R help - Apr 2005 - R-2.1.0 search engine works with mozilla browser but notfirefox

> 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.

> 
> 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 

Scott

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