[BioC] RSQLite error when using AnnotationDbi/SQLForge

[Tim Rayner]

Hi Marc, Diego,

Thank you both for your help. It turns out you're both right, it was a
permissions issue. Apparently R was trying to write something into a
directory outside my home directory and/or temporary directories
(strictly speaking, I don't think it should have to do this). It turns
out I didn't have to run R as root, but I did have to run it as the
user I originally used to install R and Bioconductor. Is there perhaps
a temporary file which is being written to somewhere in the R
installation directories, rather than tempdir()? I've had a quick look
through the code, but I can't see anything obvious.

Many thanks,

Tim Rayner



2008/7/14 Marc Carlson <mcarlson at fhcrc.org>:
> Hi Tim,
>
> I have had someone tell me that they had this problem once before, but it
> was ultimately a permissions problem.  Are you able to run this as root?
>
>   Marc
-------------------------------------------------------------------
2008/7/15 Diego Diez <diez at kuicr.kyoto-u.ac.jp>:
> 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
>