[BioC] Problem with createAnnObjs.HUMANCHIP_DB

[Martin Morgan]

Hi Wendelin --

On 05/25/2010 04:45 AM, Wendelin Waunzel wrote:
> 
>    Hello,
>    Being keen on the RmiR package I tried to install the corresponding data set
>    (hgug4112a.db_2.2.5), but failed with the following error code. I did a
>    complete update of my R/Bioconductor environment as recommended in other
>    postings, but this step didn't solve my problems. I have a fresh  2.11.0.
>    All necessary packages were installed in advance:
>    DBI_0.2-5.tar.gz
>    RSQLite_0.9-0.tar.gz
>    AnnotationDbi_1.10.1.tar.gz
>    hgug4112a.db_2.2.5.tar.gz
>    RSVGTipsDevice_1.0-1.tar.gz
>    RmiR.Hs.miRNA_1.0.6.tar.gz
>    RmiR_1.4.0.tar.gz
>    hgug4112a.db_2.2.5.tar.gz
>    Here is the R complaint
>    #######################
>    * installing *source* package 'hgug4112a.db' ...
>    ** R
>    ** inst
>    ** preparing package for lazy loading
>    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)'.
>    ** help
>    *** installing help indices
>    ** building package indices ...
>    ** testing if installed package can be loaded
>    Error : .onLoad failed in loadNamespace() for 'hgug4112a.db', details:
>      call: fun(...)
>      error: could not find function "createAnnObjs.HUMANCHIP_DB"
>    ERROR: loading failed
>    * removing '/usr/bin/R-2.11.0/library/hgug4112a.db'
>    #####################################
>    What's the problem and how can I solve it?

Are you installing this with

  source('http://bioconductor.org/biocLite.R')
  biocLite('hgug4112a.db')

? The version of hgug4112a.db relevant for R-2.11.0 is 2.4.1, as you can
see here


http://bioconductor.org/packages/2.6/data/annotation/html/hgug4112a.db.html

Also, have you followed the 'Update Installed Bioconductor packages'
directions at

  http://bioconductor.org/docs/install

?

If the problems still persist, can you provide

  library('org.Hs.eg.db')
  sessionInfo()

and the complete transcript of

  biocLite('hgug4112a.db')

Martin

>    Thank you for any suggestions
>    W
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793