#5634: installing optional R packages is broken
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Reporter: was | Owner: mabshoff
Type: defect | Status: new
Priority: major | Milestone: sage-3.4.1
Component: optional packages | Keywords:
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This email contains a bunch of good ideas for fixing this.
{{{
Mr. Stein,
I was on IRC sage-devel asking about some problems installing new packages
for R. You asked if I could fix it and unfortunately I can not completely
fix it, but I did learn more about the problems preventing it from
working. I was up late waiting for the Formula 1 race to start and so I
had a look at some of the problems with r.install_packages().
1. local/bin/R and/or local/lib/R/bin/R
Not sure why there are two or which gets called ... but one (or both)
seem to be called a lot during R package installation. Anyway, they are
both identical and have an echo line that seems to get piped into gcc
command lines causing many problems.
[from local/bin/R]
echo "WARNING: ignoring environment value of R_HOME"
This may be a total kludge in the grand scheme of things, but redirecting
echo's output to stderr seems to allow many packages (e.g., nortest) to be
built so that they can be used.
[I changed the above echo line in both files to ...]
echo "WARNING: ignoring environment value of R_HOME" 1>&2
2. local/lib/R/etc/Makeconf
Not sure what this fixes as there is still a problem with C++
packages, but the file above has:
CPPFLAGS = -I/home/rick/sage/sage-3.2.3/local/inlcude
The unfortunate character swapping is easily fixed with:
CPPFLAGS = -I/home/rick/sage/sage-3.2.3/local/include
3. local/lib/gcc-lib/i686-pc-linux-gnu/4.0.3/libgcc_s.so.1
I'm not exactly sure what the problem here is, but I believe it has to
do with building C++ libraries with a gcc version that does not match. I
use Fedora 9 and my version of gcc is 4.3.1. When, after making the
changes described above in 1 and 2, I tried to build the R package Matrix
(r.install_packages('Matrix')), the resulting library could not be loaded.
Error in dyn.load(file, ...) :
unable to load shared library
'/home/rick/sage/sage-3.2.3/local/lib/R/library/Matrix/libs/Matrix.so':
/home/rick/sage/sage-3.2.3/local/lib/gcc-lib/i686-pc-linux-
gnu/4.0.3/libgcc_s.so.1: version `GCC_4.2.0' not found (required by
/usr/lib/libstdc++.so.6)
Error: require(Matrix) is not TRUE
Execution halted
ERROR: installing package indices failed
** Removing '/home/rick/sage/sage-3.2.3/local/lib/R/library/Matrix'
There are still some mysteries to be solved but I hope the above is a
start.
Regards,
Richard Graham
}}}
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/5634>
Sage <http://sagemath.org/>
Sage - Open Source Mathematical Software: Building the Car Instead of
Reinventing the Wheel
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