[BioC] RS-DBI driver error with org.Sc.sgd.db
Robert Castelo
robert.castelo at upf.edu
Thu Jun 20 09:31:33 CEST 2013
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
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