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

[January Weiner]

Dear Martin,

thank you so much. This seems to have been the problem. I relied on
the fact that many packages report a problem with R version when they
are loaded, and usually I just updated them whenever I saw the
respective message ("this package has been build for a different
version of R") when I loaded them.

regards,

j.

On Sat, Jan 29, 2011 at 8:52 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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.
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>



-- 
-------- Dr. January Weiner 3 --------------------------------------
Max Planck Institute for Infection Biology
Charitéplatz 1
D-10117 Berlin, Germany
Web   : www.mpiib-berlin.mpg.de
Tel     : +49-30-28460514