R help - Aug 2010 - Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db'

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
- removed the zip file and downloaded and installed it again

My version of R is 2.11.1 on a Windows XP computer.

Thank you in advance,

Kind regards,

Kristel van Eijk

	[[alternative HTML version deleted]]

Hi Kristel --

On 08/27/2010 05:48 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
> - removed the zip file and downloaded and installed it again
> 
> My version of R is 2.11.1 on a Windows XP computer.
Please ask questions about Bioconductor packages on the Bioconductor
mailing list (you must be subscribed to post).

  http://bioconductor.org/help/mailing-list/

Please report sessionInfo() in your messages; a very common problem is
version mismatch between installed packages.

Please follow the instructions here to update your installed packages.

  http://bioconductor.org/install/index.html#update-bioconductor-packages

And for what it's worth,
> 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
> sessionInfo()
R version 2.11.1 Patched (2010-06-03 r52215)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] IlluminaHumanMethylation27k.db_1.2.0 org.Hs.eg.db_2.4.1

[3] RSQLite_0.9-2                        DBI_0.2-5

[5] AnnotationDbi_1.10.2                 Biobase_2.8.0


loaded via a namespace (and not attached):
[1] tools_2.11.1
>

Martin
> 
> Thank you in advance,
> 
> Kind regards,
> 
> Kristel van Eijk
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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