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

[Aedin Culhane]

Thanks Ben
I did use biocLite() to do the update, so this is surprising.  affyiio 
should have been installed as a dependency of affy.  I used:

source("http://www.bioconductor.org/biocLite.R")
biocLite()

I just installed affyio manually and now it works fine.

Thanks for your help
Aedin


Ben Bolstad wrote:
> 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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>>     


-- 
Aedín Culhane
Research Associate in Prof. J Quackenbush Lab
Harvard School of Public Health, Dana-Farber Cancer Institute

44 Binney Street, SM822
Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute
Boston, MA 02115
USA

Phone: +1 (617) 632 2468
Fax:   +1 (617) 582 7760
Email: aedin at jimmy.harvard.edu
Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html