Although it is questionable if packages should be installed as a minimal or somewhat more complete or full installation, the R package needs dev-tcltk/tktable and dev-tcltk/bwidget for X11 output. I suggest adding these to DEPEND.
Could you perhaps give short instructions how to check that they are needed? I am not familiar with the X11 output part of R. Thanks!
$ssh -Y -l user host ... $ R R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.1 (2004-11-15), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] > library(limmaGUI) Loading required package: limma Loading required package: tcltk limmaGUI can be launched by typing limmaGUI() > limmaGUI() Searching for user-defined limmaGUI commands in /usr/lib/R/library/limmaGUI/etc ... Sourced: hist.R > q() now you should have a nice graphical window. BTW: The -Y is sometimes needed to forward X11 apps (-X isn't enough in few cases). So let's see what happens: # emerge unmerge bwidget tktable $ R R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.1 (2004-11-15), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] > library(limmaGUI) Loading required package: limma Loading required package: tcltk limmaGUI can be launched by typing limmaGUI() > limmaGUI() Error in limmaGUI() : Error occurred in TclRequire("BWidget") > q() Cannot find Tcl/Tk package "BWidget". limmaGUI cannot continue. limmaGUI requires the Tcl/Tk extensions, BWidget and Tktable. You must have Tcl/Tk installed on your computer, not just the minimal Tcl/Tk installation which comes with R (for Windows). If you do have Tcl/Tk installed, including the extensions (e.g. using the ActiveTcl distribution in Windows), make sure that R can find the path to the Tcl library, e.g. C:\Tcl\lib (on Windows) or /usr/lib (on Linux/Unix) or /sw/lib on Mac OSX. If you don't know how to set environment variables in Windows, one way to make sure that R can find the Tcl/Tk extensions Tktable2.8 and bwidget1.6 is to copy them from your ActiveTcl installation e.g. in C:\Tcl\lib into the Tcl subdirectory of your R installation. If you do understand how to set environment variables... make sure that you have the TCL_LIBRARY environment variable set to the appropriate path, e.g.C:\Tcl\lib\tcl8.4 and the MY_TCLTK environment variable set to a non-empty string, e.g. "Yes". If using Windows, be sure to read the R for windows FAQ at http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html If your Tcl/Tk extensions still can't be found, try addTclPath("<path to Tcl library>"). This could be put in $HOME/.Rprofile If you need further instructions, please contact your system administrator and consider emailing r-help@stat.math.ethz.ch, or browse through the R-help archives for a similar question. The URLs for Tktable and BWidget are: http://tktable.sourceforge.net http://tcllib.sourceforge.net
Unless I am mistaken, limmaGUI is not part of the standard R distribution. It is a separate package you have to install yourself. Is that correct?
Oh, sorry, it should be required by BioConductor (www.bioconductor.org), sorry for the wrong "Summary". It's more or less about new package proposal it seems. I think I was tired. It's just hard to track down which Gentoo package to install. :(
Ok, I'll close this then, since Bioconductor is not in Portage. But I'll be warned if I ever try to add it. ;)
