xml
    C:/repositories/bioruby/lib/bio/command.rb:479:in `remove_entry_secure'
    C:/repositories/bioruby/lib/bio/command.rb:569:in `block in callback'
    C:/repositories/bioruby/lib/bio/command.rb:607:in `call'
    C:/repositories/bioruby/lib/bio/command.rb:607:in `close!'
    C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:77:in `test
_passed'
    C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:105:in `tea
rdown'
    test/runner.rb:27:in `<main>'

3704 tests, 21435 assertions, 4 failures, 7 errors, 0 skips