[BioC] Help with Affy TilingArray makePDpackage

[Owen Thomas]

I downloaded the affyio 1.7.10 source and installed, but I still have  
exactly the same error, which occurs in the ReadBPMAPFileIntoRList c  
function:

bpmap <- .Call ("ReadBPMAPFileIntoRList", "Sc03b_MF_v04.bpmap")
Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'

It seems that the Mac OS X binary of affyio 1.7.1 is compiled against  
a development version of R, would you recommend upgrading my version  
of R?

Anyway, to confirm the installation my sessionInfo is

 > 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_1.7.10

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


Regards,

Owen.


On 06/02/2008, at 2:03 PM, Benilton Carvalho wrote:

> Do you want to try a non-recommended approach?
>
> Install the devel version of affyio, I recall Ben fixing something  
> like this not long ago:
>
> http://www.bioconductor.org/packages/2.2/bioc/html/affyio.html
>
> Please let us know how it goes...
>
> b
>
> On Feb 5, 2008, at 9:43 PM, Owen Thomas wrote:
>
>> 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 an outdated version (the latest of affyio is 1.6.1).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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>>
>