R and parallel BLAS

Running R with parallel BLAS seems to be as easy under Gentoo ~amd64 as: eselect blas set atlas-threads.  Sweet.

update: and rebuild Matrix / MCMCglmm within R, since those are outside portage

update: ... rebuild R with +threads use flag...

update: MCMCglmm uses CSparse so no speed-up, but JAGS should like it.

Minimal Gentoo EBuild for simuPOP

Works on a Gentoo ~amd64

mkdir /usr/local/portage/sci-biology/simuPOP/files -p
cd /usr/local/portage/sci-biology/simuPOP/

In this directory, in a file called "simuPOP-1.0.0-r1.ebuild" put:

# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

DESCRIPTION="simuPOP is a general-purpose individual-based forward-time
population genetics simulation environment."
SRC_URI="http://downloads.sourceforge.net/project/simupop/simupop/${PV}/${P}-src.tar.gz"
HOMEPAGE="http://simupop.sourceforge.net/"
KEYWORDS="~x86 ~amd64"
SLOT="0"
LICENSE="GPL-3"
IUSE=""
DEPEND="
    dev-lang/python
    dev-libs/boost
    dev-lang/swig
    dev-util/scons"
RDEPEND=""
DOCS="README"

inherit distutils

Then add:

PORTDIR_OVERLAY="/usr/local/portage"

at the end of make.conf... or if you already define PORTDIR_OVERLAY, it's
something like (I hear...):

PORTDIR_OVERLAY="$PORTDIR_OVERLAY:/usr/local/portage" 

Then it should build/install with:

ebuild simuPOP manifest
emerge simuPOP

R LOL

R protects the objects "TRUE" and "FALSE" so this fails:

TRUE <- FALSE

The short forms "T" and "F" are defined by default, but they are not protected, so this works:

T <- FALSE

Then we can ask:

isTRUE(T)

Which turns out to return FALSE. I'm sure there is some legacy code which relies on this behavior so we can't change it.

We need an R-3.0