FYI:

I upgraded R to 2.9.0 on a Fedora 10 system:
Installation of the matrix package failed (incompatible library
issues)
------------------------------------------------------------------------------------
I recompiled all of sage to use gfortran
then, from a sage shell, ran

CPPFLAGS=-I"$SAGE_LOCAL"/include; export CPPFLAGS
LIBnn="lib"; export LIBnn

export FC=sage_fortran
export F77=sage_fortran

export SAGE_FORTRAN=/usr/bin/gfortran
export SAGE_FORTRAN_LIB=/usr/lib/

CFLAGS="-I$SAGE_LOCAL/include -L$SAGE_LOCAL/lib/ "$CFLAGS; export
CFLAGS
LDFLAGS="-L$SAGE_LOCAL/lib/ "$LDFLAGS; export LDFLAGS

./configure --prefix="$SAGE_LOCAL" --with-recommended-packages=yes --
enable-R-shlib --with-x=$XSUPPORT --with-readline="$SAGE_LOCAL" --with-
blas="-L$SAGE_LOCAL/lib -lf77blas -latlas" --with-lapack="-L
$SAGE_LOCAL/lib -llapack -lcblas" $SUN_FLAGS


make vignettes
make
make install
--------------------------
cd rpy-1.0.3/
RHOMES="$SAGE_LOCAL"/lib/R; export RHOMES
python setup.py install
--------------------------
>From R, I then installed the packages I normally use
without any further problems.

-gerhard
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