[BioC] problem in make.cdf.package of MoGene-1_0-st-v1.r3.CDF

[Benilton Carvalho]

you need to update affyio.

On Sep 7, 2009, at 6:12 PM, Peng Yu wrote:

> Hi,
>
> I use the following script to make the MoEx cdf. You can tune it to
> make MoGene cdf.
>
> $ cat make_cdf_package.R
> library(makecdfenv)
> make.cdf.package("MoEx-1_0-st-v1.text.cdf",
> packagename="moex10stv1cdf", species="Mus_musculus")
>
> Regards,
> Peng
>
> On Thu, Aug 27, 2009 at 4:56 AM, Pengcheng Yang<pengchy at gmail.com>  
> wrote:
>> Forgot to paste my session information. Thanks!
>>> sessionInfo()
>> R version 2.9.2 (2009-08-24)
>> i386-pc-mingw32
>> locale:
>> LC_COLLATE=Chinese_People's Republic of China. 
>> 936;LC_CTYPE=Chinese_People's
>> Republic of China.936;LC_MONETARY=Chinese_People's Republic of
>> China.936;LC_NUMERIC=C;LC_TIME=Chinese_People's Republic of China.936
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets   
>> methods
>> [8] base
>> other attached packages:
>> [1] makecdfenv_1.22.0 affyio_1.10.1     affy_1.20.2        
>> Biobase_2.2.2
>> loaded via a namespace (and not attached):
>> [1] preprocessCore_1.4.0
>> On Thu, Aug 27, 2009 at 5:53 PM, Pengcheng Yang <pengchy at gmail.com>  
>> wrote:
>>>
>>> Hi Peng,
>>> I want to make a cdf package of MoGene-1_0-st-v1.r3 using the cdf  
>>> file
>>> downloaded
>>> from http://www.affymetrix.com/Auth/support/downloads/library_files/MoGene-1_0-st-v1.r3.unsupported-cdf.zip 
>>> ,
>>> and did as makecdfenv package's instruction. But failed with the
>>> information:
>>> -------------------------------------------
>>>>
>>>> make.cdf.package("MoGene-1_0-st- 
>>>> v1.r3.CDF",spec="mus",version=1.0,author="yang",maintainer="yang")
>>> Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) :
>>>  VECTOR_ELT() can only be applied to a 'list', not a 'character'
>>> --------------------------------------------
>>> I googled using this error message and found that you have  
>>> encountered the
>>> same
>>> question: http://article.gmane.org/gmane.science.biology.informatics.conductor/24497
>>> Could you please tell me how to make the cdf package of this  
>>> platform? And
>>> there is another solution as this linkage
>>> suggest: https://stat.ethz.ch/pipermail/bioconductor/2008-July/023403.html 
>>> ,
>>> but I do not know the following step.
>>> Thanks in advance.
>>> --
>>> Pengcheng Yang
>>> PhD Candidate
>>> IOZ,CAS
>>
>>
>>
>> --
>> Pengcheng Yang
>> PhD Candidate
>> IOZ,CAS
>>
>
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