[BioC] [R] Make.cdf.package error

[James W. MacDonald]

Hi Elodie,

First, this isn't a question for R-help, but should be directed to the 
Bioconductor help list (redirected).

It also appears that you cross-posted, but I don't see any evidence for 
that in the header to this email (just in the subject). If you did in 
fact post to both lists, please don't do that either.

On 2/17/2011 10:14 AM, elodiem wrote:
>
> Hi everybody,
>
> I tried to analyze a custom Affymetrix 3'-biased Array. So I wanted to make
> a cdf package. (My CDF file size is 1.12Go).
>
> I tried several methods but the same error occured
>
> Method 1
>
>> #Set the working directory
>> setwd("D:/Analyse R/Cel files")
>> #library to create cdf env
>> library("makecdfenv")
>> #Create cdf environment
>> pkgpath<- tempdir()
>> make.cdf.package("file.cdf",
>             cdf.path=getwd(),
>             compress=FALSE, species = "Homo_sapiens",
>             package.path = pkgpath,
>             verbose=TRUE)
> dir(pkgpath)
>
> Method 2
> #Set the working directory
> setwd("D:/Analyse R/Cel files")
> #library to create cdf env
> library("makecdfenv")
> #Create cdf environment
> env<- make.cdf.env("file.cdf")
>
>
>> Reading CDF file.
>> Error in .Call("reaD file", as.character(file), as.integer(3),
> as.integer(compress), :promise already under evaluation: recursive default
> argument reference or earlier problems?
>
> The two methods take about one hour and use all the RAM of my computer
> (8Go).
>
> Is it a limit of memory?

Possibly. That is a gigantic CDF file; the largest 'stock' cdf I have 
seen is about an order of magnitude smaller. This is for sure a 3' 
biased array?

> Is it a non appropriated method for my array?

If in fact it is a 3' biased array, then this is the software to use. It 
may be some other incompatibility however. Please send us the output 
from sessionInfo().

Best,

Jim


>
> Thanks in advance for your response,
> Elodie

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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