[BioC] makecdfenv problem

[James W. MacDonald]

Hi Colin,

Please don't take things off-list. The intent is that the list archives 
might be a useful thing for people to search for answers.

colin clarke wrote:
> Hi James,
> 
> sessionInfo()
> 
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> base
> 
> other attached packages:
> [1] pls_2.1-0         affy_1.14.2       affyio_1.10.1     Biobase_2.2.2
> plsgenomics_1.2-2 MASS_7.2-45
> 
> 
> packageDescription("makecdfenv")$V
> [1] "1.20.0"
> 
> packageDescription("affy")$V
> [1] "1.14.2"

This is your problem. You have a very out of date version of affy. No 
idea how you got such a beast, but using biocLite() to install packages 
should make such a thing impossible.

So biocLite("affy") should get you fixed up.

Best,

Jim


> 
> Thank you,
> 
> Colin
> 
> 
> 
> 
> On Thu, Feb 12, 2009 at 4:20 PM, James W. MacDonald
> <jmacdon at med.umich.edu>wrote:
> 
>> Hi Colin,
>>
>> A sessionInfo() would be helpful, as would the output from
>>
>> packageDescription("makecdfenv")$V
>> and
>> packageDescription("affy")$V
>>
>> as this works for me:
>>
>>> library(makecdfenv)
>> 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: affy
>> Loading required package: affyio
>>> sessionInfo()
>> R version 2.8.0 (2008-10-20)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices datasets  utils     methods
>> [8] base
>>
>> other attached packages:
>> [1] makecdfenv_1.20.0 affyio_1.10.0     affy_1.21.6       Biobase_2.2.0
>>
>> loaded via a namespace (and not attached):
>> [1] preprocessCore_1.4.0
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> colin clarke wrote:
>>
>>> Hi all,
>>>
>>> R is returning the following error when attempting to load the makecdfenv
>>>
>>>  library("makecdfenv")
>>> Error : package 'affy' does not have a name space
>>> Error in as.environment(pos) :
>>>  no item called "newtable" on the search list
>>> Error: package/namespace load failed for 'makecdfenv'
>>>
>>> My version info:
>>>
>>> platform       i386-pc-mingw32
>>> arch           i386
>>> os             mingw32
>>> system         i386, mingw32
>>> status
>>> major          2
>>> minor          8.1
>>> year           2008
>>> month          12
>>> day            22
>>> svn rev        47281
>>> language       R
>>> version.string R version 2.8.1 (2008-12-22)
>>>
>>> Any help would be greatly appriciated,
>>>
>>> Colin
>>>
>>>        [[alternative HTML version deleted]]
>>>
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>>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Hildebrandt Lab
>> 8220D MSRB III
>> 1150 W. Medical Center Drive
>> Ann Arbor MI 48109-0646
>> 734-936-8662
>>
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662