[BioRuby] Installing & testing BioRuby on Windows

Mon Nov 7 13:48:48 UTC 2011

On Mon, Nov 7, 2011 at 11:38 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> 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:
>
> ...................E.EE................................................F......F.
> .......ignored attr: {}arrayType
> ................................................................................
> etc
> 3704 tests, 21435 assertions, 4 failures, 7 errors, 0 skips

Interestingly I gave Ruby the path name with Windows style slashes,
and the pattern is a little different,  3 failures, 8 errors. However, some
of these seem to be network related or stochastic, so a direct comparison
is not fair. On closer inspection it looks like the same problems.

We've got a couple of stochastic tests in Biopython and even after
relaxing the test criteria they still can fail every so often, which is
annoying.

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 214.230262s, 17.2898 tests/s, 99.9765 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) Error:
test_esearch(Bio::FuncTestPubmed):
Errno::ETIMEDOUT: A connection attempt failed because the connected party did no
t properly respond after a period of time, or established connection failed beca
use connected host has failed to respond. - connect(2)
    C:/repositories/bioruby/lib/bio/command.rb:649:in `start_http'
    C:/repositories/bioruby/lib/bio/command.rb:735:in `post_form'
    C:/repositories/bioruby/lib/bio/io/ncbirest.rb:131:in `ncbi_post_form'
    C:/repositories/bioruby/lib/bio/io/ncbirest.rb:268:in `block in esearch'
    C:/repositories/bioruby/lib/bio/io/ncbirest.rb:265:in `step'
    C:/repositories/bioruby/lib/bio/io/ncbirest.rb:265:in `esearch'
    C:/repositories/bioruby/lib/bio/io/pubmed.rb:96:in `esearch'
    C:/repositories/bioruby/test/functional/bio/io/test_pubmed.rb:26:in `test_es
earch'
    test/runner.rb:27:in `<main>'

  5) 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'

  6) 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'

  7) 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'

  8) 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\"">.

  9) 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\"">.

 10) Error:
test_simple_xml(Bio::TestPhyloXMLWriter):
Errno::EACCES: Permission denied - C:/Temp/PhyloXML20111107-3360-1ksuohs/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>'

 11) Failure:
test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandom
ize) [C:/repositories/bioruby/test/unit/bio/sequence/test_common.rb:286]:
test of chi2 < 21.666 failed (25.8).
Expected 21.666 to be > 25.8.

3704 tests, 21418 assertions, 3 failures, 8 errors, 0 skips