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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@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",p ackage="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=%28bui ld%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 > > 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 > > if the package is on my desktop, the == > 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. > >

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",pa ckage="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 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 if the package is on my desktop, the == 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.