[Bioperl-l] error running load_seqdatabase.pl
Chris Fields
cjfields at uiuc.edu
Fri Jan 6 12:20:07 EST 2006
Hilmar,
Did this ever get resolved? I tried to reinstall a biosql database using
bioperl-db and got the same problems. I'll list out everything I ran into
and what I pan on trying, as it's been a long time since I've tried this.
Currently, I'm using ActiveState Perl 5.8.7.813 on WinXP and MySQL 4.1.14.
Using nmake and installing worked fine. Loading the biosql schema and
loading taxonomy info also worked fine, although I had to manually untar the
taxonomy archive so load_ncbi_taxonomy.pl could find the files (stupid
windows). However, this is what happens when using load_seqdatabase.pl:
C:\Perl\Scripts>load_seqdatabase.pl -dbname dihydroorotase -dbuser root
NP_249092.gpt
Loading NP_249092.gpt ...
Undefined subroutine &Bio::Root::Root::debug called at
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1537, <GEN0>
line 65.
If I removed all args except the sequence file, it gives the same response,
which means it happens before the connection is made to the database:
C:\Perl\Scripts>load_seqdatabase.pl NP_249092.gpt
Loading NP_249092.gpt ...
Undefined subroutine &Bio::Root::Root::debug called at
C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1537, <GEN0>
line 65.
Going back through the test suite and setting up DBHarness.biosql.conf using
my loaded database gives a TON of errors, mostly warnings (which I'll show
in a second).
In the DBHarness.biosql.conf file, setting the database to 'biosql' w/o
giving a password gives the following summary:
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-160
Failed 158/160 tests, 1.25% okay
Failed Test Stat Wstat Total Fail Failed List of Failed
----------------------------------------------------------------------------
---
t\01dbadaptor.t 255 65280 19 30 157.89% 5-19 <------
t\02species.t 255 65280 65 126 193.85% 3-65
t\03simpleseq.t 255 65280 59 108 183.05% 6-59 <------
t\04swiss.t 255 65280 52 100 192.31% 3-52
t\05seqfeature.t 255 65280 48 92 191.67% 3-48
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 110 214 194.55% 4-110
t\12ontology.t 2 512 738 1471 199.32% 3-738
t\13remove.t 255 65280 59 116 196.61% 2-59
t\15cluster.t 255 65280 160 316 197.50% 3-160
Failed 14/15 test scripts, 6.67% okay. 1360/1411 subtests failed, 3.61%
okay.
NMAKE : U1077:
Stop.
___________________________________________________________________________
While setting the password (allowing the database to connect) gives:
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 65 126 193.85% 3-65
t\03simpleseq.t 255 65280 59 96 162.71% 12-59 <------
t\04swiss.t 255 65280 52 100 192.31% 3-52
t\05seqfeature.t 255 65280 48 92 191.67% 3-48
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 110 214 194.55% 4-110
t\12ontology.t 2 512 738 1471 199.32% 3-738
t\13remove.t 255 65280 59 116 196.61% 2-59
t\15cluster.t 255 65280 160 316 197.50% 3-160
Failed 14/15 test scripts, 6.67% okay. 1344/1411 subtests failed, 4.75%
okay.
NMAKE : U1077:
Stop.
___________________________________________________________________________
The arrows point to the difference in connectivity to the database. Angshu
had not set his password:
> :) I'm sorry again.
> After setting the DBHarness I get the following from nmake test:
>
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-160
> Failed 158/160 tests, 1.25% okay
> Failed Test Stat Wstat Total Fail Failed List of Failed
> -----------------------------------------------------------------------
> ------
> t\01dbadaptor.t 5 1280 19 30 157.89% 5-19 <------
> t\02species.t 255 65280 65 126 193.85% 3-65
> t\03simpleseq.t 5 1280 59 108 183.05% 6-59 <------
> t\04swiss.t 255 65280 52 100 192.31% 3-52
> t\05seqfeature.t 255 65280 48 92 191.67% 3-48
> 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 110 214 194.55% 4-110
> t\12ontology.t 9 2304 738 1470 199.19% 4-738
> t\13remove.t 255 65280 59 116 196.61% 2-59
> t\15cluster.t 255 65280 160 316 197.50% 3-160
> Failed 14/15 test scripts, 6.67% okay. 1359/1411 subtests failed,
> 3.69% okay.
Here's the error messages from that first test (warning it's very messy):
C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'bl
ib\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\01dbadaptor.....ok 1/19Subroutine new redefined at
C:\Perl\test\bioperl-db\bli
b\lib/Bio\DB\BioSQL\DBAdaptor.pm line 67.
Subroutine get_object_adaptor redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 112.
Subroutine _get_object_adaptor_class redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 154.
Subroutine set_object_adaptor redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 231.
Subroutine create_persistent redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 258.
Subroutine dbcontext redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 303.
Subroutine _load_object_adaptor redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 323.
Subroutine new redefined at C:\Perl\test\bioperl-db\blib\lib/Bio\BioEntry.pm
line 89.
Subroutine object_id redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\BioEntry.pm line 129.
Subroutine version redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\BioEntry.pm line 151.
Subroutine authority redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\BioEntry.pm line 172.
Subroutine namespace redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\BioEntry.pm line 193.
Subroutine display_name redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\BioEntry.pm line 218.
Subroutine description redefined at
C:\Perl\test\bioperl-db\blib\lib/Bio\BioEntry.pm line 242.
Subroutine new redefined at C:/Perl/site/lib/Bio\Root\Root.pm line 181.
Subroutine verbose redefined at C:/Perl/site/lib/Bio\Root\Root.pm line 214.
Subroutine _register_for_cleanup redefined at
C:/Perl/site/lib/Bio\Root\Root.pm line 226.
Subroutine _unregister_for_cleanup redefined at
C:/Perl/site/lib/Bio\Root\Root.pm line 236.
Subroutine _cleanup_methods redefined at C:/Perl/site/lib/Bio\Root\Root.pm
line 243.
"my" variable $class masks earlier declaration in same scope at
C:/Perl/site/lib/Bio\Root\Root.pm line 315.
Subroutine throw redefined at C:/Perl/site/lib/Bio\Root\Root.pm line 293.
Subroutine debug redefined at C:/Perl/site/lib/Bio\Root\Root.pm line 356.
Subroutine _load_module redefined at C:/Perl/site/lib/Bio\Root\Root.pm line
377.
Subroutine DESTROY redefined at C:/Perl/site/lib/Bio\Root\Root.pm line 405.
(in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at C:\Perl\test\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 177.
Undefined subroutine &Bio::Root::Root::debug called at
C:\Perl\test\bioperl-db\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
line 688.
(in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called.
(in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
during global destruction.
(in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at C:\Perl\test\bioperl-db\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
line 1860 during global destruction.
(in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
during global destruction.
(in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at C:\Perl\test\bioperl-db\blib\lib/Bio/DB/DBI/base.pm line 417 during
global destruction.
(in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
during global destruction.
(in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at C:\Perl\test\bioperl-db\blib\lib/Bio/DB/DBI/base.pm line 417 during
global destruction.
t\01dbadaptor.....dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 15-19
Failed 5/19 tests, 73.68% okay
____________________________________________________________________________
I'll end with that. At this moment, I can't see it working with the current
setup. I was using perl 5.8 with the old setup but I upgraded mysql at some
point when working with gbrowse (I can't remember what the old version was);
I'll try upgrading to the newest ActiveState version to see what happens.
Could it be the MySQL version?
Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign
More information about the Bioperl-l
mailing list