[R] problem with help.start and ?somefunction

[Berwin A Turlach]

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