[BioC] ReadAffy Error: new versions causing problems?

[Boel Brynedal]

Dear List,

I am a PhD student at Karolinska Institutet in Sweden. I have a problem
thats been evolving the last couple of days. The net result is that much
of what I do produces error messages. I'll give an example:

> raw<-ReadAffy()
Error in read.affybatch(filenames = l$filenames, phenoData = l
$phenoData,  :
        VECTOR_ELT() can only be applied to a 'list', not a 'char'

Is there something wrong with my CEL-files? I exported some of them to
another computer with the same version of R and packages, and there it
worked fine.

When I use the biocLite installing route, the installation of both
tkWidgets and tcltk seams to fail:
Loading required package: tkWidgets
Error: package 'tkWidgets' could not be loaded
In addition: Warning message:
there is no package called 'tkWidgets' in: library(pkg, character.only =
TRUE, logical = TRUE, lib.loc = lib.loc)
Execution halted
ERROR: execution of package source for 'marray' failed
** Removing '/usr/local/lib64/R/library/marray'
** Restoring previous '/usr/local/lib64/R/library/marray'

Could this be the reason for my problems; that old and new versions of
packages are mixed? 

My sessionInfo():
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
      gcrma matchprobes  simpleaffy  genefilter    survival        affy
    "2.8.1"     "1.8.1"     "2.8.0"    "1.14.1"      "2.31"    "1.14.0"
     affyio     Biobase
    "1.4.0"    "1.14.0"

Or can it be a more general problem? I just installed a new versions of
both R and bioconductor packages.

I'm not an expert in Linux or R, so I'll appreciate any advice!
Thank you,

Boel Brynedal

--~*~**~***~*~***~**~*~--
Boel Brynedal, MSc, PhD student
Karolinska  Institutet
Department of Clinical neuroscience

Karolinska University hospital Huddinge
Division of Neurology, R54
141 86 Stockholm
SWEDEN
Phone: +46 8 585 819 27
Fax:   +46 8 585 870 80
E-mail: boel.brynedal at ki.se