[Bioperl-guts-l] [Bug 2218] Change in PAML module

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Feb 22 15:46:32 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2218





------- Comment #5 from cjfields at uiuc.edu  2007-02-22 15:46 EST -------
Quick note: don't add text to patch files when creating an attachment; your
PAML patch had a comment in it.  Use the description box on the page instead.  
I also couldn't get the patch for Codeml.pm to work.

However, the PAML changes throw a lot of warnings and do not pass a significant
number of the core t/PAML.t tests.  I'm not sure about bioperl-run tests, but
we can't commit these without making sure those tests pass.  It would be nice
to also add additional tests demonstrating that using an array ref works.  

I'll note that whatever method you're using currently expects a single tree
which may explain the broken tests.  You could have it accept both a tree or an
array ref; this would prevent an API change in the method, which would possibly
confuse/anger/annoy PAML enthusiasts.

...
ok 80
No trees have been loaded, can't do anything
No trees have been loaded, can't do anything
No trees have been loaded, can't do anything
ok 81
...
ok 92
ok 93
not ok 94
# Test 94 got: <UNDEF> (t/PAML.t at line 229)
#    Expected: '4.54006'
not ok 95
# Test 95 got: <UNDEF> (t/PAML.t at line 230)
#    Expected: '-906.017440'
ok 96
ok 97
not ok 98
# Test 98 got: <UNDEF> (t/PAML.t at line 235)
#    Expected: 'alpha'
not ok 99
# Test 99 got: <UNDEF> (t/PAML.t at line 236)
#    Expected: '0.50000'
not ok 100
# Test 100 got: <UNDEF> (t/PAML.t at line 237)
#     Expected: '1.00000'
not ok 101
# Test 101 got: <UNDEF> (t/PAML.t at line 238)
#     Expected: '1.00000'
ok 102
ok 103
not ok 104
# Test 104 got: '0' (t/PAML.t at line 227 fail #2)
#     Expected: '2'
not ok 105
# Test 105 got: <UNDEF> (t/PAML.t at line 229 fail #2)
#     Expected: '4.29790'
not ok 106
# Test 106 got: <UNDEF> (t/PAML.t at line 230 fail #2)
#     Expected: '-902.503869'
ok 107
ok 108
ok 109
ok 110
not ok 111
# Test 111 got: '0' (t/PAML.t at line 227 fail #3)
#     Expected: '3'
not ok 112
# Test 112 got: <UNDEF> (t/PAML.t at line 229 fail #3)
#     Expected: '5.12250'
not ok 113
# Test 113 got: <UNDEF> (t/PAML.t at line 230 fail #3)
#     Expected: '-900.076500'
ok 114
ok 115
not ok 116
# Test 116 got: <UNDEF> (t/PAML.t at line 241)
#     Expected: '0.38160'
not ok 117
# Test 117 got: <UNDEF> (t/PAML.t at line 242)
#     Expected: '1.00000'
not ok 118
# Test 118 got: <UNDEF> (t/PAML.t at line 249)
#     Expected: '15'
not ok 119
# Test 119 got: <UNDEF> (t/PAML.t at line 250)
#     Expected: 'L'
not ok 120
# Test 120 got: <UNDEF> (t/PAML.t at line 251)
#     Expected: '0.6588'
ok 121
No trees have been loaded, can't do anything
No trees have been loaded, can't do anything
not ok 122
# Test 122 got: '0' (t/PAML.t at line 261)
#     Expected: '1'
not ok 123
# Test 123 got: <UNDEF> (t/PAML.t at line 263)
#     Expected: '1.00000'
not ok 124
# Test 124 got: <UNDEF> (t/PAML.t at line 264)
#     Expected: '0.09213'
ok 125
ok 126

...

ok 160
No trees have been loaded, can't do anything
ok 161


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