[Bioc-sig-seq] Package affy and its depencies

[James W. MacDonald]

Hi Ivan,

On 5/10/2011 4:41 PM, Ivan Gregoretti wrote:
> There seems to be a dependency error that comes up when running an
> analysis with affy. It only takes three commands.
>
> ###################################################################
> library(affy)
>
> Data<- ReadAffy(file="/home/johndoe/GSM492799.CEL.gz")
>
> eset<- rma(Data)
>
> Warning in install.packages(cdfname, lib = lib, repos =
> Biobase:::biocReposList(),  :
>    'lib = "/usr/local/lib64/R/library"' is not writable
> Would you like to create a personal library
> ~/R/x86_64-unknown-linux-gnu-library/2.14
> to install packages into?  (y/n)
> ###################################################################
>
> Is this error reproducible by others?

I don't see an error here. But perhaps you are referring to the warning?

I'm not sure how it could be made clearer, however. The gist is that you 
are running R as non-root (as you should), and therefore don't have 
write access to the /usr/local/lib64/R/library, (which you should not), 
so R is stating that fact and asking you if you want it to create a 
personal library in your home directory, where in future it will look 
for any packages that aren't found in the 'usual' place.

So, long story short, if you had simply typed a 'y' after that warning, 
you would have got the package downloaded and gone about your business.

Best,

Jim


>
> Thank you
>
> Ivan
>
>
> sessionInfo()
> R version 2.14.0 Under development (unstable) (2011-04-14 r55450)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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] affy_1.31.1    Biobase_2.13.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.21.0         preprocessCore_1.15.0 tools_2.14.0
>
>
> Ivan Gregoretti, PhD
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> 5 Memorial Dr, Building 5, Room 205.
> Bethesda, MD 20892. USA.
> Phone: 1-301-496-1016 and 1-301-496-1592
> Fax: 1-301-496-9878
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing

-- 
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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