[R] R packages install problems linux - X not found (WhiteBoxEL 3)
subianto at cs.uu.nl
Mon Aug 9 17:46:38 CEST 2004
Maybe you can try with the other RHEL clone like CentOS-3:
On this day 09/08/2004 04:12 PM, Marc Schwartz wrote:
> On Mon, 2004-08-09 at 08:13, Dr Mike Waters wrote:
>>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
> 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
>>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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