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