[BioC] make.cdf.package

[Lana Schaffer]

Jim,
Sorry no time for lemon bars for you now.
But next time I see you, you are going to get them.
Lana

----- Original Message ----- 
From: "James W. MacDonald" <jmacdon at med.umich.edu>
To: "Lana Schaffer" <schaffer at scripps.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Friday, January 19, 2007 4:51 PM
Subject: Re: [BioC] make.cdf.package


> 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
>
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not 
> be used for urgent or sensitive issues.
>
>