From marc_schwartz at comcast.net  Wed Nov 26 05:52:34 2008
From: marc_schwartz at comcast.net (Marc Schwartz)
Date: Tue, 25 Nov 2008 22:52:34 -0600
Subject: [Rd] Fedora 10, R and yes...help.start()...deja vu all over again...
Message-ID: <492CD612.3040000@comcast.net>

Hi all,

I installed F10 Final today. This was a clean install, not an upgrade
from F9.

Kudos the the Fedora team as the level of maturity noted in the install
process, including using encrypted partitions, keeps getting better with
each release. I'd still like to see easier options in the GUI with
respect to selecting entire groups of applications, rather than having
to go through individual check-boxes. That part of the process took
almost as long as the installation itself.

Nice also to see the RPMFusion repo fully in place, to centralize the
use of multiple former repos (Livna, FreshRPMS, etc.).

I built R version 2.8.0 Patched (2008-11-24 r47019) from SVN and have a
few observations:

1. F10 is using gcc (GCC) 4.3.2 20081105 (Red Hat 4.3.2-7)

2. R passed 'make check-all' without issue

3. When using the help.start() search engine, the "Applet started."
messages appears in the Firefox status line. However, when searching on
any term (eg. "plot") the Search Results page shows:

  No matches for "plot" have been found!

Thus, it would appear that the Java-Javascript bridge is still
non-functional in the OpenJDK (formerly IcedTea) plugin. The following
error messages appear in the R Console when using the search applet with
OpenJDK:

  > ICEDTEAPLUGIN_DEBUG = (null)
  Initializing JVM...
  NOT IMPLEMENTED: virtual nsresult IcedTeaPluginInstance::Start()
  JNLPRuntime already initialized
  NOT IMPLEMENTED: virtual nsresult IcedTeaPluginInstance::Stop()


The instructions available here:

  http://www.mjmwired.net/resources/mjm-fedora-f10.html#java

provide a step by step process to get the Sun JRE installed on F10, with
one additional step not noted there, required due to SELinux. So follow
the steps on the above page. After which, using the search applet you
may still see:

  No matches for "plot" have been found!

If you are running SELinux in Enforcing Mode, you may see an AVC error
pop-up in the SELinux Troubleshooting Panel Applet. Use the following
command:

  sudo restorecon -v /opt/jre1.6/plugin/i386/ns7/libjavaplugin_oji.so

which will re-set the SELinux context for the newly installed Java
plug-in file.

At that point, if all is well, you should subsequently get proper
results from the search applet. You may need to exit from Firefox and
use help.start() again just to be sure that any residual issues are not
present.

If there are any problems, be sure that the 'alternatives' command is
configured to use the Sun JRE. This is a two step process:

1. Use:

  sudo /usr/sbin/alternatives --config java

and be sure that /opt/jre1.6/bin/java is selected as designated by the '+':

There are 3 programs which provide 'java'.

  Selection    Command
-----------------------------------------------
 + 1           /usr/lib/jvm/jre-1.6.0-openjdk/bin/java
   2           /usr/lib/jvm/jre-1.5.0-gcj/bin/java
*  3           /opt/jre1.6/bin/java

Enter to keep the current selection[+], or type selection number: 3


2. Use:

  sudo /usr/sbin/alternatives --config libjavaplugin.so

and be sure that '/opt/jre1.6/plugin/i386/ns7/libjavaplugin_oji.so' is
selected as designated by the '+':

There are 2 programs which provide 'libjavaplugin.so'.

  Selection    Command
-----------------------------------------------
 + 1           /usr/lib/jvm/jre-1.6.0-openjdk/lib/i386/IcedTeaPlugin.so
*  2           /opt/jre1.6/plugin/i386/ns7/libjavaplugin_oji.so

Enter to keep the current selection[+], or type selection number: 2


All in all, everything else is going well so far (save of course my
ongoing frustration with nVidia, but that's another story for another
thread....).

Hope that the above is helpful. Off to bed...

Regards,

Marc Schwartz



[Rd] Fedora 10, R and yes...help.start()...deja vu all over again...
Marc Schwartz