[BioRuby] Errors from ruby test/runner.rb

Mitsuteru Nakao n at bioruby.org
Wed Mar 28 10:45:50 UTC 2007


Hi Trevor,

I am going to check the unit tests for the next release.
Please check error message below and attached errors from
"% ruby -r lib/bio/util/restriction_enzyme/cut_symbol.rb test/runner.rb",
and make sure test/runner.rb (and/or ruby install.rb test)
to be "0 failures, 0 errors."


------ ruby test/runner.rb -------
% ruby test/runner.rb
./lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb:51:
uninitialized constant
Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation::CutSymbol
(NameError)
	from ./lib/bio/util/restriction_enzyme/single_strand.rb:14:in `require'
	from ./lib/bio/util/restriction_enzyme/single_strand.rb:14
	from ./lib/bio/util/restriction_enzyme/double_stranded.rb:19:in `require'
	from ./lib/bio/util/restriction_enzyme/double_stranded.rb:19
	from ./lib/bio/util/restriction_enzyme.rb:12:in `require'
	from ./lib/bio/util/restriction_enzyme.rb:12
	from ./lib/bio/util/restriction_enzyme/cut_symbol.rb:14
	from ./lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb:15:in
`require'
	 ... 25 levels...
	from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:198:in `[]'
	from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:198:in `run'
	from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run'
	from test/runner.rb:10



Best,
Mitsuteru
-
Mitsuteru Nakao Ph.D
n at bioruby.org

Kazusa DNA Research Institute
mn at kazusa.or.jp
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Loaded suite .
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Finished in 65.205477 seconds.

  1) Error:
test_dataset(Bio::TestSOFT):
Errno::ENOENT: No such file or directory - ../../../data/soft/GSE3457_family_partial.soft
    ./test/unit/bio/db/test_soft.rb:22:in `readlines'
    ./test/unit/bio/db/test_soft.rb:22:in `setup'

  2) Error:
test_series(Bio::TestSOFT):
Errno::ENOENT: No such file or directory - ../../../data/soft/GSE3457_family_partial.soft
    ./test/unit/bio/db/test_soft.rb:22:in `readlines'
    ./test/unit/bio/db/test_soft.rb:22:in `setup'

  3) Error:
test_argument_error(Bio::TestDoubleStrandedCutLocationPair):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup'

  4) Error:
test_complement(Bio::TestDoubleStrandedCutLocationPair):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup'

  5) Error:
test_contents(Bio::TestDoubleStrandedCutLocationPair):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup'

  6) Error:
test_primary(Bio::TestDoubleStrandedCutLocationPair):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup'

  7) Error:
test_argument_error(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup'

  8) Error:
test_complement(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup'

  9) Error:
test_contents(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup'

 10) Error:
test_primary(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup'

 11) Error:
test_complement(Bio::TestDoubleStrandedCutLocations):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup'

 12) Error:
test_contents(Bio::TestDoubleStrandedCutLocations):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup'

 13) Error:
test_primary(Bio::TestDoubleStrandedCutLocations):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup'

 14) Error:
test_complement(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

 15) Error:
test_complement_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

 16) Error:
test_complement_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

 17) Error:
test_contents(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

 18) Error:
test_primary(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

 19) Error:
test_primary_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

 20) Error:
test_primary_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

 21) Error:
test_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

 22) Error:
test_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation):
ArgumentError: Range is an invalid class type to initalize CutLocationPair.
    ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new'
    ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup'

1282 tests, 2443 assertions, 0 failures, 22 errors


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