On 10/08/2010 09:14 AM, danieladna wrote:
> Hello,
> I have been running the affy package for a while now without running into any 
> problems.
> Now I would like to use affyPara as I have 600 .CEL files to analyze.
> All my packages are up to date and all cdf files are installed.
> Unfortunately affyPara cannot load any cdf files. I am not sure why. Does 
>anyone 
>
> have an idea how I can fix this problem?
> The failure message I get is following:
> Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
>   31 nodes produced errors; first error: Could not obtain CDF environment, 
> problems encountered:
> Specified
 environment does not contain HuEx-1_0-st-v2
> Library - package huex10stv2cdf not installed
> Bioconductor - could not connect
> Calls: rmaPara -> preproPara -> clusterCall -> checkForRemoteErrors
> Execution halted
>
> I am positive that huex10stv2cdf is installed, as I have been running it with 
> affy successfully from the same location.
> Many thanks for your help and ideas,
> Daniela
>
>
>   

Hi Daniela,

Seeing more of your code would be helpful for troubleshooting the
problem.  Please provide a chunk of code that describes how you are
inputting the cdf files and what you are distributing to the nodes. 

Also include the output of sessionInfo() from one of the nodes.
For example, if cl is your cluster then
clusterEvalQ(cl, sessionInfo())

I am
 also ccing the package maintainer on this response.

Valerie


Hi Valerie,
Many thanks for your reply.
My code looks like this:

library(affyPara)
library(snow)
library(huex10stv2hsensecdf)

cl<-makeCluster()
clusterEvalQ(cl, sessionInfo())

path<-"/home/daniela/test"
files <- list.celfiles(path,full.names = T)
distList<-distributeFiles(files,protocol="SCP")
eset<-rmaPara(distList$files, cdfname="huex10stv2hsensecdf ",cluster=cl)
sessionInfo()
e<-exprs(eset)

write.exprs(file="samples.txt")


removeDistributedFiles("/home/daniela/test")
stopCluster(cl)

The session info like this: and is repeated for all processors I have been 
requesting.
[[3]]
R version 2.11.1 (2010-05-31) 
x86_64-unknown-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 datasets  utils     methods   base     

other attached packages:
[1] snow_0.3-3 Rmpi_0.5-8

And this is the error message I get:

There were 24 warnings (use warnings() to see them)
Error in .getObjectType(object) : Object has an unknown type
Calls: rmaPara -> preproPara -> .getObjectType
Execution halted

Do I really need to manually distribute the files with the distributeFiles 
command? Or could I leave this command out since
I am working on a cluster and all the files are already on all the available 
nodes because our shared file system.
I think that that distributeFiles command might cause following error: 
Permission denied (publickey,keyboard-interactive).
lost connection. Is this a possible cause for my problems?

I very much appreciate your help,
Daniela


      
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