On Tue, 13 Apr 2004, Simon Kidd wrote: ... > others) packages. Other than some problems with tcltk and limmaGUI ... Yes, last time I installed limmaGUI on Mac OS X, it certainly took some effort. One issue with Mac OS X is that there are two different tcltk's : Aqua Tcl/Tk and X11 Tcl/Tk, and they are not compatible. So if you are installing the Tcl/Tk extensions requied by limmaGUI (Tktable and BWidget) you have to be careful you don't mix these Tcl/Tk versions, otherwise you will get strange errors like "undefined systemWindowBody color". To see your Tcl/Tk search path, type : library(tcltk) tclvalue("auto_path") I think the R-Mac experts (Jan de Leeuw, Stefano Iacus etc.) have been working pretty hard to make the R-Tcl/Tk stuff easier to install on OS X. While I don't use a Mac regularly, I do have access to Macs so if anyone has any specific questions about installing limmaGUI on OS X, I'd be happy to help. There are a few rough notes on http://bioinf.wehi.edu.au/limmaGUI/ Regards, James

Patient Colleagues -- Further follow-up, thanks mostly to Robert Gentleman and Stefano Iacus... It was suggested that I not live with the permissions open in the R framework (because of the security holes that leaves), and that I take another shot at installing the latest version of R GUI for the Mac and the packages as pre-compiled binaries. I dragged the permission- changed R.framework directory tree to the trash, emptied the trash, and started over with the fresh package. Slightly longer story made short: this all worked. I installed the package from the CRAN website, and then used the menu option Packages|Bioconductor|Individual Packages|Ready-to-use Binary to install biobase, affy, and the widget tools. Then I ran the X windows server in Mac OS X (to accommodate the Tcl/tk stuff) before calling expresso with widget=TRUE. Viola. Thanks for the help. Now to converge on some consistent, credible, coherent expression measures... Best regards, Marc Salit -- Dr. Marc Salit Research Chemist NIST Chemical Science and Technology Laboratory 100 Bureau Drive, Stop 8391 Gaithersburg, MD 20899-8391 email: Salit domain NIST.gov voice: +1 301 975-3646 fax: +1 301 869-0413 On Apr 21, 2004, at 6:43 PM, Marc Salit wrote: > Dear Colleagues -- > > A little follow-up is in order -- I've got things going, more or less. > Mostly more. Thanks for the suggestions, which mostly got me on track. > Bioconductor things seem to work in general, it was the affy package > I was having trouble with. I am still having problems with the > 'widget' tools, but have received some leads on that (problems with > tcltk). > > Ok, so I'm running R release version Version 1.9.0 (2004-04-12) , on > Mac OS X 10.3.3 on a PowerMac G5 2.0 GHz dual processor. > > Some things that I did in order to get going: > 1) I installed the Apple Mac OSX developer's tools, which are needed > to compile source. > > 2) I changed owner and permissions on the R.Framework directory, and > everything underneath it to permit r/w access to all users. (From some > of the error messages I was receiving, it seemed that this was > necessary, though your mileage may vary...) > > 3) I downloaded the development version of the affy package > (affy_1.4.23.tar.gz) and installed from the command line. The > 'released' version (affy_1.3.28.tar.gz) would not install this way, it > died while building help for normalize.invariantset (see below). > > normalize.contrast text html latex example > normalize.invariantset text html latex > > ERROR: command (e.g. \url) inside \link > ERROR: building help failed for package 'affy' > ** Removing > '/Library/Frameworks/R.framework/Versions/1.9.0/Resources/library/ > affy' > > And, my problems with tcltk: > > > package.manager() > loading package: widgetTools > Loading required package: tcltk > Error in fun(...) : this isn't a Tk applicationcouldn't connect to > display ":0" > Error: .onLoad failed in loadNamespace > Error in f(libname, pkgname) : Package tcltk not able to be loaded! > Error in library(pkgs[i], character.only = TRUE) : > .First.lib failed > > dchip <- expresso(widget=TRUE) > Loading required package: tkWidgets > Error in expresso(widget = TRUE) : library tkWidgets could not be > found ! > In addition: Warning message: > There is no package called 'tkWidgets' in: library(package, > character.only = TRUE, logical = TRUE, warn.conflicts = > warn.conflicts, > > package.manager() > loading package: tcltk > Error in fun(...) : this isn't a Tk applicationcouldn't connect to > display ":0" > Error: .onLoad failed in loadNamespace > Error in library(pkgs[i], character.only = TRUE) : > package/namespace load failed > > Best regards, > Marc Salit > > On Apr 13, 2004, at 5:15 PM, Marc Salit wrote: > >> Dear Colleagues -- >> >> I've been trying unsuccessfully to use Bioconductor (mostly the affy >> package) on a Mac with OS X 10.3.3, running R with a GUI, either >> 1.8.1 or 1.9.0 beta. I've tried to install Bioconductor with >> getBioC.R, which doesn't work all the way, and also tried to use a >> shell command to install downloaded packages, a la R CMD INSTALL >> /path/to/pkg_version.tar.gz , which also doesn't work all the way >> (stops when it can't find a 'make' command in SHLIB. >> >> Suggestions? Caveats? Will this work? Shall I give up and 'switch' >> back to a PC??? >> >> Cheers & TIA, >> Marc Salit >> >> -- >> Dr. Marc Salit >> Research Chemist >> NIST >> Chemical Science and Technology Laboratory >> 100 Bureau Drive, Stop 8391 >> Gaithersburg, MD 20899-8391 >> email: Salit@NIST.gov >> voice: +1 301 975-3646 >> fax: +1 301 869-0413_______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 5364 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040422/ea79ed40/attachment.bin