Hi all, I'm having some trouble loading Biobase properly upon start up using .Rprofile in a Windows environment. I saw this problem before, but I mistakenly attributed it to a problem in the affy package affecting hist() in my post on 3/21/06 (https://stat.ethz.ch/pipermail/bioconductor/2006-March/012421.html). I get an error when trying to load Biobase itself, or when loading one of the packages that depend on it (see below for examples and sessionInfo) using an .Rprofile file in the working directory that is automatically sourced upon starting R. The error appears to happen because of a problem with the Windows menu in the Rgui, i.e., not finding functions "winMenuNames" or ""winMenuAddItem". I know Windows is not the ideal OS for R, but I'm stuck with it for a while... I should also point out that the error message does not always appear if you are loading several different libraries, in particular when "library(RWinEdt)" comes first, which can lead to problems with functions later like the one I put in my original post. RWinEdt also adds an item on to the menu but doesn't seem to have any problems, so perhaps it's doing something correctly that Biobase is not doing? Thanks, Jenny Example 1) This is with just "library(affy) in the .Rprofile file, although "library(Biobase)" alone produces the same error message: R : Copyright 2006, The R Foundation for Statistical Computing Version 2.3.0 (2006-04-24) 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 Loading required package: methods 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. Error in inherits(x, "factor") : could not find function "winMenuNames" Error: .onAttach failed in 'attachNamespace' Error: package 'Biobase' could not be loaded > source(".rprofile") Loading required package: affy Loading required package: Biobase 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: matchprobes > sessionInfo() Version 2.3.0 (2006-04-24) i386-pc-mingw32 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "tools" "base" other attached packages: gcrma matchprobes affy affyio Biobase "2.4.0" "1.4.0" "1.10.0" "1.0.0" "1.10.0" > Example 2) With only "library(limma)" in the .Rprofile (R welcome stuff deleted): Loading required package: methods Error in f(libname, pkgname) : could not find function "winMenuAddItem" Error in library(limma) : .First.lib failed for 'limma' > ?winMenuAddItem > Example 3) With "library(RWinEdt)" then "library(limma)" in the .Rprofile; no error message, but Biobase is not loaded: Loading required package: methods Loading required package: utils > sessionInfo() Version 2.3.0 (2006-04-24) i386-pc-mingw32 attached base packages: [1] "stats" "graphics" "grDevices" "datasets" "utils" "methods" [7] "base" other attached packages: limma RWinEdt "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

Hi Jenny, Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: > I'm having some trouble loading Biobase properly upon start up using > .Rprofile in a Windows environment. I saw this problem before, but I > mistakenly attributed it to a problem in the affy package affecting hist() > in my post on 3/21/06 > (https://stat.ethz.ch/pipermail/bioconductor/2006-March/012421.html). I get > an error when trying to load Biobase itself, or when loading one of the > packages that depend on it (see below for examples and sessionInfo) using > an .Rprofile file in the working directory that is automatically sourced > upon starting R. The error appears to happen because of a problem with the > Windows menu in the Rgui, i.e., not finding functions "winMenuNames" or > ""winMenuAddItem". Thanks for the detailed report. We will look into and provide a fix as soon as we find one. > I know Windows is not the ideal OS for R, but I'm stuck with it for > a while... I think what you are trying to do is reasonable and we will work for a fix. It should work fine on Windows. In other words, no need for an excuse here :-) > I should also point out that the error message does not always > appear if you are loading several different libraries, in particular > when "library(RWinEdt)" comes first, which can lead to problems with > functions later like the one I put in my original post. RWinEdt also > adds an item on to the menu but doesn't seem to have any problems, > so perhaps it's doing something correctly that Biobase is not doing? That could be a good hint. We'll take a look. And if you haven't heard from us by this time next week, please bug me about it. Thanks, + seth

Hi Jenny -- I guess you have a line like library("Biobase") in .Rprofile. From reading ?.Rprofile, it sounds like what happens is that the code in .Rprofile gets sourced before the standard packages are loaded. So when Biobase goes looking for winMenuNames (which is in the 'utils' package) it doesn't find it. The right thing to do is to have in your .Rprofile something like local({ old <- getOption("defaultPackages") options(defaultPackages = c(old, "Biobase")) }) which adds Biobase to the list of 'default' packages. Martin Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: > Hi all, > > I'm having some trouble loading Biobase properly upon start up using > .Rprofile in a Windows environment. I saw this problem before, but I > mistakenly attributed it to a problem in the affy package affecting hist() > in my post on 3/21/06 > (https://stat.ethz.ch/pipermail/bioconductor/2006-March/012421.html). I get > an error when trying to load Biobase itself, or when loading one of the > packages that depend on it (see below for examples and sessionInfo) using > an .Rprofile file in the working directory that is automatically sourced > upon starting R. The error appears to happen because of a problem with the > Windows menu in the Rgui, i.e., not finding functions "winMenuNames" or > ""winMenuAddItem". I know Windows is not the ideal OS for R, but I'm stuck > with it for a while... I should also point out that the error message does > not always appear if you are loading several different libraries, in > particular when "library(RWinEdt)" comes first, which can lead to problems > with functions later like the one I put in my original post. RWinEdt also > adds an item on to the menu but doesn't seem to have any problems, so > perhaps it's doing something correctly that Biobase is not doing? > > Thanks, > Jenny > > Example 1) This is with just "library(affy) in the .Rprofile file, although > "library(Biobase)" alone produces the same error message: > > R : Copyright 2006, The R Foundation for Statistical Computing > Version 2.3.0 (2006-04-24) > 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 > Loading required package: methods > > 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. > > > Error in inherits(x, "factor") : could not find function "winMenuNames" > Error: .onAttach failed in 'attachNamespace' > Error: package 'Biobase' could not be loaded > > > source(".rprofile") > Loading required package: affy > Loading required package: Biobase > > 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: matchprobes > > sessionInfo() > Version 2.3.0 (2006-04-24) > i386-pc-mingw32 > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > [7] "tools" "base" > > other attached packages: > gcrma matchprobes affy affyio Biobase > "2.4.0" "1.4.0" "1.10.0" "1.0.0" "1.10.0" > > > > > Example 2) With only "library(limma)" in the .Rprofile (R welcome stuff > deleted): > > Loading required package: methods > Error in f(libname, pkgname) : could not find function "winMenuAddItem" > Error in library(limma) : .First.lib failed for 'limma' > > ?winMenuAddItem > > > > Example 3) With "library(RWinEdt)" then "library(limma)" in the .Rprofile; > no error message, but Biobase is not loaded: > > Loading required package: methods > Loading required package: utils > > > sessionInfo() > Version 2.3.0 (2006-04-24) > i386-pc-mingw32 > > attached base packages: > [1] "stats" "graphics" "grDevices" "datasets" "utils" "methods" > [7] "base" > > other attached packages: > limma RWinEdt > "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

Hi Jenny -- Probably in Windows you want to go to Start --> Settings --> Control Panel --> System --> Advanced --> Environment variables and create a new 'User' variable called HOME and with value equal to the path to a directory that 'belongs' to you, e.g., c:\DOCUME~1\jdrnevich Then use the file c:\DOCUME~1\jdrnevich\.Rprofile to store your profile information. The help page for .Rprofile says that R will find this file. There are two advantages to doing things this way. The first is that the .Rprofile will still be found even after you update R. The second is that other users of your computer don't get the 'benefit' of your customization. ('DOCUME~1' is the short name for 'Documents and Settings', and provides a path that has no spaces in it. R handles path names with spaces, but the 'HOME' directory is used by a number of non-windows applications and not all of them are as smart as R. You can figure out what the 'short' name is by going to Start --> Run --> cmd, using DOS commands to navigate to the directory above the directory you are interested in (in this case, c:\), and typing dir /x) Hope that helps, Martin Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: > Hi Martin, > > Thanks for the suggestion. I'm getting better at understanding what's > in the ?.Rprofile help page... The code below works whether it is in a > file called ".Rprofile" in the working directory, or in a file called > "Rprofile.site" in the $R_HOME/etc/ folder (which on my Windows > system, is C:/Program Files/R/R-2.3.0/etc/ for those of you like me > who didn't quite get what $R_HOME means!). I'm going to use the > "Rprofile.site" method so I can continue to set up shortcuts to R with > different default working directories to keep all my projects separate. > > Cheers, > Jenny > > > At 03:27 PM 5/23/2006, Martin Morgan wrote: >>Hi Jenny -- >> >>I guess you have a line like >> >>library("Biobase") >> >>in .Rprofile. From reading ?.Rprofile, it sounds like what happens is >>that the code in .Rprofile gets sourced before the standard packages >>are loaded. So when Biobase goes looking for winMenuNames (which is in >>the 'utils' package) it doesn't find it. >> >>The right thing to do is to have in your .Rprofile something like >> >>local({ >> old <- getOption("defaultPackages") >> options(defaultPackages = c(old, "Biobase")) >>}) >> >>which adds Biobase to the list of 'default' packages. >> >>Martin >> >>Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: >> >> > Hi all, >> > >> > I'm having some trouble loading Biobase properly upon start up using >> > .Rprofile in a Windows environment. I saw this problem before, but I >> > mistakenly attributed it to a problem in the affy package affecting hist() >> > in my post on 3/21/06 >> > >> (https://stat.ethz.ch/pipermail/bioconductor/2006-March/012421.html). I >> get >> > an error when trying to load Biobase itself, or when loading one of the >> > packages that depend on it (see below for examples and sessionInfo) using >> > an .Rprofile file in the working directory that is automatically sourced >> > upon starting R. The error appears to happen because of a problem with the >> > Windows menu in the Rgui, i.e., not finding functions "winMenuNames" or >> > ""winMenuAddItem". I know Windows is not the ideal OS for R, but I'm stuck >> > with it for a while... I should also point out that the error message does >> > not always appear if you are loading several different libraries, in >> > particular when "library(RWinEdt)" comes first, which can lead to problems >> > with functions later like the one I put in my original post. RWinEdt also >> > adds an item on to the menu but doesn't seem to have any problems, so >> > perhaps it's doing something correctly that Biobase is not doing? >> > >> > Thanks, >> > Jenny >> > >> > Example 1) This is with just "library(affy) in the .Rprofile file, >> although >> > "library(Biobase)" alone produces the same error message: >> > >> > R : Copyright 2006, The R Foundation for Statistical Computing >> > Version 2.3.0 (2006-04-24) >> > 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 >> > Loading required package: methods >> > >> > 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. >> > >> > >> > Error in inherits(x, "factor") : could not find function "winMenuNames" >> > Error: .onAttach failed in 'attachNamespace' >> > Error: package 'Biobase' could not be loaded >> > >> > > source(".rprofile") >> > Loading required package: affy >> > Loading required package: Biobase >> > >> > 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: matchprobes >> > > sessionInfo() >> > Version 2.3.0 (2006-04-24) >> > i386-pc-mingw32 >> > >> > attached base packages: >> > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" >> > [7] "tools" "base" >> > >> > other attached packages: >> > gcrma matchprobes affy affyio Biobase >> > "2.4.0" "1.4.0" "1.10.0" "1.0.0" "1.10.0" >> > > >> > >> > >> > Example 2) With only "library(limma)" in the .Rprofile (R welcome stuff >> > deleted): >> > >> > Loading required package: methods >> > Error in f(libname, pkgname) : could not find function "winMenuAddItem" >> > Error in library(limma) : .First.lib failed for 'limma' >> > > ?winMenuAddItem >> > > >> > >> > Example 3) With "library(RWinEdt)" then "library(limma)" in the .Rprofile; >> > no error message, but Biobase is not loaded: >> > >> > Loading required package: methods >> > Loading required package: utils >> > >> > > sessionInfo() >> > Version 2.3.0 (2006-04-24) >> > i386-pc-mingw32 >> > >> > attached base packages: >> > [1] "stats" "graphics" "grDevices" "datasets" "utils" "methods" >> > [7] "base" >> > >> > other attached packages: >> > limma RWinEdt >> > "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