[BioC] CDF environment for a custom Affy chip

[Oleg Moskvin]

Hi Seth,

Thanks for the reply. The error message does not look too informative:


 -----------------------------------------------------------------
 C:\Program Files\R\R-2.3.0\bin>R CMD INSTALL uwyrhodo1acdf

 *** Installation of uwyrhodo1acdf failed ***

 Removing 'C:/PROGRA~1/R/R-23~1.0/library/uwyrhodo1acdf'

 C:\Program Files\R\R-2.3.0\bin>
 -----------------------------------------------------------------

 As you see, this is run from the "bin" directory of R. I've copied the
 folder generated by makecdfenv there. This may look weird but running it
 from other places (such as /library) results in not finding the R 
executable
 at all! See below.

 -----------------------------------------------------------------
 C:\Program Files\R\R-2.3.0\bin>R CMD INSTALL uwyrhodo1acdf

 *** Installation of uwyrhodo1acdf failed ***

 Removing 'C:/PROGRA~1/R/R-23~1.0/library/uwyrhodo1acdf'

 C:\Program Files\R\R-2.3.0\bin>
 -----------------------------------------------------------------

 This looks like the "path" problem, but frankly, I do not now how to fix
 this in Windows XP (years ago I did edit this under DOS ;)).

 As another possibility, I could supply the original cdf file, if it is
 possible to generate the cdf-environment remotely and then install it from
 zip file. BTW, several other laboratories would be interested in it (the
 Rhodobacter genechip will be commercially available soon).

 Thanks for all the help.

 Oleg


> ----- Original Message ----- 
> From: "Seth Falcon" <sfalcon at fhcrc.org>
> To: "Oleg Moskvin" <ovm at uwyo.edu>
> Sent: Tuesday, May 30, 2006 4:51 PM
> Subject: Re: [BioC] CDF environment for a custom Affy chip
>
>
>> Hi Oleg,
>>
>> "Oleg Moskvin" <ovm at uwyo.edu> writes:
>>> After using Bioconductor with pre-built CDF evironments, I've finally 
>>> faced
>>> a problem of generating a CDF environment for a custom Affy chip. The
>>> makecdfenv utility worked just fine under Linux and the custom CDF
>>> environment is already usable there. However, under Windows (and I do 
>>> need
>>> this as well) the final step of installation (R CMD INSTALL 
>>> uwyrhodo1acdf)
>>> from a command prompt keeps failing, regardless to presence of installed
>>> Perl (as recommened in the manual) etc., etc. The contents of the folder
>>> with the name of the new environment seem to be equal under both Linux
>>> (after installation which is functional) and Windows (after incomplete
>>> installation). Could someone help me with this issue? (I use the latest
>>> R/Bioconductor).
>>
>> Can you provide some further detail on the errors you get on Windows?
>> Perhaps copy/paste the relevant part of the terminal session.
>>
>> Please try to give us as much detail as possible.  For example, exact
>> R version.
>>
>> + seth
>>
>