Re: [R] Fedora Core 4

From: Marc Schwartz <MSchwartz_at_mn.rr.com>
Date: Sat 18 Jun 2005 - 22:33:27 EST

In follow up to Prof. Ripley's post, having participated in the referenced r-devel thread, I would note that I have been able to build Version 2.1.1 beta (2005-06-17) and all CRAN packages from source using both FC4 fortran compilers.

However, I am back to using g77 based upon Prof. Ripley's recommendations.

As mentioned, the problem below is likely the mixing and matching of compiled R executables from FC3 and FC4.

Jon, I would recommend re-compiling a full and clean installation of R (including any CRAN packages), using which ever version of R you are running at the moment.

If you did not install the referenced compatibility RPMs during the initial installation, it is available via the Add/Remove Applications GUI: GNOME menu -> Desktop -> System Settings -> Add/Remove Applications

Once the GUI is up, scroll down and select "Development". Then select the 2 packages in the "Legacy Software Development" set, which includes the two "compat" sets of programs. You will need your install CD/DVD to load the RPMS.

Alternatively, you can use:

# yum groupinstall "Legacy Software Development"

from a console as root.

HTH, Marc Schwartz

On Sat, 2005-06-18 at 13:00 +0100, Prof Brian Ripley wrote:
> There has been discussion of this on R-devel in the context of the release
> of 2.1.1.
>
> FC4 contains gfortran, not g77 (unless you install everything when you
> get g77 from gcc-3.2.3 in some compatibility RPM). This is not a bug: R
> compiled on one OS (or even machine) is not expected to work on another.
> -lg2c is part of gcc-3.x.y, and gfortran uses something like -lgfortran
> (FC3's gcc4 didn't use the standard name, so I am being cautious).
>
> I think it is fortuitous that R runs in your tests without crashing:
> libRlapack.so is linked against libg2c.0.0 and actually calls entry points
> in it. (The R executable is also linked but seems to contain no such
> entry points.)
>
> I would suggest installing 2.1.1 on Monday from the sources, or waiting
> for a 2.1.1 RPM. I believe gcc-3.4.4 is still a better choice than
> gcc-4.0.0 on ix86: it runs faster and there are several cases in which
> 4.0.0 appears to give incorrect answers. I am waiting for the eventual
> release of 4.0.1 to test these more thoroughly. (See the notes in the
> R-admin manual: fortunately FC4's gcc4 is just recent enough to avoid the
> showstopper bug.)
>
> On Sat, 18 Jun 2005, Jonathan Baron wrote:
>
> > I had installed R from source on Fedora Core 3. Then I upgraded
> > to Fedora Core 4, but left R alone. R worked fine, until I trued
> > to update.packages(). Even then, many packages updated just
> > fine, but two of them, cluster and mgcv, failed with the
> > following error message (using cluster as an example):
> >
> > gcc -shared -L/usr/local/lib -o cluster.so clara.o daisy.o
> > dysta.o fanny.o meet.o mona.o pam.o spannel.o twins.o -lg2c -lm -lgcc_s
> > /usr/bin/ld: cannot find -lg2c
> > collect2: ld returned 1 exit status
> > make: *** [cluster.so] Error 1
> >
> > I tracked this down as far as I could and got to this page:
> > http://gcc.gnu.org/fortran/usage.html
> > in the section about "Compatability with g77." The problem seems
> > to have something to do with Fortran.
>
> Interesting spelling!
>
> > Before I invest more time, I wonder if someone knows what to do.
> > Options:
> > 1. Re-install R from source.
> > 2. Try the RPM for Fedora Core 4. It isn't in CRAN, but it is in
> > Fedora "extras". R is now part of the Fedora distribution,
> > albeit one of the many things they have put in "extras" in an
> > effort to limit the distribution to 4 CDs.
> > 3. Report a bug. But where? Is it a bug in R?
> > 4. Something else.
>



R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Jun 18 22:52:00 2005

This archive was generated by hypermail 2.1.8 : Fri 03 Mar 2006 - 03:32:51 EST