[Bioperl-l] Error retrieving sequence from BioSQL

Seth Johnson johnson.biotech at gmail.com
Sat Sep 30 23:35:24 UTC 2006 

Here're complete test details:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(1,
'blib\lib', 'blib\arch')" t\01dbadaptor.t t\02species.t t\03simpleseq.t
t\04swiss.t t\05seqfeature.t t\06comment.t t\07dblink.t t\08genbank.t
t\09fuzzy2.t t\10ensembl.t t\11locuslink.t t\12ontology.t t\13remove.t
t\14query.t t\15cluster.t t\16obda.t
t\01dbadaptor.....1..19
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
t\02species.......1..65
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
not ok 63
# Test 63 got: <UNDEF> (t\02species.t at line 97)
#    Expected: '1'
ok 64
not ok 65
# Test 65 got: <UNDEF> (t\02species.t at line 101)
#    Expected: 'Bio::DB::Persistent::PersistentObject=HASH(0x1d9f77c)'
FAILED tests 63, 65
    Failed 2/65 tests, 96.92% okay
t\03simpleseq.....1..59
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
dubious
    Test returned status 1 (wstat 256, 0x100)
DIED. FAILED tests 7-59
    Failed 53/59 tests, 10.17% okay
t\04swiss.........1..52
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
not ok 25
# Test 25 got: '10097078' (t\04swiss.t at line 79)
#    Expected: '91309150'
ok 26
not ok 27
# Test 27 got: 'Jiang,J., Zhang,Y., Krainer,A.R. and Xu,R.M.' (t\04swiss.t
at line 85)
#    Expected: 'Krainer,A.R., Mayeda,A., Kozak,D. and Binns,G.'
not ok 28
# Test 28 got: 'Crystal structure of human p32, a doughnut-shaped acidic
mitochondrial matrix protein' (t\04swiss.t at line 86)
#    Expected: 'Functional expression of cloned human splicing factor SF2:
homology to RNA-binding proteins, U1 70K, and Drosophila splicing
regulators'
not ok 29
# Test 29 got: 'Proc. Natl. Acad. Sci. U.S.A. 96 (7), 3572-3577 (1999)'
(t\04swiss.t at line 87)
#    Expected: 'Cell 66 (2), 383-394 (1991)'
not ok 30
# Test 30 got: <UNDEF> (t\04swiss.t at line 88)
#    Expected: '91309150'
not ok 31
# Test 31 got: 'Krainer,A.R., Mayeda,A., Kozak,D. and Binns,G.' (t\04swiss.t
at line 85 fail #2)
#    Expected: 'Honore,B., Madsen,P., Rasmussen,H.H., Vandekerckhove,J.,
Celis,J.E. and Leffers,H.'
not ok 32
# Test 32 got: 'Functional expression of cloned human splicing factor SF2:
homology to RNA-binding proteins, U1 70K, and Drosophila splicing
regulators' (t\04swiss.t at line 86 fail #2)
#    Expected: 'Cloning and expression of a cDNA covering the complete
coding region of the P32 subunit of human pre-mRNA splicing factor SF2'
not ok 33
# Test 33 got: 'Cell 66 (2), 383-394 (1991)' (t\04swiss.t at line 87 fail
#2)
#    Expected: 'Gene 134 (2), 283-287 (1993)'
not ok 34
# Test 34 got: <UNDEF> (t\04swiss.t at line 88 fail #2)
#    Expected: '94085792'
ok 35
ok 36
ok 37
not ok 38
# Test 38 got: <UNDEF> (t\04swiss.t at line 88 fail #3)
#    Expected: '94253723'
not ok 39
# Test 39 got: 'Honore,B., Madsen,P., Rasmussen,H.H., Vandekerckhove,J.,
Celis,J.E. and Leffers,H.' (t\04swiss.t at line 85 fail #4)
#    Expected: 'Jiang,J., Zhang,Y., Krainer,A.R. and Xu,R.M.'
not ok 40
# Test 40 got: 'Cloning and expression of a cDNA covering the complete
coding region of the P32 subunit of human pre-mRNA splicing factor SF2'
(t\04swiss.t at line 86 fail #4)
#    Expected: 'Crystal structure of human p32, a doughnut-shaped acidic
mitochondrial matrix protein'
not ok 41
# Test 41 got: 'Gene 134 (2), 283-287 (1993)' (t\04swiss.t at line 87 fail
#4)
#    Expected: 'Proc. Natl. Acad. Sci. U.S.A. 96 (7), 3572-3577 (1999)'
not ok 42
# Test 42 got: <UNDEF> (t\04swiss.t at line 88 fail #4)
#    Expected: '99199225'
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
FAILED tests 25, 27-34, 38-42
    Failed 14/52 tests, 73.08% okay
t\05seqfeature....1..48
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok
t\06comment.......1..11
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok
t\07dblink........1..18
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t\08genbank.......1..18
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t\09fuzzy2........1..21 todo 17;
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
not ok 17
# Test 17 got: <UNDEF> (t\09fuzzy2.t at line 71 *TODO*)
#    Expected: 'Q9QYG8'
ok 18
ok 19
ok 20
ok 21
ok
t\10ensembl.......1..15
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
t\11locuslink.....1..110
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok
t\12ontology......1..738
ok 1
ok 2
not ok 3
# Failed test 3 in t\12ontology.t at line 29
dubious
    Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 3-738
    Failed 736/738 tests, 0.27% okay
t\13remove........1..59
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok
t\14query.........1..18
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t\15cluster.......1..160
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok
t\16obda..........1..12
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
FAILED tests 10-12
    Failed 3/12 tests, 75.00% okay
Failed Test     Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t\02species.t                 65    2   3.08%  63 65
t\03simpleseq.t    1   256    59  106 179.66%  7-59
t\04swiss.t                   52   14  26.92%  25 27-34 38-42
t\12ontology.t     2   512   738 1471 199.32%  3-738
t\16obda.t                    12    3  25.00%  10-12

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