Hi,
On Sat, Oct 21, 2017 at 10:47:54AM +1300, François Bissey wrote:
>
>
> > On 21/10/2017, at 10:37, Michael Orlitzky <mich...@orlitzky.com> wrote:
> >
> > On 10/20/2017 11:30 AM, Nils Bruin wrote:
> >> Do we actually get real benefit from packaging R with sage? It seems to
> >> me R is a very popular, very mature piece of software. Isn't it easy to
> >> install R on any of the platforms supported by sage? If that is the
> >> case, wouldn't it be much easier to let sage just work with the
> >> system-wide R if that is available?
> >
> >
> > No, yes, yes.
>
>
> Of course we had those conversations before. sage interfaces with R in two
> ways:
> * directly with the R command line through the pexpect interface
> * through rpy
>
> The first way can happily use system wide R.
> The second is more complicated. We have to build sage’s rpy and rpy
> links directly to libR and that’s where the potential madness comes in,
> libR links to blas/lapack. So there is a potential clash between
> system blas/lapack and sage blas/lapack in rpy.
> This may (or not) be dealt with by being careful in building rpy in sage.
For what it worth, in Sage Debian Live, since i ship R-studio,
R-commander, JGR and Deducer interfaces (they were asked by some people
using SDL to teach R), i modify Sage not to compile R, but to use Debian's
one. For installing rpy2, i just replace
export RHOMES="$SAGE_LOCAL"/lib/R
with
export RHOMES=/usr/lib/R/
in spkg-install (r-base-dev Debian package is supposed to be installed
before Sage is compiled).
So, i guess it could be doable to provide a configure option of the kind
--with-r PATH
for the users that do not want to compile Sage's R but still be able to
use the system's one from Sage.
As of Sage 7.4, doctests pass, but perhaps they are not strong enough to
show a possible blas/lapack conflict (before your email, i supposed that
rpy2 just calls R which calls the blas/lapack it is linked to,
independently of Sage's one, i guess that if rpy2 used local blas/lapack,
then it would have been written in its dependencies).
Ciao,
Thierry
> François
>
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