[Rd] R and F9

[Marc Schwartz]

Hi all,

Being the glutton for self-inflicted punishment that I am, I did a clean
install of F9 yesterday.  :-)

As it relates to R:

1. Building R from SVN:

   R version 2.7.0 Patched (2008-05-12 r45683)

It builds and passes make check all without issue. F9 is using:

   gcc (GCC) 4.3.0 20080428 (Red Hat 4.3.0-8)


2. As was noted with F8, the lack of the Java-JavaScript bridge in the
default IcedTea Java engine still precludes the functioning of the
help.start() search engine. Note that the R java applet WILL start, but
the actual search function will not execute.

I had reported this for F8 last December in:

   https://bugzilla.redhat.com/show_bug.cgi?id=420781

but the key bug report to follow for updates will be:

   https://bugzilla.redhat.com/show_bug.cgi?id=304021

In the mean time, one will need to install and use the Sun Java engine
in order to get the R search engine to work properly.



Other miscellaneous observations:

1. F9 is using a pre-release version of Xorg. As a consequence, those
with nVidia cards are going to find themselves between a rock and a hard
place since nVidia is not yet formally supporting this version. The only
real option, which imposes no 3D graphics and no compositing (eg.
CompizFusion) is to use the beta version (173.08) of the nVidia driver
referenced here:

   http://www.nvnews.net/vbulletin/showthread.php?t=111460

Note that I could not get the patched versions of the current release
driver for 2.6.25 kernels to work as is noted in other posts on NVNews.

I have not yet figured out how to boot into 'init 5' successfully, as
one needs to pass the '-ignoreABI' argument to X. I spent some time last
night tracking through the startup scripts and searching through some
posts with suggested fixes, but no joy yet. Thus, for the time being, I
am booting to 'init 3' and using:

   startx -- -ignoreABI

to get into X from the console. Note the use of the two sets of hyphens
in the above. A double hyphen surrounded by spaces followed by the
single hyphen and argument. The use of the -ignoreABI argument will
enable X to start despite that lack of GLX and other module support,
since the current ABI version would otherwise result in conflicts and
errors.

If you want to follow progress and the current flame wars over this
situation, keep an eye on:

   http://www.nvnews.net/vbulletin/forumdisplay.php?s=&forumid=14

One option which has been noted in several forums is to revert F9 to the
F8 version of Xorg and then be careful in using yum and its brethren
when upgrading RPMS.

Note to self: By a laptop with an Intel GPU next time...


2. F9 is also using a beta version of Firefox (version 3 beta 5). I had
played around with it under F8 and it is notably faster than version 2.
Many of the memory leaks have also been resolved. However, note that
many of the extensions for Firefox (eg. Google toolbar) will not yet
function with Firefox 3.


3. The good news is that the install went very well. Anaconda now
supports install-time encryption of disk partitions, which makes this
process easier. I ended up re-partitioning my drive to use LVM, so that
I now have effectively two actual partitions, one for boot, which is in
the clear and the other an LVM group which includes all other partitions
and is encrypted. So far, other than the issues noted above, all seems
stable so far.


I think that covers the key issues. Fedora has definitely moved from
leading edge to bleeding edge with the inclusion of pre-release versions
of key components, so I would urge anyone without a strong stomach to
hold off on the upgrade for a while.

Regards,

Marc Schwartz