[BioC] Prokaryotic_Rhodobacter capsulatus GEP

[dorothyc]

Hi Jim,

Thanks very much for your advice.  It works now.

Regards,
Dorothy

On Dec 1, 2008, at 5:41 AM, James W. MacDonald wrote:

> Looking at the output that the OP has provided implies to me that  
> she used the makecdfenv package to create a cdf package, but  
> installed it incorrectly.
>
> Dorothy - you did everything correctly up until the last step. You  
> have to use R CMD INSTALL to install any package, whether or not it  
> has a .tar.gz suffix (which you could make using R CMD build, but  
> this is not necessary).
>
> So just move the folder back out onto e.g., your desktop and then  
> install.
>
> Best,
>
> Jim
>
>
> Martin Morgan wrote:
>> Mark Robinson <mrobinson at wehi.EDU.AU> writes:
>>> Hi Dorothy.
>>>
>>> In general you can't install packages by copying files to your  
>>> library
>>> directory.  And, my guess is that your CDF *file* is not a CDF
>>> *package*, as required by affy.  Or, is it?
>>>
>>> Is your file a text file ... something of the this format?
>>> http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html
>>>
>>> If it is, you could use 'convertCdf' in the affxparser package,  
>>> giving
>>> you a CDF *file*, which you could use within aroma.affymetrix.   
>>> There
>>> also may be a way of converting this into a CDF package, but I don't
>>> know how.  Anyone else?
>> The Bioconductor makecdfenv package makes cdf environments from cdf
>> files.
>> Martin
>>> If it is not of this format, please let us know what it is.
>>>
>>> Mark
>>>
>>>
>>>
>>> On 28/11/2008, at 12:14 PM, dorothyc wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm a computational biologist at Genome Sciences Centre, Vancouver,
>>>> BC, Canada.  I'm working on Affymetrix custom bacterial ship,
>>>> Prokaryotic_Rhodobacter capsulatus GEP.
>>>>
>>>> I've encountered some problems with the CDF file.  I've copied the
>>>> rcapex1a520469fcdf directory to /Library/Frameworks/R.framework/
>>>> Versions/2.7/Resources/library.  However, I got an error as  
>>>> follows:
>>>> --------------
>>>>> require(rcapex1a520469fcdf)
>>>> Loading required package: rcapex1a520469fcdf
>>>> Error in library(package, lib.loc = lib.loc, character.only = TRUE,
>>>> logical.return = TRUE,  :
>>>>  'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0?
>>>>
>>>>> raw.data <- ReadAffy()
>>>>> eset <<- rma(raw.data)
>>>> Error in library("rcapex1a520469fcdf", lib.loc = NULL,  
>>>> character.only
>>>> = TRUE) :
>>>>  'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0?
>>>>
>>>>> library()
>>>> ....
>>>> plier                   Implements the Affymetrix PLIER algorithm
>>>> preprocessCore          A collection of pre-processing functions
>>>> rcapex1a520469fcdf      ** No title available (pre-2.0.0  
>>>> install?) **
>>>> rpart                   Recursive Partitioning
>>>> ...
>>>> ------------------
>>>> Was the CDF not installed properly?  I was given the cdf file,  
>>>> not the
>>>> tar.gz file; otherwise, I'd have used R CMD INSTALL.
>>>>
>>>> Your feedback is very much appreciated.
>>>>
>>>> Thanks,
>>>> Dorothy
>>>> 	[[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
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>>> ------------------------------
>>> Mark Robinson
>>> Epigenetics Laboratory, Garvan
>>> Bioinformatics Division, WEHI
>>> e: m.robinson at garvan.org.au
>>> e: mrobinson at wehi.edu.au
>>> p: +61 (0)3 9345 2628
>>> f: +61 (0)3 9347 0852
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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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