[R] R packages install problems linux - X not found (WhiteBoxEL 3)

Marc Schwartz MSchwartz at MedAnalytics.com
Mon Aug 9 16:12:40 CEST 2004

On Mon, 2004-08-09 at 08:13, Dr Mike Waters wrote:


> Marc,
> Sorry for the confusion yesterday - in my defence, it was very hot and humid
> here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). 
> What had happened was that I had done a clean install of WB Linux, including
> the XFree86 and other developer packages. However, the on-line updating
> system updated the XFree86 packages to a newer sub version. It seems that it
> didn't do this correctly for the XFree86 developer package, which was
> missing vital files. However it showed up in the rpm database as being
> installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another
> rpm for this manually and I only forced the upgrade because it was the same
> version as already 'installed' (as far as the rpm database was concerned). I
> assumed that all dependencies were sorted out through the install in the
> first place.

OK, that helps. I still have a lingering concern that, given the facts
above, there may be other integrity issues in the RPM database, if not

>From reading the WB web site FAQ's
(http://www.whiteboxlinux.org/faq.html) , it appears that they are using
up2date/yum for system updates. Depending upon the version in use, there
have been issues especially with up2date (hangs, incomplete updates,
etc.) which could result in other problems. I use yum via the console
here (under FC2), though I note that a GUI version of yum has been
created, including replacing the RHN/up2date system tray alert icon.

A thought relative to this specifically:

If there is or may be an integrity problem related to the rpm database,
you should review the information here:


which provides instructions on repairing the database. Note the
important caveats regarding backups, etc.

The two key steps there are to remove any residual lock files using (as

rm -f /var/lib/rpm/__*

and then rebuilding the rpm database using (also as root):

rpm -vv --rebuilddb

I think that there needs to be some level of comfort that this basic
foundation for the system is intact and correct.

> I only mentioned RH9 to show that I had some familiarity with the RedHat
> policy of separating out the 'includes' etc into a separate developer
> package.
> Once all this had been sorted out, I was then left with a compilation error
> which pointed to a missing dependency or similar, which was not due to
> missing developer packages, but, as you and Prof Ripley correctly point out,
> from the R installation itself. Having grown fat and lazy on using R under
> the MS Windows environment, I was struggling to identify the precise nature
> of this remaining problem.
> As regards the R installation, I did this from the RH9 binary for version
> 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate
> here. Perhaps I should now compile from the source instead?

I would not use the FC2 RPM, since FC2 has many underlying changes not
the least of which includes the use of the 2.6 kernel series and the
change from XFree86 to x.org. Both changes resulted in significant havoc
during the FC2 testing phases and there was at least one issue here with
R due to the change in X.

According to the WB FAQs:

"If you cannot find a package built specifically for RHEL3 or WBEL3 you
can try a package for RH9 since many of the packages in RHEL3 are the
exact same packages as appeared in RH9."

Thus, it would seem reasonable to use the RH9 RPM that Martyn has
created. An alternative would certainly be to compile R from the source

In either case, I would remove the current installation of R and after
achieving a level of comfort that your RPM database is OK, reinstall R
using one of the above methods. Pay close attention to any output during
the installation process, noting any error or warning messages that may

If you go the RPM route, be sure that the MD5SUM of the RPM file matches
the value that Martyn has listed on CRAN to ensure that the file has
been downloaded in an intact fashion.

These are my thoughts at this point. You need to get to a point where
the underlying system is stable and intact, then get R to the same state
before attempting to install new packages.



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