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

[January Weiner]

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":

> 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.

-- 
-------- 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