[Bioperl-l] bioperl-db question

gang wu gwu at molbio.mgh.harvard.edu
Mon Nov 20 10:57:48 EST 2006


Hi Hilmar,

Thanks for your message. Below are several tests for Oracle and MySQL. 
MySQL actually also has two tests with failed items which may be related 
to data in BioSQL database.

Could it be my Oracle installation/configuration has some issues?

Thanks.

Gang


Output of 'make test' for Oracle
=======================================================
[root at elegans bioperl-db-1.5.2-RC3]# make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" 
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01dbadaptor.....ok 14/19Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939.
t/01dbadaptor.....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 15-19
        Failed 5/19 tests, 73.68% okay
t/02species.......ok 5/65Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939.
t/02species.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-65
        Failed 60/65 tests, 7.69% okay
t/03simpleseq.....ok 5/59Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 1.
t/03simpleseq.....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-59
        Failed 54/59 tests, 8.47% okay
t/04swiss.........ok 5/52Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 78.
t/04swiss.........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-52
        Failed 47/52 tests, 9.62% okay
t/05seqfeature....ok 3/48Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
t/05seqfeature....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 4-48
        Failed 45/48 tests, 6.25% okay
t/06comment.......ok 2/11Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
t/06comment.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-11
        Failed 9/11 tests, 18.18% okay
t/07dblink........ok 2/18Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
t/07dblink........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-18
        Failed 16/18 tests, 11.11% okay
t/08genbank.......ok 2/18Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
t/08genbank.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-18
        Failed 16/18 tests, 11.11% okay
t/09fuzzy2........ok 2/21Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 64.
t/09fuzzy2........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-21
        Failed 19/21 tests, 9.52% okay
t/10ensembl.......ok 2/15Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 1420.
t/10ensembl.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-15
        Failed 13/15 tests, 13.33% okay
t/11locuslink.....ok 4/110Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 1.
t/11locuslink.....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-110
        Failed 106/110 tests, 3.64% okay
t/12ontology......ok 4/738Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 98.
t/12ontology......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-738
        Failed 734/738 tests, 0.54% okay
t/13remove........ok 1/59Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 41.
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 41.
t/13remove........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-59
        Failed 58/59 tests, 1.69% okay
t/14query.........ok
t/15cluster.......ok 5/160Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 1.
t/15cluster.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-160
        Failed 155/160 tests, 3.12% okay
t/16obda..........ok 2/12Can't call method "bind_param" on an undefined 
value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
t/16obda..........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-12
        Failed 10/12 tests, 16.67% okay
Failed Test      Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/01dbadaptor.t   255 65280    19   10  52.63%  15-19
t/02species.t     255 65280    65  120 184.62%  6-65
t/03simpleseq.t   255 65280    59  108 183.05%  6-59
t/04swiss.t       255 65280    52   94 180.77%  6-52
t/05seqfeature.t  255 65280    48   90 187.50%  4-48
t/06comment.t     255 65280    11   18 163.64%  3-11
t/07dblink.t      255 65280    18   32 177.78%  3-18
t/08genbank.t     255 65280    18   32 177.78%  3-18
t/09fuzzy2.t      255 65280    21   38 180.95%  3-21
t/10ensembl.t     255 65280    15   26 173.33%  3-15
t/11locuslink.t   255 65280   110  212 192.73%  5-110
t/12ontology.t    255 65280   738 1468 198.92%  5-738
t/13remove.t      255 65280    59  116 196.61%  2-59
t/15cluster.t     255 65280   160  310 193.75%  6-160
t/16obda.t        255 65280    12   20 166.67%  3-12
Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% 
okay.
make: *** [test_dynamic] Error 255
=======================================================

Output of 'make test TEST_VERBOSE=1' for Oracle
=======================================================
[root at elegans bioperl-db-1.5.2-RC3]# make test TEST_VERBOSE=1
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" 
"test_harness(1, 'blib/lib', 'blib/arch')" t/*.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
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 15-19
        Failed 5/19 tests, 73.68% okay
t/02species.......1..65
ok 1
ok 2
ok 3
ok 4
ok 5
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-65
        Failed 60/65 tests, 7.69% okay
t/03simpleseq.....1..59
ok 1
ok 2
ok 3
ok 4
ok 5
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 1.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-59
        Failed 54/59 tests, 8.47% okay
t/04swiss.........1..52
ok 1
ok 2
ok 3
ok 4
ok 5
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 78.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-52
        Failed 47/52 tests, 9.62% okay
t/05seqfeature....1..48
ok 1
ok 2
ok 3
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 4-48
        Failed 45/48 tests, 6.25% okay
t/06comment.......1..11
ok 1
ok 2
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-11
        Failed 9/11 tests, 18.18% okay
t/07dblink........1..18
ok 1
ok 2
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-18
        Failed 16/18 tests, 11.11% okay
t/08genbank.......1..18
ok 1
ok 2
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-18
        Failed 16/18 tests, 11.11% okay
t/09fuzzy2........1..21 todo 17;
ok 1
ok 2
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 64.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-21
        Failed 19/21 tests, 9.52% okay
t/10ensembl.......1..15
ok 1
ok 2
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 1420.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-15
        Failed 13/15 tests, 13.33% okay
t/11locuslink.....1..110
ok 1
ok 2
ok 3
ok 4
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 1.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-110
        Failed 106/110 tests, 3.64% okay
t/12ontology......1..738
ok 1
ok 2
ok 3
ok 4
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 98.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-738
        Failed 734/738 tests, 0.54% okay
t/13remove........1..59
ok 1
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 41.
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 41.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-59
        Failed 58/59 tests, 1.69% okay
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
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 1.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-160
        Failed 155/160 tests, 3.12% okay
t/16obda..........1..12
ok 1
ok 2
Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939, <GEN0> line 72.
dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-12
        Failed 10/12 tests, 16.67% okay
Failed Test      Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/01dbadaptor.t   255 65280    19   10  52.63%  15-19
t/02species.t     255 65280    65  120 184.62%  6-65
t/03simpleseq.t   255 65280    59  108 183.05%  6-59
t/04swiss.t       255 65280    52   94 180.77%  6-52
t/05seqfeature.t  255 65280    48   90 187.50%  4-48
t/06comment.t     255 65280    11   18 163.64%  3-11
t/07dblink.t      255 65280    18   32 177.78%  3-18
t/08genbank.t     255 65280    18   32 177.78%  3-18
t/09fuzzy2.t      255 65280    21   38 180.95%  3-21
t/10ensembl.t     255 65280    15   26 173.33%  3-15
t/11locuslink.t   255 65280   110  212 192.73%  5-110
t/12ontology.t    255 65280   738 1468 198.92%  5-738
t/13remove.t      255 65280    59  116 196.61%  2-59
t/15cluster.t     255 65280   160  310 193.75%  6-160
t/16obda.t        255 65280    12   20 166.67%  3-12
Failed 15/16 test scripts, 6.25% okay. 1347/1423 subtests failed, 5.34% 
okay.
make: *** [test_dynamic] Error 255
=======================================================


Output of 'make test' for MySQL
===================================================
[root at elegans bioperl-db-1.5.2-RC3]# make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" 
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01dbadaptor.....ok
t/02species.......FAILED tests 11, 14-40, 49-119
        Failed 99/65 tests, -52.31% okay
t/03simpleseq.....ok
t/04swiss.........ok
t/05seqfeature....ok
t/06comment.......ok
t/07dblink........ok
t/08genbank.......ok
t/09fuzzy2........ok
t/10ensembl.......ok
t/11locuslink.....ok
t/12ontology......ok
t/13remove........ok
t/14query.........ok
t/15cluster.......ok 155/160
-------------------- WARNING ---------------------
MSG: failed to store one or more child objects for an instance of class 
Bio::Cluster::UniGene (PK=168)
---------------------------------------------------
t/15cluster.......ok
t/16obda..........ok
Failed Test   Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/02species.t               65  136 209.23%  11 14-40 49-119
Failed 1/16 test scripts, 93.75% okay. 28/1423 subtests failed, 98.03% okay.
make: *** [test_dynamic] Error 255
======================================================


Output of 'make test_02species TEST_VERBOSE=1' for MySQL
======================================================
[root at elegans bioperl-db-1.5.2-RC3]# make test_02species TEST_VERBOSE=1
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi 
-I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); 
$verbose=1; runtests @ARGV;' t/02species.t
t/02species....1..65
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
not ok 11
# Test 11 got: '29' (t/02species.t at line 45)
#    Expected: '11'
ok 12
ok 13
not ok 14
# Test 14 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 49 fail #3)
#    Expected: 'Hominidae'
not ok 15
# Test 15 got: 'Hominidae' (t/02species.t at line 49 fail #4)
#    Expected: 'Catarrhini'
not ok 16
# Test 16 got: 'Hominoidea' (t/02species.t at line 49 fail #5)
#    Expected: 'Primates'
not ok 17
# Test 17 got: 'Catarrhini' (t/02species.t at line 49 fail #6)
#    Expected: 'Eutheria'
not ok 18
# Test 18 got: 'Simiiformes' (t/02species.t at line 49 fail #7)
#    Expected: 'Mammalia'
not ok 19
# Test 19 got: 'Haplorrhini' (t/02species.t at line 49 fail #8)
#    Expected: 'Vertebrata'
not ok 20
# Test 20 got: 'Primates' (t/02species.t at line 49 fail #9)
#    Expected: 'Chordata'
not ok 21
# Test 21 got: 'Euarchontoglires' (t/02species.t at line 49 fail #10)
#    Expected: 'Metazoa'
not ok 22
# Test 22 got: 'Eutheria' (t/02species.t at line 49 fail #11)
#    Expected: 'Eukaryota'
not ok 23
# Failed test 23 in t/02species.t at line 49 fail #12
not ok 24
# Failed test 24 in t/02species.t at line 49 fail #13
not ok 25
# Failed test 25 in t/02species.t at line 49 fail #14
not ok 26
# Failed test 26 in t/02species.t at line 49 fail #15
not ok 27
# Failed test 27 in t/02species.t at line 49 fail #16
not ok 28
# Failed test 28 in t/02species.t at line 49 fail #17
not ok 29
# Failed test 29 in t/02species.t at line 49 fail #18
not ok 30
# Failed test 30 in t/02species.t at line 49 fail #19
not ok 31
# Failed test 31 in t/02species.t at line 49 fail #20
not ok 32
# Failed test 32 in t/02species.t at line 49 fail #21
not ok 33
# Failed test 33 in t/02species.t at line 49 fail #22
not ok 34
# Failed test 34 in t/02species.t at line 49 fail #23
not ok 35
# Failed test 35 in t/02species.t at line 49 fail #24
not ok 36
# Failed test 36 in t/02species.t at line 49 fail #25
not ok 37
# Failed test 37 in t/02species.t at line 49 fail #26
not ok 38
# Failed test 38 in t/02species.t at line 49 fail #27
not ok 39
# Failed test 39 in t/02species.t at line 49 fail #28
not ok 40
# Failed test 40 in t/02species.t at line 49 fail #29
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
not ok 49
# Test 49 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 63 fail #3)
#    Expected: 'Hominidae'
not ok 50
# Test 50 got: 'Hominidae' (t/02species.t at line 63 fail #4)
#    Expected: 'Catarrhini'
not ok 51
# Test 51 got: 'Hominoidea' (t/02species.t at line 63 fail #5)
#    Expected: 'Primates'
not ok 52
# Test 52 got: 'Catarrhini' (t/02species.t at line 63 fail #6)
#    Expected: 'Eutheria'
not ok 53
# Test 53 got: 'Simiiformes' (t/02species.t at line 63 fail #7)
#    Expected: 'Mammalia'
not ok 54
# Test 54 got: 'Haplorrhini' (t/02species.t at line 63 fail #8)
#    Expected: 'Vertebrata'
not ok 55
# Test 55 got: 'Primates' (t/02species.t at line 63 fail #9)
#    Expected: 'Chordata'
not ok 56
# Test 56 got: 'Euarchontoglires' (t/02species.t at line 63 fail #10)
#    Expected: 'Metazoa'
not ok 57
# Test 57 got: 'Eutheria' (t/02species.t at line 63 fail #11)
#    Expected: 'Eukaryota'
not ok 58
# Failed test 58 in t/02species.t at line 63 fail #12
not ok 59
# Failed test 59 in t/02species.t at line 63 fail #13
not ok 60
# Failed test 60 in t/02species.t at line 63 fail #14
not ok 61
# Failed test 61 in t/02species.t at line 63 fail #15
not ok 62
# Failed test 62 in t/02species.t at line 63 fail #16
not ok 63
# Failed test 63 in t/02species.t at line 63 fail #17
not ok 64
# Failed test 64 in t/02species.t at line 63 fail #18
not ok 65
# Failed test 65 in t/02species.t at line 63 fail #19
not ok 66
# Failed test 66 in t/02species.t at line 63 fail #20
not ok 67
# Failed test 67 in t/02species.t at line 63 fail #21
not ok 68
# Failed test 68 in t/02species.t at line 63 fail #22
not ok 69
# Failed test 69 in t/02species.t at line 63 fail #23
not ok 70
# Failed test 70 in t/02species.t at line 63 fail #24
not ok 71
# Failed test 71 in t/02species.t at line 63 fail #25
not ok 72
# Failed test 72 in t/02species.t at line 63 fail #26
not ok 73
# Failed test 73 in t/02species.t at line 63 fail #27
not ok 74
# Failed test 74 in t/02species.t at line 63 fail #28
not ok 75
# Failed test 75 in t/02species.t at line 63 fail #29
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
not ok 90
# Test 90 got: 'Homo/Pan/Gorilla group' (t/02species.t at line 91 fail #3)
#    Expected: 'Hominidae'
not ok 91
# Test 91 got: 'Hominidae' (t/02species.t at line 91 fail #4)
#    Expected: 'Catarrhini'
not ok 92
# Test 92 got: 'Hominoidea' (t/02species.t at line 91 fail #5)
#    Expected: 'Primates'
not ok 93
# Test 93 got: 'Catarrhini' (t/02species.t at line 91 fail #6)
#    Expected: 'Eutheria'
not ok 94
# Test 94 got: 'Simiiformes' (t/02species.t at line 91 fail #7)
#    Expected: 'Mammalia'
not ok 95
# Test 95 got: 'Haplorrhini' (t/02species.t at line 91 fail #8)
#    Expected: 'Vertebrata'
not ok 96
# Test 96 got: 'Primates' (t/02species.t at line 91 fail #9)
#    Expected: 'Chordata'
not ok 97
# Test 97 got: 'Euarchontoglires' (t/02species.t at line 91 fail #10)
#    Expected: 'Metazoa'
not ok 98
# Test 98 got: 'Eutheria' (t/02species.t at line 91 fail #11)
#    Expected: 'Eukaryota'
not ok 99
# Failed test 99 in t/02species.t at line 91 fail #12
not ok 100
# Failed test 100 in t/02species.t at line 91 fail #13
not ok 101
# Failed test 101 in t/02species.t at line 91 fail #14
not ok 102
# Failed test 102 in t/02species.t at line 91 fail #15
not ok 103
# Failed test 103 in t/02species.t at line 91 fail #16
not ok 104
# Failed test 104 in t/02species.t at line 91 fail #17
not ok 105
# Failed test 105 in t/02species.t at line 91 fail #18
not ok 106
# Failed test 106 in t/02species.t at line 91 fail #19
not ok 107
# Failed test 107 in t/02species.t at line 91 fail #20
not ok 108
# Failed test 108 in t/02species.t at line 91 fail #21
not ok 109
# Failed test 109 in t/02species.t at line 91 fail #22
not ok 110
# Failed test 110 in t/02species.t at line 91 fail #23
not ok 111
# Failed test 111 in t/02species.t at line 91 fail #24
not ok 112
# Failed test 112 in t/02species.t at line 91 fail #25
not ok 113
# Failed test 113 in t/02species.t at line 91 fail #26
not ok 114
# Failed test 114 in t/02species.t at line 91 fail #27
not ok 115
# Failed test 115 in t/02species.t at line 91 fail #28
not ok 116
# Failed test 116 in t/02species.t at line 91 fail #29
ok 117
ok 118
ok 119
FAILED tests 11, 14-40, 49-119
        Failed 99/65 tests, -52.31% okay
Failed Test   Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/02species.t               65  136 209.23%  11 14-40 49-119
Failed 1/1 test scripts, 0.00% okay. 28/65 subtests failed, 56.92% okay.
make: *** [test_02species] Error 255
=======================================================

Output of 'make test_15cluster TEST_VERBOSE=1' for MySQL
=======================================================
[root at elegans bioperl-db-1.5.2-RC3]# make test_15cluster TEST_VERBOSE=1
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi 
-I/usr/lib/perl5/5.8.5 -e 'use Test::Harness qw(&runtests $verbose); 
$verbose=1; runtests @ARGV;' t/15cluster.t
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

-------------------- WARNING ---------------------
MSG: failed to store one or more child objects for an instance of class 
Bio::Cluster::UniGene (PK=201)
---------------------------------------------------
ok 156
ok 157
ok 158
ok 159
ok 160
ok
All tests successful.
Files=1, Tests=160, 18 wallclock secs ( 4.39 cusr +  0.37 csys =  4.76 CPU)

=======================================================



Hilmar Lapp wrote:
> This is very odd. I would mean that preparing the statement failed, 
> i.e., that the generated SQL was not accepted by the server (or the 
> Oracle client library).
>
> Which test does this happen with?
>
> Could you run the test alone in which it happens with TEST_VERBOSE 
> turned on? E.g.,
>
>     $ make test_03simpleseq TEST_VERBOSE=1
>
> if it's the simpleseq test that's causing the failure. Capture the 
> output in a file and send it to me.
>
>     -hilmar
>
> On Nov 18, 2006, at 3:57 AM, gang wu wrote:
>
>> Hi everyone,
>>
>> I used to use MySQL to host the BioSQL schema and load Genbank into it
>> with the 'load_seqdatabase.pl' without problem(except extremely slow. It
>> took about 12 hours to load Arabidopsis thaliana). I just loaded the
>> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without
>> problem.
>>
>> When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with
>> MySQL while always saw an error with Oracle:
>>       Can't call method "bind_param" on an undefined value at
>> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
>>
>> line 939.
>>
>> , where the code is $sth->bind_param();
>>
>> Any idea what the problem is?
>>
>> Gang
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>



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