[BioC] make.cdf.package

[James W. MacDonald]

Hi Lana,

Lana Schaffer wrote:
> Hi, I am having the same problem installing a cdf package that I
> usually have. Would you be able to help me out? R version 2.4.0
> (2006-10-03) 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" "methods" "stats" "graphics" "grDevices"
> "utils" [7] "datasets" "base" other attached packages: makecdfenv
> affy affyio Biobase "1.12.0" "1.12.2" "1.2.0" "1.12.2"
> 
>> make.cdf.package("GLYCOv3_Mm.cdf",cdf.path=system.file("extdata",package="makecdfenv"),compress=FALSE,author="Lana
>> Schaffer",maintainer="Lana
>> Schaffer",species="Mus_musculus",package.path=pkgpath)

I'm not sure where you got the idea to build the package like that, but 
it won't work. In all instances, you have to do a two step process.

1.) Make the package
2.) Install the package

Making the package and sticking it in your library directory won't work. 
In addition, to install the package on Windows requires a bit of setup 
because Windows is missing most of the functionality that comes standard 
with more reasonable operating systems. You need to start here:

http://cran.fhcrc.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f

then go here to get the tools you will need:

http://www.murdoch-sutherland.com/Rtools/

You will need everything up to 'Building R itself' except for the cross 
compilers and unicode support. Installing things and getting them 
correct can be a hair-pulling exercise, so you have to be very careful 
to do exactly what is described. Another source of info is here:

http://wiki.fhcrc.org/bioc/HowTo/Build_R_on_Windows?highlight=%28build%29

Scroll down to the section about Tools.

Once you are set up, all you have to do is set your working directory 
somewhere reasonable (_not_ the library directory of your R 
installation) I usually use the desktop. Then make your package:

make.cdf.package("GLYCOv3_Mm.cdf", species="Mus_musculus) ## none of 
that other stuff

Then open a command prompt, and type

RCMD INSTALL <path to package>

This assumes you have your PATH set up correctly. I usually forgo 
putting my path to R in my PATH because it changes. Instead, I cd to (in 
your case)

cd \progra~1\R\R-2.4.0\bin

then

R CMD INSTALL <path to package>

if the package is on my desktop, the <path to package> == 
c:\docume~1\jim\desktop\glycov3mmcdf

note that I use the windows short name for Documents and Settings - you 
cannot have spaces in the path to the package, so type the first six 
letters without a space, then add ~1.

Or, you can send the cdf file to me, and FedEx some lemon bars to my 
lab. When I get the lemon bars, I will build the package for you and 
send it back ;-D Not some packaged lemon bars either - I want real 
lemons and lots of egg yolks...

Best,

Jim


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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