I am trying to get affylmGUI working in Rv2.0 on a Mac OS 10.3 machine. The only trouble I am having is with tkrplot. When I try and install it from source, the package installer, or from the "install.packages2" command, I get the following error: > install.packages2("tkrplot") Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download tkrplot from http://www.bioconductor.org//CRANrepository" [1] "Download complete." [1] "Installing tkrplot" * Installing *source* package 'tkrplot' ... configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -I/usr/local/include -I/usr/X11R6/include -I/usr/local/include -fno-common -g -O2 -c tcltkimg.c -o tcltkimg.o tcltkimg.c:1: tk.h: No such file or directory make: ** Removing '/Users/rkakkar/Library/R/library/tkrplot' ** Restoring previous '/Users/rkakkar/Library/R/library/tkrplot' *** [tcltkimg.o] Error 1 ERROR: compilation failed for package 'tkrplot' From URL: http://www.bioconductor.org//CRANrepository tkrplot version 0.0-10 Warning message: Installation of package tkrplot had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > any ideas? Many thanks, Rahul

> -I/usr/local/include -I/usr/local/include -I/usr/X11R6/include > -I/usr/local/include -fno-common -g -O2 -c tcltkimg.c -o tcltkimg.o > tcltkimg.c:1: tk.h: No such file or directory > make: ** Removing '/Users/rkakkar/Library/R/library/tkrplot' > ** Restoring previous '/Users/rkakkar/Library/R/library/tkrplot' > *** [tcltkimg.o] Error 1 > ERROR: compilation failed for package 'tkrplot' > From URL: http://www.bioconductor.org//CRANrepository > tkrplot version 0.0-10 > any ideas? It would appear that you don't have the proper system libraries installed. What that would be specifically, I'm not sure unfortunately.

On Mon, Nov 22, 2004 at 12:03:05PM -0600, Rahul Kakkar wrote: > gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/usr/local/include -I/usr/local/include -I/usr/X11R6/include > -I/usr/local/include -fno-common -g -O2 -c tcltkimg.c -o tcltkimg.o > tcltkimg.c:1: tk.h: No such file or directory Do you have the TclTk headers and libs installed? Guessing not since tk.h isn't found. There are notes on installing TclTk at www.r-project.org under the Mac OS X FAQ. You could also install via fink. + seth

At 12:03pm -0600 22/11/04, Rahul Kakkar wrote: >I am trying to get affylmGUI working in Rv2.0 on a Mac OS 10.3 >machine. The only trouble I am having is with tkrplot. When I try >and install it from source, the package installer, or from the >"install.packages2" command, I get the following error: > I have affylmGUI working in r2.01 and Mac OSX 10.36. I installed R from <http: cran.stat.ucla.edu="" src="" base="" r-2="" r-2.0.1.tar.gz=""> and I also installed tcltk which came with it (its in /usr/local/lib). I installed the Tktable2.8 folder <http: bioinf.wehi.edu.au="" affylmgui="" tktable2.8macosx_x11.zip=""> as was suggested on this list in /usr/local/lib. I then installed the appropriate packages mainly as source. affylmGUI launches ok though I have not done an analysis with this version. Simon

Hi Rahul, I have found tkrplot to be a little tricky to build from source on MacOS X. The reasons for using tkrplot in limmaGUI and affylmGUI were actually only relevant to the Windows operating system when using the MDI (Multiple Document Interface) for R, (avoiding R graphics device and Tk windows "fighting" over which window was on top / focussed). So in the latest affylmGUI, (post-BioC release), you can choose whether to use tkrplot or the regular R graphics device (Quartz for Mac?) from the Plot menu, and on on Mac, the regular R graphics device should be the default now. The latest affylmGUI is at http://bioinf.wehi.edu.au/affylmGUI/ Perhaps tkrplot will be phased out of limmaGUI and affylmGUI eventually - especially as the plots cannot be resized by dragging a corner. Regards, James On Mon, 22 Nov 2004, Rahul Kakkar wrote: > I am trying to get affylmGUI working in Rv2.0 on a Mac OS 10.3 machine. > The only trouble I am having is with tkrplot. When I try and install > it from source, the package installer, or from the "install.packages2" > command, I get the following error: > > > install.packages2("tkrplot") > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download tkrplot from > http://www.bioconductor.org//CRANrepository" > [1] "Download complete." > [1] "Installing tkrplot" > * Installing *source* package 'tkrplot' ... > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/usr/local/include -I/usr/local/include -I/usr/X11R6/include > -I/usr/local/include -fno-common -g -O2 -c tcltkimg.c -o tcltkimg.o > tcltkimg.c:1: tk.h: No such file or directory > make: ** Removing '/Users/rkakkar/Library/R/library/tkrplot' > ** Restoring previous '/Users/rkakkar/Library/R/library/tkrplot' > *** [tcltkimg.o] Error 1 > ERROR: compilation failed for package 'tkrplot' > From URL: http://www.bioconductor.org//CRANrepository > tkrplot version 0.0-10 > > Warning message: > Installation of package tkrplot had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > > > > any ideas? > > Many thanks, > > Rahul > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- ---------------------------------------------------------------------- ---- James Wettenhall Tel: (+61 3) 9345 2629 Division of Genetics and Bioinformatics Fax: (+61 3) 9347 0852 The Walter & Eliza Hall Institute E-mail: wettenhall@wehi.edu.au of Medical Research, Mobile: (+61 / 0 ) 438 527 921 1G Royal Parade, Parkville, Vic 3050, Australia http://www.wehi.edu.au