[R] problem with help.start and ?somefunction

[drnevich at uiuc.edu]

Hi all,

I am going to be teaching a workshop next week using R and Bioconductor in one of our university's computer labs. They have recently installed R 2.4.1 for me, and I'm checking all my scripts. I just noticed that using the ?somefunction call to access the documentation for that function is not working. On my own PC, the ? call output changed between R 2.3 and 2.4; before it would open some sort of plain text file and now it opens a nice browser with all the functions of that package listed in a side frame and the function documentation listed in the main window. At the computer lab, calling ?somefunction opens the browser with the functions in the side frame, but the main window says "The page cannot be displayed"

If I try help.start(), I get the warnings below, but it does open the html search page. I'm guessing the two are related, and it might have something to do with this message from 2004:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/30360.html

What do I do? I'm not sure what to tell the sys admin about how to fix the problem... I should mention that I used this same lab over a year ago with R 2.2.1, and didn't have the ? help problem - probably because it wasn't the new browser version of help.

Thanks,
Jenny

> help.start()
updating HTML package listing
updating HTML search index
Warning messages:
1: cannot update HTML package index in: make.packages.html(.libPaths()) 
2: cannot open file 'P:\xpapps\R\R-2.4.1/doc/html/search/index.txt', reason 'Permission denied' 
If nothing happens, you should open 'P:\xpapps\R\R-2.4.1\doc\html\index.html' yourself
Warning message:
cannot update HTML search index in: make.search.html(.libPaths()) 

> sessionInfo()
R version 2.4.1 (2006-12-18) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"    
[7] "datasets"  "methods"   "base"     

other attached packages:
        made4 scatterplot3d          ade4 affycoretools       annaffy 
      "1.8.0"      "0.3-24"       "1.4-2"       "1.7.5"       "1.6.1" 
       xtable         gcrma   matchprobes       biomaRt         RCurl 
      "1.4-3"       "2.6.0"       "1.6.0"       "1.8.1"       "0.8-0" 
          XML       GOstats      Category    genefilter      survival 
      "1.4-0"       "2.0.4"       "2.0.3"      "1.12.0"        "2.30" 
         KEGG          RBGL      annotate            GO         graph 
     "1.14.1"      "1.10.0"      "1.12.1"      "1.14.1"      "1.12.0" 
        limma          affy        affyio       Biobase 
      "2.9.8"      "1.12.2"       "1.2.0"      "1.12.2" 
> 
Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066 
e-mail: drnevich at uiuc.edu