[BioC] RSQLite error when using AnnotationDbi/SQLForge

[Tim Rayner]

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