R help - Feb 2007 - problem with help.start and ?somefunction

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

G'day Jenny,

On Wed, 28 Feb 2007 16:41:18 -0600 (CST)
<drnevich at uiuc.edu> wrote:
> 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. 
Yes, as far as I know, one of the changes on MS Windows from R 2.3.x to
R 2.4.x was that the compiled html help system became the default.  
> 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"
On MS Windows (which is not my preferred platform, so I might use some
inaccurate terminology in the sequel) I always preferred the compiled
html help system.  So I usually asked our IT guys to make that the
default via the etc/Rprofile.site configuration file, and ran into the
same problem you have about a year ago.

In a nutshell, yet another security issue was discovered if compiled
html help files are run over a network.  Hence MS released a patch that
switched this possibility off.  If I remember correctly, the discussion
at:
	http://forums.techarena.in/showthread.php?t=322640&goto=nextnewest

proved to be very helpful to us and enabled us to allow again the use
of compiled help files over the network.  But I never really understood
what the security implications are and what issues really existed.  I
trusted our IT guys to understand that and to decide whether it was
o.k. to make the necessary registry changes to allow compiled html help
again. :-)
> 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, 
No, they are not related. :-)

As the warnings message says, if you say help.start() R tries to update
a file to which it does not have write permissions.  

As I understand it, help.start() runs by default with "update=TRUE"
(you
may want to try "update=FALSE") on MS Windows.  The
"update=TRUE"
options means that the functions make.packages.html() and
make.search.html() are called to update some information (details are
on the help pages of these two functions).  The updated information is
written to a file, in your case
P:\xpapps\R\R-2.4.1/doc/html/search/index.txt, but you have no write
access to this file.  Hence the warning.  This is a problem with how
the permissions are set up on your lab/network.  Not sure how to solve
this one, our lab had a setup where users had write access to the
location of that file, so we never experienced the problem (except
once, when due to a server upgrade the permissions on the lab machines
got messed up).

Hope this helps.

Cheers,

	Berwin