[BioC] Error loading Affymetrix Human Genome U133plus2 Set annotation data

Seth Falcon sfalcon at fhcrc.org
Tue Nov 17 02:12:19 CET 2009

Hi Lei,

On 11/16/09 1:22 PM, Lei Huang wrote:
> I received an error message when trying to load library(hgu133plus2.db)

>> library(hgu133plus2.db)
> Loading required package: AnnotationDbi
> Loading required package: Biobase
> 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
> Error in sqliteFetch(rs, n = -1, ...) :
>    RSQLite driver: (RS_SQLite_fetch: failed first step: disk I/O error)
> Error : .onLoad failed in 'loadNamespace' for 'hgu133plus2.db'
> Error: package/namespace load failed for 'hgu133plus2.db'

Hmm, that error looks like it is coming from SQLite.  A bit difficult to 
debug from here, but a few suggestions:

1. Try reinstalling this package using biocLite.  Possibly try 
installing the package to a different package library (see .libPaths()).

2. Consider upgrading your R and Bioc packages to the latest release.

+ seth
Seth Falcon
Program in Computational Biology | Fred Hutchinson Cancer Research Center

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