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

[Marc Carlson]

Hi Robert,

The annotation package will not be updated (for this reason anyways) as 
there is nothing wrong with the data.  The software (AnnotationDbi) was 
updated for this right after you mentioned it.  You should be able to 
update it by installing it via biocLite.

biocLite("AnnotationDbi")


   Marc



On 06/20/2013 12:31 AM, Robert Castelo wrote:
> 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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>>
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>