Hi Martin, The patched version works fine - thanks for pointing it out! As for problems installing RWinEdt, do you have WinEdt downloaded and installed? www.winedt.com I've found it to be a useful editor for R - well worth the nominal fee after the trial period has ended. Cheers, Jenny At 01:01 PM 8/11/2006, Martin Morgan wrote: >Hi Jenny -- > >This sounds like a problem that is addressed in the 'patched' version >of 2.3.1, from the CHANGES file: > >R 2.3.1 patched >=============== > >winMenuAdd() could crash when too many menus were added. (PR#8961) > >The patched version is at CRAN: > >R Binaries --> windows --> Base and then hunt fort the link 'r-patched >snapshot build'. > >I haven't been able to test this explicitly with RWinEdt, which does >not seem to want to install easily on my computer. If this is the >solution, then perhaps you could forward a 'solved!' note to the list? > >Martin >-- >Bioconductor > >Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: > > > Hi again, > > > > I have been playing around with the order of loading packages, and as far > > as I can tell, there's nothing specific with affycoretools that's causing > > my Rgui to crash (i.e., shuts down and the Microsoft 'please send error > > report' box pops up). Instead, it has something to do with the order & > type > > of packages that are loaded that add items to the menu bar by themselves, > > or adding more options under 'Vignettes'. Specific combinations of any 3 > > of: affycoretools, RWinEdt, affyPLM or affylmGUI can cause the crash. So > > far, I haven't been able to get it to crash without affycoretools, even if > > I load all the dependencies by themselves, but that may just be because I > > don't know of another package that adds to the menu bar. After playing > > around with this for a while, even combinations of two packages (that > > loaded fine before) started to crash the Rgui until I rebooted my PC. I > > remember having similar sorts of trouble a while back when manually > > downloading zipped packages and installing them via the menu - after doing > > a few, clicking on the menu again in the same R session would cause the > > Rgui to crash. As this may not be specific to Bioconductor (except that > you > > may not put so many items in the menu unless you're using BioC packages), > > I'm cross posting to the R mailing list. > > > > Cheers, > > Jenny > > > > > > At 12:37 PM 8/10/2006, Jenny Drnevich wrote: > >>Hi Jim & all, > >> > >>I'm having trouble getting affycoretools to work. I apparently had > >>downloaded & installed affycoretools before, but had never used it. When I > >>tried to load it today, I got an error message saying I was missing a > >>dependent package, GOstats. So I used biocLite() to download & install > >>GOstats & it's dependencies. Then when I tried to load affycoretools, I > >>crashed my Rgui. I restarted the Rgui a few times in different ways, and > >>each time I tried to load affycoretools, it crashed the Rgui. So then I > >>went and deleted R_HOME/library/affycoretools and tried using biocLite() to > >>get it again. This time it didn't crash, but it gave a warning message > >>about it not containing a vignette (see below for output & sessionInfo). I > >>checked on bioconductor.org, and there is a vignette for affycoretools. I > >>haven't tried any of the functions yet, but I'm worried that something's > >>amiss. Any suggestions on what to check or reload? > >> > >>Thanks, > >>Jenny > >> > >>P.S. It was great to finally meet many of you at the BioC2006 conference! > >> > >> > >>R : Copyright 2006, The R Foundation for Statistical Computing > >>Version 2.3.1 (2006-06-01) > >>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. > >> > >> Natural language support but running in an English locale > >> > >>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 an HTML browser interface to help. > >>Type 'q()' to quit R. > >> > >>Loading required package: affy > >>Loading required package: Biobase > >>Loading required package: tools > >> > >>Welcome to Bioconductor > >> > >> > >> Vignettes contain introductory material. > >> > >> To view, simply type 'openVignette()' or start with 'help(Biobase)'. > >> > >> For details on reading vignettes, see the openVignette help page. > >> > >> > >>Loading required package: affyio > >>Loading required package: affydata > >>Loading required package: Biobase > >>Loading required package: gcrma > >>Loading required package: matchprobes > >>Loading required package: reposTools > >>Loading required package: simpleaffy > >>Loading required package: genefilter > >>Loading required package: survival > >>Loading required package: splines > >>Welcome to 'affyQCReport' V 1.6-1 > >>Further information available at: www.bifix.org > >> mailto: craig.parman at bifix.org > >>Loading required package: ade4 > >>Loading required package: scatterplot3d > >> > >> > source("http://bioconductor.org/biocLite.R") > >> > biocLite("affycoretools") > >> > >>Running getBioC version 0.1.6 with R version 2.3.1 > >>Running biocinstall version 1.8.4 with R version 2.3.1 > >>Your version of R requires version 1.8 of Bioconductor. > >>trying URL > >>'http://bioconductor.org/packages/1.8/bioc/bin/windows/contrib/2.3 /affyc > oretools_1.4.0.zip' > >>Content type 'application/zip' length 10626563 bytes > >>opened URL > >>downloaded 10377Kb > >> > >>package 'affycoretools' successfully unpacked and MD5 sums checked > >> > >>The downloaded packages are in > >> C:\Documents and Settings\drnevich\Local > >>Settings\Temp\RtmpfRnlqb\downloaded_packages > >>updating HTML package descriptions > >> > >> > library(affycoretools) > >> > >>Loading required package: GOstats > >>Loading required package: graph > >>Loading required package: Ruuid > >>Loading required package: GO > >>Loading required package: annotate > >>Loading required package: RBGL > >>Loading required package: xtable > >> > >>Attaching package: 'xtable' > >> > >> > >> The following object(s) are masked from package:graph : > >> > >> label > >> > >>Loading required package: multtest > >>Loading required package: Category > >>Loading required package: KEGG > >>Loading required package: hgu95av2 > >>Warning message: > >>affycoretools contains no vignette, nothing is added to the menu bar in: > >>addVigs2WinMenu("affycoretools") > >> > >> > sessionInfo() > >>Version 2.3.1 (2006-06-01) > >>i386-pc-mingw32 > >> > >>attached base packages: > >>[1] "splines" "tools" "methods" "stats" "graphics" "grDevices" > >>[7] "utils" "datasets" "base" > >> > >>other attached packages: > >>affycoretools GOstats Category hgu95av2 KEGG > >> "1.4.0" "1.6.0" "1.4.1" "1.12.0" "1.12.0" > >> multtest xtable RBGL annotate GO > >> "1.10.2" "1.3-2" "1.8.1" "1.10.0" "1.12.0" > >> graph Ruuid made4 scatterplot3d ade4 > >> "1.10.4" "1.10.0" "1.6.0" "0.3-24" "1.4-1" > >> affyQCReport simpleaffy genefilter survival reposTools > >> "1.10.0" "2.6.0" "1.10.1" "2.26" "1.10.0" > >> affyPLM gcrma matchprobes affydata affy > >> "1.8.0" "2.4.1" "1.4.0" "1.8.0" "1.10.0" > >> affyio Biobase limma RWinEdt > >> "1.0.0" "1.10.0" "2.7.2" "1.7-4" > >> > > >> > >> > >>Jenny Drnevich, Ph.D. > >> > >>Functional Genomics Bioinformatics Specialist > >>W.M. Keck Center for Comparative and Functional Genomics > >>Roy J. Carver Biotechnology Center > >>University of Illinois, Urbana-Champaign > >> > >>330 ERML > >>1201 W. Gregory Dr. > >>Urbana, IL 61801 > >>USA > >> > >>ph: 217-244-7355 > >>fax: 217-265-5066 > >>e-mail: drnevich at uiuc.edu > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor at stat.math.ethz.ch > >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >>Search the archives: > >>http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > Jenny Drnevich, Ph.D. > > > > Functional Genomics Bioinformatics Specialist > > W.M. Keck Center for Comparative and Functional Genomics > > Roy J. Carver Biotechnology Center > > University of Illinois, Urbana-Champaign > > > > 330 ERML > > 1201 W. Gregory Dr. > > Urbana, IL 61801 > > USA > > > > ph: 217-244-7355 > > fax: 217-265-5066 > > e-mail: drnevich at uiuc.edu > > > > ______________________________________________ > > R-help at stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code.

Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: > Hi Martin, > > The patched version works fine - thanks for pointing it out! As for > problems installing RWinEdt, do you have WinEdt downloaded and > installed? www.winedt.com I've found it to be a useful editor for R - > well worth the nominal fee after the trial period has ended. You might also want to take a look at Tinn-R (http://www.sciviews.org/Tinn-R/). It provides a nice IDE for R code on Windows and it is free. + seth