[BioC] RSQLite error when using AnnotationDbi/SQLForge

[Diego Diez]

Hi,

you have to run this in a root session, i.e. making "sudo R".

Diego.


On Tue, Jul 15, 2008 at 1:11 AM, Tim Rayner <tfrayner at gmail.com> wrote:
> Hi,
>
> I'm having a problem building a custom AnnotationDbi-style package
> using the SQLForge functions. It appears that something from the
> RSQLite package is disagreeing with the makeHUMANCHIP_DB function,
> such that there's an "attempt to write a readonly database". See below
> for a full transcript:
>
>> library('AnnotationDbi')
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: DBI
> Loading required package: RSQLite
>> makeHUMANCHIP_DB(
>    affy=FALSE,
>    prefix='Human25kOligoSet.db',
>    fileName='refseq.txt',
>    baseMapType='refseq',
>    outputDir='.',
>    version='0.1',
>    manufacturer='MRC',
>    chipName='Human 25k Oligo Set',
>    manufacturerUrl='http://www.geneservice.co.uk')
> baseMapType is refseq
> Prepending Metadata
> Creating Genes table
> Error in sqliteExecStatement(con, statement, bind.data) :
>  RS-DBI driver: (RS_SQLite_exec: could not execute1: attempt to write
> a readonly database)
>> sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-apple-darwin8.10.1
>
> locale:
> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] AnnotationDbi_1.2.2 RSQLite_0.6-9       DBI_0.2-4
> [4] Biobase_2.0.1
>
>
> All the packages were installed with biocLite(..., type='source'). The
> "refseq.txt" file is a two-column file with arbitrary probe
> identifiers linked to Refseq accessions, as described in the SQLForge
> vignette. Has anyone else seen this problem? Can anyone point me to
> where my error might be?
>
> Many thanks in advance,
>
> Tim Rayner
>
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-- 
Diego Diez, Ph
Bioinformatics center,
Institute for Chemical Research,
Kyoto University.
Gokasho, Uji, Kyoto 611-0011 JAPAN
diez at kuicr.kyoto-u.ac.jp