[BioC] Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db'

[James W. MacDonald]

Hi Kristel,

On 8/30/2010 5:37 AM, Kristel van Eijk wrote:
> Hello everyone,
>
> I have a problem when loading the library: IlluminaHumanMethylation27k.db
> I installed the package from zip (from the Bioconductor website), and also
> installed all the packages it asked for. It went all succesfull:
>
> "package 'IlluminaHumanMethylation27k.db' successfully unpacked and MD5 sums
> checked"
>
> But when I am trying to load this library I get an error:
>
>> library(IlluminaHumanMethylation27k.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: org.Hs.eg.db
> Loading required package: DBI
> Error : .onLoad failed in loadNamespace() for
> 'IlluminaHumanMethylation27k.db', details:
>    call: sqliteExecStatement(con, statement, bind.data)
>    error: RS-DBI driver: (error in statement: near "s": syntax error)
> Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db'
>
> I have tried the following things:
> - I reinstalled the packages from Bioconductor (AnnotationDbi, Biobase,
> org.Hs.eg.db and DBI)
> - restarted R

Did you try re-installing IlluminaHumanMethylation27k.db? I get this 
package to load without problems.

Also, you indicate that you are going to the website to get the files 
for installation. This is not the best way to do things. Instead, use 
biocLite().

source("http://www.bioconductor.org/biocLite.R")
biocLite("IlluminaHumanMethylation27k.db")

Best,

Jim



>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252
> LC_MONETARY=Dutch_Netherlands.1252
> [4] LC_NUMERIC=C                       LC_TIME=Dutch_Netherlands.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] org.Hs.eg.db_2.4.1   RSQLite_0.9-2        DBI_0.2-5
> AnnotationDbi_1.10.2 Biobase_2.8.0
>
>> traceback()
> 2: stop(gettextf("package/namespace load failed for '%s'", package),
>         call. = FALSE, domain = NA)
> 1: library(IlluminaHumanMethylation27k.db)
>
>
> Thank you in advance,
>
> Kind regards,
>
> Kristel van Eijk
> PhD student (University Medical Center Utrecht, The Netherlands)
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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