Maybe you can try with the other RHEL clone like CentOS-3: http://install.linux.duke.edu/pub/linux/add-on/distrib/centos-3.1/i386/rpms/R-1.9.0-0.duke.1.el3.i386.rpm http://install.linux.duke.edu/pub/linux/add-on/distrib/centos-3.1/i386/srpms/R-1.9.0-0.duke.1.el3.src.rpm
Best wishes, Muhammad Subianto
On this day 09/08/2004 04:12 PM, Marc Schwartz wrote:
On Mon, 2004-08-09 at 08:13, Dr Mike Waters wrote:
<snip>
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 elsewhere.
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:
http://www.rpm.org/hintskinks/repairdb/
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 root):
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 tarball.
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 occur.
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.
HTH,
Marc
______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html