[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
-------------- next part --------------
Loaded suite .
Started
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................EE.............................................................................................................................................................................................................................................................................................................................................................................................................................................EEEEEEEEEEEEEEEEEEEE.....
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
More information about the BioRuby
mailing list