[Bioperl-l] Problems with bioperl-db
Alex Zelensky
alex_zelensky@mac.com
Sat, 20 Oct 2001 03:39:25 +1000
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Hi Elia,
Thanks a lot for a prompt reply and help.
I have just updated bioperl-db form cvs, and some problems are solved. I
don't get exceptions telling that genbank/swissprot database can't be found.
However, many tests still fail, complaining that method new/is_remote can'
t be found (see log at the bottom).
Is it possible that these problems arise because I have 0.9.0 release
installed instead of the most current one from CVS?
Thanks again!
Alex.
[alex-z:~/Documents/Download/bioperl-db] 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 1/3Can't locate object method "new" via package "Bio:
:DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 225.
t/ePCRdb............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-3
Failed 2/3 tests, 33.33% okay
t/ensembl...........ok 4/14Can't locate object method "is_remote" via
package "Bio::Location::Simple" at blib/lib/Bio/DB/SQL/SeqLocationAdaptor.
pm line 212, <GEN0> line 3931.
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 1/6Can't locate object method "new" via package "Bio:
:DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 225.
t/map...............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-6
Failed 5/6 tests, 16.67% okay
t/marker............ok 1/19Can't locate object method "new" via package
"Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 225.
t/marker............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-19
Failed 18/19 tests, 5.26% 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 4/20Can't locate object method "is_remote" via
package "Bio::Location::Simple" at blib/lib/Bio/DB/SQL/SeqLocationAdaptor.
pm line 212, <GEN0> line 72.
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 4/16Can't locate object method "is_remote" via
package "Bio::Location::Simple" at blib/lib/Bio/DB/SQL/SeqLocationAdaptor.
pm line 212, <GEN0> line 78.
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 3 2 66.67% 2-3
t/ensembl.t 255 65280 14 10 71.43% 5-14
t/map.t 255 65280 6 5 83.33% 2-6
t/marker.t 255 65280 19 18 94.74% 2-19
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. 76/130 subtests failed, 41.54% okay.
make: *** [test_dynamic] Error 2
On Friday, October 19, 2001, at 11:31 PM, Elia Stupka wrote:
> Hello Alex,
> cc:bioperl
>
> I have fixed all tests, you should update bioperl-db on the main trunk,
> and all should be well. We had to skip tests related to markers, because
> as Jason said the schema and object layer is in flux, so we are down to
> 130 tests, all pass. This marker problem does not affect at all however
> the sequence database in bioperl-db used to store genbank,EMBL,etc.
> records.
>
> Make sure that you not only have the DBHarness.conf file, but also a
> DBHarness.marker.conf file, which is the same, but just loading the marker
> schema instead of the seqdb schema.
>
> Let me know if everything looks ok on your side.
>
> Elia Stupka
>
> ******************************
> * http://www.ebi.ac.uk/~elia *
> * tel: +44 1223 49 44 31 *
> * mobile: +44 7971 59 03 69 *
> * fax: +44 1223 49 44 68 *
> ******************************
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
---------------------------------------------------------------------------
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 Elia,
Thanks a lot for a prompt reply and help.=20
I have just updated bioperl-db form cvs, and some problems are solved.
I don't get exceptions telling that genbank/swissprot database can't
be found. =20
However, many tests still fail, complaining that method new/is_remote
can't be found (see log at the bottom).=20
Is it possible that these problems arise because I have 0.9.0 release
installed instead of the most current one from CVS?=20
Thanks again!
Alex.=20
[alex-z:~/Documents/Download/bioperl-db] anz% make test
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 1/3Can't locate object method "new" via package
"Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 225.
t/ePCRdb............dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-3
Failed 2/3 tests, 33.33% okay
t/ensembl...........ok 4/14Can't locate object method "is_remote" via
package "Bio::Location::Simple" at
blib/lib/Bio/DB/SQL/SeqLocationAdaptor.pm line 212, <<GEN0> line 3931.
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 1/6Can't locate object method "new" via package
"Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 225.
t/map...............dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-6
Failed 5/6 tests, 16.67% okay
t/marker............ok 1/19Can't locate object method "new" via
package "Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 225.
t/marker............dubious =
=20
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-19
Failed 18/19 tests, 5.26% 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 4/20Can't locate object method "is_remote" via
package "Bio::Location::Simple" at
blib/lib/Bio/DB/SQL/SeqLocationAdaptor.pm line 212, <<GEN0> line 72.
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 4/16Can't locate object method "is_remote" via
package "Bio::Location::Simple" at
blib/lib/Bio/DB/SQL/SeqLocationAdaptor.pm line 212, <<GEN0> line 78.
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
=
--------------------------------------------------------------------------=
-----
t/ePCRdb.t 255 65280 3 2 66.67% 2-3
t/ensembl.t 255 65280 14 10 71.43% 5-14
t/map.t 255 65280 6 5 83.33% 2-6
t/marker.t 255 65280 19 18 94.74% 2-19
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. 76/130 subtests failed, 41.54%
okay.
make: *** [test_dynamic] Error 2
On Friday, October 19, 2001, at 11:31 PM, Elia Stupka wrote:
<excerpt>Hello Alex,
cc:bioperl
I have fixed all tests, you should update bioperl-db on the main trunk,
and all should be well. We had to skip tests related to markers,
because
as Jason said the schema and object layer is in flux, so we are down to
130 tests, all pass. This marker problem does not affect at all however
the sequence database in bioperl-db used to store genbank,EMBL,etc.
records.
Make sure that you not only have the DBHarness.conf file, but also a
DBHarness.marker.conf file, which is the same, but just loading the
marker
schema instead of the seqdb schema.
Let me know if everything looks ok on your side.
Elia Stupka
******************************
* http://www.ebi.ac.uk/~elia *
* tel: +44 1223 49 44 31 *
* mobile: +44 7971 59 03 69 *
* fax: +44 1223 49 44 68 *
******************************
_______________________________________________
Bioperl-l mailing list
Bioperl-l@bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-l
</excerpt>
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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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