G'day Jenny, On Wed, 28 Feb 2007 16:41:18 -0600 (CST) <[EMAIL PROTECTED]> 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 ______________________________________________ R-help@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.