[BioC] ReadAffy - Error VECTOR_ELT() can only be applied to a 'list', not a 'char'

[Ben Bolstad]

You have a mismatch between your version of affy and your version of
affyio. You need 1.4.0 or later (the version released with BioC2.0).

As a general rule people should not be mixing and matching packages
between different versions of BioC/R. It is always safest to re-install
the release using biocLite() or getBioC() rather than trying to install
packages manually and hoping it works.

Best,

Ben






On Wed, 2007-06-20 at 19:38 -0400, aedin culhane wrote:
> Hi BioC,
> I am having problems getting ReadAffy to work on fc5. Any ideas?
> Thanks.
> Aedin
> 
>  > example(ReadAffy)
> 
> RdAffy> if(require(affydata)){
> RdAffy+      celpath <- system.file("celfiles", package="affydata")
> RdAffy+      fns <- list.celfiles(path=celpath,full.names=TRUE)
> RdAffy+
> RdAffy+      cat("Reading files:\n",paste(fns,collapse="\n"),"\n")
> RdAffy+      ##read a binary celfile
> RdAffy+      abatch <- ReadAffy(filenames=fns[1])
> RdAffy+      ##read a text celfile
> RdAffy+      abatch <- ReadAffy(filenames=fns[2])
> RdAffy+      ##read all files in that dir
> RdAffy+      abatch <- ReadAffy(celfile.path=celpath)
> RdAffy+ }
> Loading required package: affydata
> Reading files:
>  
> /home/aedin/R/i686-redhat-linux-gnu-library/2.5/affydata/celfiles/binary.cel
> /home/aedin/R/i686-redhat-linux-gnu-library/2.5/affydata/celfiles/text.cel
> Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  :
>          VECTOR_ELT() can only be applied to a 'list', not a 'char'
> 
> 
> 
>  > sessionInfo()
> R version 2.5.0 (2007-04-23)
> i686-redhat-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGE 
>  
> S=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI 
>                        CATION=C
> 
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "methods"   "base"
> 
> other attached packages:
> affydata     affy   affyio  Biobase
> "1.11.2" "1.14.1"  "1.0.0" "1.14.0"
> 
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