[BioC] RS-DBI driver error with org.Sc.sgd.db

[Robert Castelo]

hi Marc,

when do you think this annotation package will be updated with the 
solution? (as far as the website tells, it's still on the same version 
2.9.1)

thanks!
robert.

On 06/04/2013 10:22 PM, Marc Carlson wrote:
> Hi Robert,
>
> That's a pretty good one. The problem here is that someone decided to
> name their gene symbol: IMP2' (presumably to go with IMP2). This creates
> a problem when we query the DB since all these gene symbols get written
> into a query, and part of that query looks like this:
>
> ... 'IMP2', 'IMP2'', 'IMP3' ...
>
> And this ends up confusing SQL, as it doesn't know what to make of two
> single quote characters in a row like that...
>
>
> I have a simple fix, it should be in place about as soon as it can
> percolate out through our build system.
>
>
> Marc
>
>
>
>
> On 06/04/2013 12:42 AM, Robert Castelo wrote:
>> hi,
>>
>> while i was using the gene-centric organism-level package for yeast
>> org.Sc.sgd.db i encountered the following error:
>>
>> library(org.Sc.sgd.db)
>>
>> select(org.Sc.sgd.db, cols="ORF", keys=keys(org.Sc.sgd.db,
>> keytype="GENENAME"), keytype="GENENAME")
>> Error in sqliteExecStatement(con, statement, bind.data) :
>> RS-DBI driver: (error in statement: near "IMP3": syntax error)
>>
>> it looks like the sqlite engine does not like some symbol name in
>> "GENENAME".
>>
>>
>> cheers,
>>
>> robert.
>> ps: sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8
>> LC_COLLATE=en_US.UTF8
>> [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8 LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] org.Sc.sgd.db_2.9.1 RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.5
>> Biobase_2.20.0
>> [6] BiocGenerics_0.6.0 vimcom_0.9-8 setwidth_1.0-3 colorout_1.0-0
>>
>> loaded via a namespace (and not attached):
>> [1] IRanges_1.18.1 stats4_3.0.0
>>
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-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550