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

[Robert Castelo]

hi Marc,

i see, i misunderstood where the problem was. i've updated AnnotationDbi 
and it works like a charm.

thanks!
robert.

On 06/22/2013 04:00 PM, Marc Carlson wrote:
> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>
>

-- 
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