On Fri, 2005-04-29 at 13:04 -0700, Waichler, Scott R wrote: > > I believe the problem is related to the change in the > > installation directory for the updated JVM from Sun. > > > > If you use the jre1.5.0_02 from java.sun.com, then the plugin > > is installed in: > > > > /usr/java/jre1.5.0_02/plugin/i386/ns7/libjavaplugin_oji.so > > Ok, the above pathname is the exact one. Yes, this is the one I used. > > > > > > I just downloaded the updated RPM binary installer from java.sun.com. > > > > A key step here is that you need to remove the old 1.5 version: > > > > rpm -e jre-1.5.0-fcs > > This is not installed on my machine.
OK. That was just in case you have a prior version installed. Though you might want to check in /usr/java to be sure that there are no other versions present. > > > > With both versions installed, there appear to be conflicts. > > The new installer appears to use "rpm -i" rather than "rpm > > -U", which leaves both versions in place. Testing at the site > > below with both versions installed fails. > > > > Once you have properly done the above, then go here: > > > > http://www.java.com/en/download/help/testvm.xml > > > > to test your java plug-in installation. > > Yes, this test page works fine in my Firefox, and about:plugins shows > the Java stuff is present and enabled. And the boxes under Preferences > are checked. > > Java is working in my Firefox, but there is something about the R search > engine it doesn't like. Just to be really clear, this is the page that > appears, but the links and search box inside it don't work: > file:///tmp/RtmpB32234/.R/doc/html/search/SearchEngine.html That is correct. R uses dynamically created pages, which will be in /tmp. Scott, do you have a lot of CRAN/BioC packages installed? If the list of your installed packages is not overly long, why don't you post it back here, or if it is, send it to me offlist. I am wondering if there is an installed package causing problems for the search engine. I am not sure of other possible issues. I did find that there seems to be at least four CRAN packages: 1. PHYLOGR 2. sfsmisc 3. survrec 4. vardiag that seem to have problems with UTF-8 locales. If I run help.start() in my default locale of en_US.UTF-8, I get the following for each of the above packages: > help.start() Making links in per-session dir ... Error in gsub(pattern, replacement, x, ignore.case, extended, fixed) : input string 28 is invalid in this locale The number of the input string does change. I believe that the above error occurs within make.packages.html(). If I change to LANG=C, the above packages do not cause problems, so perhaps they need to be updated for R 2.1.0. I'll drop a separate e-mail to each of the package authors above. Marc ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
