Dear listers, 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' > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.iso88591;LC_NUMERIC=C;LC_TIME=en_US.iso88591;LC_COLLATE =en_US.iso88591;LC_MONETARY=C;LC_MESSAGES=en_US.iso88591;LC_PAPER=en_U S.iso88591;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US. iso88591;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RSQLite_0.7-3 DBI_0.2-4 AnnotationDbi_1.6.1 [4] Biobase_2.4.1 However I can successfully load library(hgu133a.db) and others. I logged in as root to run the same command and got the same error. After looking up Bioconductor mailing list archives I found few clue about this issue. Could anyone give me a hint on solving the problem? Thanks a lot, Lei Huang Bioengineering/Bioinformatics Program University of Illinois at Chicago 821 S Wood Street, RM103 Chicago, IL 60612

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

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