[BioC] About Affy TilingArray makePDpackage

[Feng Tian]

Hi Ben,

I've followed your instructions and got the same error:

cbc03:~/mkCDF feng$ R

R version 2.6.1 (2007-11-26)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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Type 'contributors()' for more information and
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> dir()
[1] "AFFY_TILING.bpmap"               "AFFY_TILING.cif"                
[3] "Dm35b_MR_v02-3_BDGPv4h.NR.bpmap"
> library(affyio)
> bpmapFile <- "AFFY_TILING.bpmap"
> bpmap <- .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE="affyio")
Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> traceback()
1: .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE = "affyio")
>

Also:
> sessionInfo()
R version 2.6.1 (2007-11-26) 
powerpc-apple-darwin8.10.1 

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] affyio_1.6.1

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

Thanks!

Feng



-----Original Message-----
From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] 
Sent: Thursday, January 24, 2008 9:10 PM
To: joseph
Cc: Feng Tian; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] About Affy TilingArray makePDpackage

could you, please, provide the results of:

traceback()

right after the error?

also, i'd appreciate if you could quit and reload R and do exactly the  
following:

library(affyio)
bpmapFile <- "Dm35b_MF_v02-3_BDGPv4h.bpmap"
bpmap <- .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE="affyio")

and let me know how it goes...

thanks,
b


On Jan 24, 2008, at 9:32 PM, joseph wrote:

> I refer you to Naira's response where you might find the solution:
> https://stat.ethz.ch/pipermail/bioconductor/2007-December/020468.html
> However, I did not go any further because I did not have enough  
> memory on my PC. Also, you can check Henrik's solution to the memory  
> problem
> https://stat.ethz.ch/pipermail/bioconductor/2007-December/020479.html
> Good Luck
>
> ----- Original Message ----
> From: Feng Tian <firmly at gmail.com>
> To: jdsandjd at yahoo.com; jmacdon at med.umich.edu
> Cc: Frank Liu <xliu26 at uic.edu>; parantu shah <parantu.shah at gmail.com>
> Sent: Thursday, January 24, 2008 2:12:41 PM
> Subject: About Affy TilingArray makePDpackage
>
>
> Hi, Joseph,
>
>> From the Bioconductor mail list,  I found that you had ever met the  
>> same problem as I do now. When trying to create environment for  
>> Drosophila tiling array,
>
>> makePDpackage("Dm35b_MF_v02-3_BDGPv4h.bpmap",  
>> file1="Dm35b_MF_v02.cif", manufacturer="affymetrix", type="tiling")
>
>
> I got the same error:
>
> affymetrix tiling
> The package will be called pd.dm35b.mr.v02.3.bdgpv4h.nr
> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) :
>
>  SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
>
> Have you solved your problems, and how? Thanks!
>
>
>
> I'm using the latest version of R and packages:
>
>> sessionInfo()
>
> R version 2.6.1 (2007-11-26)
> powerpc-apple-darwin8.10.1
>
> locale:
> C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils      
> datasets
> [8] methods   base
>
> other attached packages:
>
> [1] makePlatformDesign_1.2.0 oligo_1.2.2               
> oligoClasses_1.0.3
> [4] affxparser_1.10.2        AnnotationDbi_1.0.6       
> preprocessCore_1.0.0
> [7] RSQLite_0.6-4            DBI_0.2-4                Biobase_1.16.2
>
> [10] affyio_1.6.1
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-17
>
>
>
>
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