[BioC] CDF package in R (windows)

[Salim Charaniya]

Thanks a lot...
I was able to execute the command R CMD INSTALL cdfpackage. unfortunately there is an error during execution.
the first few steps go well (adding build stamp to DESCRIPTION, installing R files, data files, man source files,....installing help)
(i noticed that a subdirectory named 'chm' is created in packagecdf during execution)
The execution malfunctions at this point and i get the following error 
hhc: not found
cp: cannot stat 'c://packagecdf/chm/packagecdf.chm' no such file or directory
make[1]: ***[chm-packagecdf] Error 1
*** Installation of packagecdf failed ***


Acc to the manual .chm file is created by microsoft help html workshop which i have installed on the computer (and also added to the path). Any idea why i am still getting this error?
Sorry for bothering you guys
Thanks again
Salim


----- Original Message ----
From: Seth Falcon <sfalcon at fhcrc.org>
To: Salim Charaniya <sal_charaniya at yahoo.com>
Cc: bioconductor at stat.math.ethz.ch
Sent: Wednesday, June 6, 2007 4:35:40 PM
Subject: Re: [BioC] CDF package in R (windows)

Salim Charaniya <sal_charaniya at yahoo.com> writes:

> Hi all, i am a relatively new user of bioconductor. i am using R 2.5.0
> installed on windows. I have used bioconductor for processing affy
> data. Last few days i have been trying to develop a CDF package for a
> custom affy array. I downloaded the makecdfenv package and used the
> commands in there to create a cdf package (using the .cdf file). but
> it seems that is not enough in windows environment. I have read the
> instructions in R installation and admin manual. Accordingly i
> installed the windows toolset (active perl, command line tools and
> MinGW compilers (Rtools.exe), inno setup installer). I have also
> changed the path according to the instructions in Rtools.txt. However,
> I cannot understand the following statement in the R manual:
>
> There are a number of options available: use R CMD INSTALL
>
>    
> The same command works in Windows if you have the source-code package
> files (option “Source Package Installation Files” in the installer)
> and toolset (see The Windows toolset) installed.
>
>    
>
> I have tried this command (R cmd install path_for_cdfpackage). But it
> is not recognized as a command and i get an error.  What are these
> source-code package files? Where can i get them? Is there anything
> else that i need to do to create the cdf package?

Is the bin directory of your R also in your PATH?  Your efforts with
makecdfenv should have produced a source package directory.  Can you
try:

c:\<your_path_here>\R-2.5.0\bin\R CMD INSTALL somecdfpackagedir

I think you are close to getting things to work.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org





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