[ensembl-dev] Variant Effect Predictor 2.2 A global symbol error

[Saeed Al Turki]

A fresh cvs checkout solved it!

Many thanks Daniel.

Saeed

On Wed, 28 Sep 2011 12:49:59 +0100, Daniel Sobral <sobral at ebi.ac.uk>
wrote:
> Hi Saeed,
> 
> These lines probably affect variation predictions in Transcription 
> Factor binding sites.
> 
> The error is coming from a variable that is exported by 
> Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor,  from which 
> MotifFeatureAdaptor inherits.
> 
> I would think there is something wrong with your ensembl instalation or 
> PERL5LIB  because I try the same and I don't get errors. All ensembl 
> modules need to be checked out from the same release (64).
> Try a fresh cvs checkout.
> 
> The PERL5LIB I used to test:
>
PERL5LIB=$ENS_SRC/bioperl-live/:$ENS_SRC/ensembl/modules/:$ENS_SRC/ensembl-variation/modules/:$ENS_SRC/ensembl-functgenomics/modules/
> 
> Hope it helps,
> Daniel
> 
> On 28/09/2011 11:31, Saeed Al Turki wrote:
>> Hi,
>>
>> I trying to run VEP 2.2 with Ensembl API 64 but I ran into this error:
>>
>> $ perl variant_effect_predictor_2.2.pl  --help
>>
>> ------------------------------
>> Global symbol "%true_tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 69.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 70.
>> Global symbol "%true_tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 70.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 99.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 107.
>> Global symbol "%true_tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 107.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 135.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 149.
>> Global symbol "%true_tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 149.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 184.
>> Global symbol "%true_tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 184.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 215.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 227.
>> Global symbol "%true_tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 227.
>> Global symbol "%tables" requires explicit package name at
>>
/software/pubseq/PerlModules/Ensembl/www_64_1/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/MotifFeatureAdaptor.pm
>> line 271.
>> Compilation failed in require at variant_effect_predictor_2.2.pl line
>> 480.
>> BEGIN failed--compilation aborted at variant_effect_predictor_2.2.pl
line
>> 480.
>> ------------------------------
>> If I comment lines from 479 to 483 , the script seems to work but I
don't
>> know how this would affect the final output.
>>
>> What do you think the cause of the error? Is it save to keep lines
>> 479-483
>> commented out?
>>
>> Cheers,
>> Saeed
>>
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> 
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