[BioC] Help with Affy TilingArray makePDpackage

[Owen Thomas]

Hi,

I am running affyio 1.6.1,

as confirmed by the sessionInfo:

 > 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


Thanks,

Owen.

On 06/02/2008, at 1:30 PM, Benilton Carvalho wrote:

> You didn't provide the results of your sessionInfo()
>
> But the error is given by affyio, suggesting that you're running an  
> outdated version (the latest of affyio is 1.6.1).
>
> Please, ensure you're running this version and let us know what  
> your sessionInfo() is.
>
> best,
> b
>
>
> On Feb 5, 2008, at 9:11 PM, Owen Thomas wrote:
>
>> Hi,
>>
>> I am having trouble using the makePDpackage function, other people
>> have had the same problem:
>>
>> https://stat.ethz.ch/pipermail/bioconductor/2008-January/020922.html
>>
>> I have found no solution though, if anyone could help me understand
>> what's going on I would greatly appreciate it.
>>
>> The concise problem is:
>>
>> makePDpackage ("Sc03b_MF_v04.bpmap", file1="Sc03b_MF_v04.cif",
>> manufacturer="affymetrix", type="tiling")
>> affymetrix tiling
>>
>> The package will be called pd.sc03b.mf.v04
>>
>> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) :
>>   SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
>>
>> Thanks,
>>
>> Owen.
>>
>> Full R session:
>>
>> 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
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> library (makePlatformDesign)
>> Loading required package: affyio
>> Loading required package: oligo
>> Loading required package: Biobase
>> Loading required package: tools
>>
>> Welcome to Bioconductor
>>
>>   Vignettes contain introductory material. To view, type
>>   'openVignette()'. To cite Bioconductor, see
>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>> Loading required package: splines
>> Loading required package: RSQLite
>> Loading required package: DBI
>> Loading required package: preprocessCore
>> Loading required package: AnnotationDbi
>> Loading required package: affxparser
>> Loading required package: oligoClasses
>> This is the oligo package
>>> makePDpackage ("Sc03b_MF_v04.bpmap", file1="Sc03b_MF_v04.cif",
>> manufacturer="affymetrix", type="tiling")
>> affymetrix tiling
>> The package will be called pd.sc03b.mf.v04
>> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) :
>>   SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
>>> traceback ()
>> 3: .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE = "affyio")
>> 2: makeBPMAPenv(designFile, file1, genomebuild = genomebuild)
>> 1: makePDpackage("Sc03b_MF_v04.bpmap", file1 = "Sc03b_MF_v04.cif",
>>        manufacturer = "affymetrix", type = "tiling")
>>
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>