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

[Marc Carlson]

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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