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

[Marc Carlson]

Hi Peng,

I have no problems building this, but my sessionInfo() looks a little
more current than yours:

R version 2.9.1 Patched (2009-06-29 r48872)
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] affy_1.22.0          affyio_1.12.0        base_2.9.1
 [4] Biobase_2.4.1        graphics_2.9.1       grDevices_2.9.1
 [7] methods_2.9.1        preprocessCore_1.6.0 stats_2.9.1
[10] tools_2.9.1          utils_2.9.1


So you might want to run update.packages().  You can see some nice
examples of this by looking in the manual for update.packages or on our
website here:

http://www.bioconductor.org/docs/install/


Please let us know if you have other questions or concerns,



  Marc





Peng Yu wrote:
> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
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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
>>>
>>>       
>
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>