[Bioperl-l] Problems with bioperl-db
Alex Zelensky
Alex.Zelensky@anu.edu.au
Fri, 19 Oct 2001 18:41:23 +1000
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Hi,
I'm trying to compile bioperl-db package, and fail on most of the tests.
BioPerl version that I've got is 0.9.0 and I'm running it on MacOS X 10.0.
4.
MySQL server seems to be working OK.
I have edited the DBHarness.conf to reflect my local settings.
Can anybody please give me a hint on what am I doing wrong?
Thank you!
Here is what I get:
anz% make test
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
-I/System/Library/Perl/darwin -I/System/Library/Perl -e 'use Test::Harness
qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/comment...........ok
t/dbadaptor.........ok
t/dblink............ok
t/ePCRdb............ok 1/5Can't locate object method "new" via package "Bio:
:DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
t/ePCRdb............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-5
Failed 4/5 tests, 20.00% okay
t/ensembl...........ok 4/14--------------------
EXCEPTION --------------------
MSG: Could not find db for name genbank
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name blib/lib/Bio/DB/SQL/
BioDatabaseAdaptor.pm:121
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed blib/
lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
STACK toplevel t/ensembl.t:39
-------------------------------------------
t/ensembl...........dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-14
Failed 10/14 tests, 28.57% okay
t/map...............ok 1/15Can't locate object method "new" via package
"Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
t/map...............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-15
Failed 14/15 tests, 6.67% okay
t/marker............ok 1/34Can't locate object method "new" via package
"Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
t/marker............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-34
Failed 33/34 tests, 2.94% okay
t/seqfeature........ok 3/9Can't locate object method "is_remote" via
package "Bio::Location::Simple" at blib/lib/Bio/DB/SQL/SeqLocationAdaptor.
pm line 212.
t/seqfeature........dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 4-9
Failed 6/9 tests, 33.33% okay
t/seqfeaturekey.....ok
t/seqlocation.......ok 3/10Can't locate object method "is_remote" via
package "Bio::Location::Simple" at blib/lib/Bio/DB/SQL/SeqLocationAdaptor.
pm line 212.
t/seqlocation.......dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 4-10
Failed 7/10 tests, 30.00% okay
t/simpleseq.........ok 4/20--------------------
EXCEPTION --------------------
MSG: Could not find db for name genbank
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name blib/lib/Bio/DB/SQL/
BioDatabaseAdaptor.pm:121
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed blib/
lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
STACK toplevel t/simpleseq.t:40
-------------------------------------------
t/simpleseq.........dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-20
Failed 16/20 tests, 20.00% okay
t/species...........ok
t/swiss.............ok 4/16--------------------
EXCEPTION --------------------
MSG: Could not find db for name swissprot
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name blib/lib/Bio/DB/SQL/
BioDatabaseAdaptor.pm:121
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed blib/
lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
STACK toplevel t/swiss.t:38
-------------------------------------------
t/swiss.............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-16
Failed 12/16 tests, 25.00% okay
Failed Test Status Wstat Total Fail Failed List of failed
-------------------------------------------------------------------------------
t/ePCRdb.t 255 65280 5 4 80.00% 2-5
t/ensembl.t 255 65280 14 10 71.43% 5-14
t/map.t 255 65280 15 14 93.33% 2-15
t/marker.t 255 65280 34 33 97.06% 2-34
t/seqfeature.t 255 65280 9 6 66.67% 4-9
t/seqlocation.t 255 65280 10 7 70.00% 4-10
t/simpleseq.t 255 65280 20 16 80.00% 5-20
t/swiss.t 255 65280 16 12 75.00% 5-16
Failed 8/13 test scripts, 38.46% okay. 102/156 subtests failed, 34.62% okay.
make: *** [test_dynamic] Error 2
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Alex Zelensky,
Computational Molecular Biology & Drug Design Group
John Curtin School of Medical Research
PO Box 334, Canberra ACT 2601
Phone: +61-2-6125-8303
Fax: +61-2-6125-0415
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Hi,
I'm trying to compile bioperl-db package, and fail on most of the
tests. BioPerl version that I've got is 0.9.0 and I'm running it on
MacOS X 10.0.4.=20
MySQL server seems to be working OK.=20
I have edited the DBHarness.conf to reflect my local settings.
Can anybody please give me a hint on what am I doing wrong?
Thank you!
Here is what I get:
anz% make test=20
PERL_DL_NONLAZY=3D1 /usr/bin/perl -Iblib/arch -Iblib/lib
-I/System/Library/Perl/darwin -I/System/Library/Perl -e 'use
Test::Harness qw(&runtests $verbose); $verbose=3D0; runtests @ARGV;'
t/*.t
t/comment...........ok =
=20
t/dbadaptor.........ok =
=20
t/dblink............ok =
=20
t/ePCRdb............ok 1/5Can't locate object method "new" via package
"Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
t/ePCRdb............dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-5
Failed 4/5 tests, 20.00% okay
t/ensembl...........ok 4/14-------------------- EXCEPTION
--------------------
MSG: Could not find db for name genbank
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name
blib/lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:121
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed
blib/lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
STACK toplevel t/ensembl.t:39
-------------------------------------------
t/ensembl...........dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-14
Failed 10/14 tests, 28.57% okay
t/map...............ok 1/15Can't locate object method "new" via
package "Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
t/map...............dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-15
Failed 14/15 tests, 6.67% okay
t/marker............ok 1/34Can't locate object method "new" via
package "Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
t/marker............dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-34
Failed 33/34 tests, 2.94% okay
t/seqfeature........ok 3/9Can't locate object method "is_remote" via
package "Bio::Location::Simple" at
blib/lib/Bio/DB/SQL/SeqLocationAdaptor.pm line 212.
t/seqfeature........dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 4-9
Failed 6/9 tests, 33.33% okay
t/seqfeaturekey.....ok =
=20
t/seqlocation.......ok 3/10Can't locate object method "is_remote" via
package "Bio::Location::Simple" at
blib/lib/Bio/DB/SQL/SeqLocationAdaptor.pm line 212.
t/seqlocation.......dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 4-10
Failed 7/10 tests, 30.00% okay
t/simpleseq.........ok 4/20-------------------- EXCEPTION
--------------------
MSG: Could not find db for name genbank
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name
blib/lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:121
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed
blib/lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
STACK toplevel t/simpleseq.t:40
-------------------------------------------
t/simpleseq.........dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-20
Failed 16/20 tests, 20.00% okay
t/species...........ok =
=20
t/swiss.............ok 4/16-------------------- EXCEPTION
--------------------
MSG: Could not find db for name swissprot
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name
blib/lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:121
STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed
blib/lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
STACK toplevel t/swiss.t:38
-------------------------------------------
t/swiss.............dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-16
Failed 12/16 tests, 25.00% okay
Failed Test Status Wstat Total Fail Failed List of failed
=
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-----
t/ePCRdb.t 255 65280 5 4 80.00% 2-5
t/ensembl.t 255 65280 14 10 71.43% 5-14
t/map.t 255 65280 15 14 93.33% 2-15
t/marker.t 255 65280 34 33 97.06% 2-34
t/seqfeature.t 255 65280 9 6 66.67% 4-9
t/seqlocation.t 255 65280 10 7 70.00% 4-10
t/simpleseq.t 255 65280 20 16 80.00% 5-20
t/swiss.t 255 65280 16 12 75.00% 5-16
Failed 8/13 test scripts, 38.46% okay. 102/156 subtests failed, 34.62%
okay.
make: *** [test_dynamic] Error 2
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Alex Zelensky,
Computational Molecular Biology & Drug Design Group
John Curtin School of Medical Research
PO Box 334, Canberra ACT 2601
Phone: +61-2-6125-8303
Fax: +61-2-6125-0415
=
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