[BioC] Problems with affy on Ubuntu 10.10: "extended" option in sub/R missing

[Martin Morgan]

On 01/29/2011 11:01 AM, January Weiner wrote:
> Hello,
> 
> I cannot use ReadAffy() in Ubuntu 10.10 (it works in Ubuntu 10.04).
> 
>> ab <- ReadAffy()
> Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) :
>   unused argument(s) (extended = TRUE)
> 
> The reason is that the sub() function from R lacks the optional
> argument "extended":

Hi January --

This is likely a version mismatch between your R and Bioc packages;
follow instructions at

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

and

source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE)

Or update your R and create a fresh bioc install.

Martin

> 
>> a <- rep( "a", 10 )
>> sub( "a", "b", a )
>  [1] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b"
>> sub( "a", "b", a, extended=TRUE )
> Error in sub("a", "b", a, extended = TRUE) :
>   unused argument(s) (extended = TRUE)
> 
> No such errors occur in Ubuntu 10.04.
> 
> The R version that comes with Ubuntu 10.10 is 2.11.1:
> 
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> i686-pc-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] affy_1.22.1   Biobase_2.4.1
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0        preprocessCore_1.6.0
> 
> 
> In Ubuntu 10.04, the version of R is 2.10.1
> 
> My question: is that a general problem with R 2.11.1, or a problem
> with Ubuntu? Is anyone aware of that problem? I am trying to figure
> out what would be the easiest way of getting back the 2.10.1 version
> (short of deinstalling all R packages and libraries and manually
> reinstalling them again), I will post a solution if I find an easy
> one.
> 
> best regards,
> 
> j.
> 


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