[Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
Hilmar Lapp
hlapp at gnf.org
Wed Oct 8 20:00:41 EDT 2003
This is definitely related to the perl setup I'd claim. Have you been able
to run the bioperl test suite without similar trouble?
Again, I'm cc'ing the bioperl list in case anybody has seen this also and
has clues as to what the cause is and how to remedy it.
-hilmar
On 10/8/03 3:18 PM, "Robert Roth" <robert.roth at home.se> wrote:
> Hi,
>
> I've tried to run the test suite and most tests failed with outputs like the
> one below. Only the
> test_dbadaptor was succesful and but also there a lot of comments about
> redefined subroutines like the ones below were generated.
> I will reinstall everything tomorrow to see if that helps.
>
> /Robert
>
> E:\temp\bioperl-db>e:\Perl\bin\perl.exe -Iblib\arch -Ilib\lib -IE:\perl\lib
> -IE:
> Perl\lib -e "use Test::Harness qw(&runtests $verbose); $verbose=0; runtests
> @ARG
> V;" t/comment.t
> t/comment...........ok 2/11Subroutine new redefined at
> e:/Perl/site/lib/Bio\Seq\
> RichSeq.pm line 112, <GEN0> line 72.
> Subroutine division redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 172, <
> GEN0> line 72.
> Subroutine molecule redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 193, <
> GEN0> line 72.
> Subroutine add_date redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 215, <
> GEN0> line 72.
> Subroutine get_dates redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 234,
> <GEN0> line 72.
> Subroutine pid redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line 253,
> <GEN0>
> line 72.
> Subroutine accession redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 279,
> <GEN0> line 72.
> Subroutine add_secondary_accession redefined at
> e:/Perl/site/lib/Bio\Seq\RichSeq
> .pm line 296, <GEN0> line 72.
> Subroutine get_secondary_accessions redefined at
> e:/Perl/site/lib/Bio\Seq\RichSe
> q.pm line 315, <GEN0> line 72.
> Subroutine seq_version redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 332
> , <GEN0> line 72.
> Subroutine keywords redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 353, <
> GEN0> line 72.
> Subroutine each_date redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 369,
> <GEN0> line 72.
> Subroutine each_secondary_accession redefined at
> e:/Perl/site/lib/Bio\Seq\RichSe
> q.pm line 376, <GEN0> line 72.
> Subroutine sv redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line 383,
> <GEN0>
> line 72.
> Subroutine new redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm line
> 146,
> <GEN0> line 72.
> Subroutine set_attributes redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 188, <GEN0> line 72.
> Subroutine direct_new redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 253, <GEN0> line 72.
> Subroutine location redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line
> 274, <GEN0> line 72.
> Subroutine start redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 30
> 4, <GEN0> line 72.
> Subroutine end redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm line
> 321,
> <GEN0> line 72.
> Subroutine length redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 3
> 38, <GEN0> line 72.
> Subroutine strand redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 3
> 55, <GEN0> line 72.
> Subroutine score redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 37
> 2, <GEN0> line 72.
> Subroutine frame redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 39
> 7, <GEN0> line 72.
> Subroutine primary_tag redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm l
> ine 423, <GEN0> line 72.
> Subroutine source_tag redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 444, <GEN0> line 72.
> Subroutine has_tag redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line
> 465, <GEN0> line 72.
> Subroutine add_tag_value redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 480, <GEN0> line 72.
> Subroutine get_tag_values redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 499, <GEN0> line 72.
> Subroutine get_all_tags redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 521, <GEN0> line 72.
> Subroutine remove_tag redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 537, <GEN0> line 72.
> Subroutine attach_seq redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 562, <GEN0> line 72.
> Subroutine seq redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm line
> 592,
> <GEN0> line 72.
> Subroutine entire_seq redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 633, <GEN0> line 72.
> Subroutine seq_id redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 6
> 58, <GEN0> line 72.
> Subroutine display_name redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 677, <GEN0> line 72.
> Subroutine annotation redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 702, <GEN0> line 72.
> Subroutine get_SeqFeatures redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.
> pm line 733, <GEN0> line 72.
> Subroutine add_SeqFeature redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 763, <GEN0> line 72.
> Subroutine remove_SeqFeatures redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Gener
> ic.pm line 800, <GEN0> line 72.
> Subroutine gff_format redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 832, <GEN0> line 72.
> Subroutine gff_string redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 862, <GEN0> line 72.
> Subroutine slurp_gff_file redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 885, <GEN0> line 72.
> Subroutine _from_gff_string redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic
> .pm line 921, <GEN0> line 72.
> Subroutine _expand_region redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 943, <GEN0> line 72.
> Subroutine _parse redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 9
> 73, <GEN0> line 72.
> Subroutine _tag_value redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 991, <GEN0> line 72.
> Subroutine seqname redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line
> 1006, <GEN0> line 72.
> Subroutine display_id redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 1012, <GEN0> line 72.
> Subroutine each_tag_value redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 1019, <GEN0> line 72.
> Subroutine all_tags redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line
> 1020, <GEN0> line 72.
> Subroutine sub_SeqFeature redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 1024, <GEN0> line 72.
> Subroutine add_sub_SeqFeature redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Gener
> ic.pm line 1025, <GEN0> line 72.
> Subroutine flush_sub_SeqFeatures redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Ge
> neric.pm line 1026, <GEN0> line 72.
> Subroutine flush_sub_SeqFeature redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Gen
> eric.pm line 1028, <GEN0> line 72.
> Subroutine new redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 195,
> <GEN0> l
> ine 72.
> Subroutine verbose redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 228,
> <GEN
> 0> line 72.
> Subroutine _register_for_cleanup redefined at
> e:/Perl/site/lib/Bio\Root\Root.pm
> line 240, <GEN0> line 72.
> Subroutine _unregister_for_cleanup redefined at
> e:/Perl/site/lib/Bio\Root\Root.p
> m line 250, <GEN0> line 72.
> Subroutine _cleanup_methods redefined at e:/Perl/site/lib/Bio\Root\Root.pm
> line
> 257, <GEN0> line 72.
> Subroutine throw redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 307,
> <GEN0>
> line 72.
> Subroutine debug redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 370,
> <GEN0>
> line 72.
> Subroutine _load_module redefined at e:/Perl/site/lib/Bio\Root\Root.pm line
> 390,
> <GEN0> line 72.
> Subroutine DESTROY redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 416,
> <GEN
> 0> line 72.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at e:
> /Perl/site/lib/Bio\DB\BioSQL\DBAdaptor.pm line 173, <GEN0> line 72.
> Undefined subroutine &Bio::Root::Root::debug called at
> e:/Perl/site/lib/Bio/DB/B
> ioSQL/BasePersistenceAdaptor.pm line 689, <GEN0> line 72.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at e:
> /Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1756 during
> global d
> estruction.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> durin
> g global destruction.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at e:
> /Perl/site/lib/Bio/DB/DBI/base.pm line 411 during global destruction.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> durin
> g global destruction.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> durin
> g global destruction.
> t/comment...........dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-11
> Failed 9/11 tests, 18.18% okay
> Failed Test Status Wstat Total Fail Failed List of Failed
> ----------------------------------------------------------------------------
> ----
>
> t/comment.t 255 65280 11 9 81.82% 3-11
> Failed 1/1 test scripts, 0.00% okay. 9/11 subtests failed, 18.18% okay.
>
> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gnf.org]
> Sent: 08 October 2003 20:54
> To: Robert Roth; OBDA BioSQL
> Cc: BioPerl
> Subject: Re: [BioSQL-l] Error using load_seqdatabase.pl
>
>
> This has nothing to do with the input file but everything with run-time
> loading of modules in perl on Windows. The error you get is generated by the
> following line of code:
>
> $self->debug("attempting to load driver for adaptor class $class\n");
>
> The class Bio::DB::BioSQL::BasePersistenceAdaptor.pm has a 'use
> Bio::Root::Root' statement, it inherits directly from Bio::Root::Root, and
> Bio::Root::Root does have a debug() method as you can (and should) easily
> convince yourself of.
>
> Have you run the bioperl-db test suite? If so, what was the result? If not,
> run it.
>
> So, I'm copying the bioperl list here in case somebody has more clues as to
> why you might be seeing this error on WinXP. We've had a case before on the
> list where it turned out eventually that there had been a version mix-up on
> the machine and everything worked fine after re-installing from scratch.
>
> -hilmar
>
> On 10/8/03 4:24 AM, "Robert Roth" <robert.roth at home.se> wrote:
>
>>
>> Hello,
>>
>> I'm using Mysql 4.0.15, Bioperl 1.2.3, bioperl-db from the cvs and perl
>> 5.6.1 on WinXP.
>> After installation I pre-loaded the the biosql database with the NCBI
> taxon
>> database using
>> load_ncbi_taxonomy.pl. Now when I try to load sequence data with
>> load_seqdatabase.pl I get
>> the following error,
>>
>> perl load_seqdatabase.pl --host localhost --dbname biosql --dbus
>> er root --namespace bioperl --debug --safe --testonly --format
>> genbank test.genbank
>> Loading test.genbank ...
>> attempting to load adaptor class for Bio::Seq::RichSeq
>> attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
>> attempting to load adaptor class for Bio::Seq
>> attempting to load module Bio::DB::BioSQL::SeqAdaptor
>> instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
>> attempting to load adaptor class for Bio::SeqFeature::Generic
>> attempting to load module Bio::DB::BioSQL::GenericAdaptor
>> attempting to load adaptor class for Bio::Root::Root
>> attempting to load module Bio::DB::BioSQL::RootAdaptor
>> Undefined subroutine &Bio::Root::Root::debug called at
>> E:/Perl/site/lib/Bio/DB/B
>> ioSQL/BasePersistenceAdaptor.pm line 1502, <GEN0> line 41.
>>
>> I've tried different formats (swiss and genbank) and different files with
>> the same
>> result. The line number given in the error always correspond to the end of
>> the first
>> record (and it doesn't matter if the file contains one or more records).
>> Any ideas?
>>
>> Many thanks in advance,
>>
>> Robert
>>
>>
>> _______________________________________________
>> BioSQL-l mailing list
>> BioSQL-l at open-bio.org
>> http://open-bio.org/mailman/listinfo/biosql-l
>>
>
> --
> -------------------------------------------------------------
> Hilmar Lapp email: lapp at gnf.org
> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>
>
>
>
>
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
-------------------------------------------------------------
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