[BioC] makecdfenv's error (with MoGene-1_0-st-v1.r3.cdf)

[Peng Yu]

Here is the session info when the package makecdfenv is loaded.

> sessionInfo("makecdfenv")
R version 2.9.1 (2009-06-26)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
character(0)

other attached packages:
[1] makecdfenv_1.22.0

loaded via a namespace (and not attached):
[1] affyio_1.8.1    base_2.9.1      Biobase_2.0.1   graphics_2.9.1
[5] grDevices_2.9.1 methods_2.9.1   stats_2.9.1     tools_2.9.1
[9] utils_2.9.1


On Tue, Aug 4, 2009 at 2:58 PM, Peng Yu<pengyu.ut at gmail.com> wrote:
> Here is it.
>
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> On Tue, Aug 4, 2009 at 2:39 PM, Robert Gentleman<rgentlem at fhcrc.org> wrote:
>> Please give your sessionInfo as requested in the posting guide.
>>
>> It looks like  you might have mixed versions (or old versions) so you could
>> check and update if so, before coming back to the list.
>>
>> Peng Yu wrote:
>>>
>>> Hi,
>>>
>>> I downloaded MoGene-1_0-st-v1.r3.cdf from
>>>
>>> http://www.affymetrix.com/products_services/arrays/specific/mousegene_1_st.affx#1_4
>>>
>>> Then, I run the following command in R.
>>>
>>> library("makecdfenv")
>>>
>>> make.cdf.package("~/download/MoGene-1_0-st-v1.r3.unsupported-cdf/MoGene-1_0-st-v1.r3.cdf",
>>> species="Mus_musculus")
>>>
>>> But I got the following error.
>>>
>>> Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) :
>>>  VECTOR_ELT() can only be applied to a 'list', not a 'character'
>>> Calls: make.cdf.package -> make.cdf.env -> isCDFXDA -> .Call
>>> Execution halted
>>>
>>> Can somebody let me what the problem is? Do I call the command
>>> incorrectly?
>>>
>>> Regards,
>>> Peng
>>>
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>>
>> --
>> Robert Gentleman, PhD
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> PO Box 19024
>> Seattle, Washington 98109-1024
>> 206-667-7700
>> rgentlem at fhcrc.org
>>
>