Hi James,

That worked a treat!

Thanks a million for your help,

Cheers,

Colin

On Thu, Feb 12, 2009 at 5:11 PM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> 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 You have a very out of date version of affy.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@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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>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>  --
>>> 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
>

	[[alternative HTML version deleted]]

