8 files changed, 52 insertions, 5 deletions
diff --git a/config/simple-deprules.d/dev-libs b/config/simple-deprules.d/dev-libs
index 05e4d3b..0303be7 100644
--- a/config/simple-deprules.d/dev-libs
+++ b/config/simple-deprules.d/dev-libs
@@ -16,7 +16,10 @@ dev-libs/boost {
 	The Boost 'program_options' library(http://boost.org) is required.
 }
 
-~dev-libs/glib :: glib
+~dev-libs/glib {
+	glib
+	glib2
+}
 
 ~dev-libs/gmp {
 	libgmp
diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text
index 34f11eb..d6effd6 100644
--- a/config/simple-deprules.d/ignored_text
+++ b/config/simple-deprules.d/ignored_text
@@ -29,6 +29,15 @@
 	rgdal OSX binary packages are also available at the samesite.
 	rgdal OSX binary packages are also available at the same site.
 	probably)
+	Linux and Mac
+	MPICH2 (>= 1.4.1p1) on Windows
+	which is included with standard Mac and Windowsinstallations of Csound. Some Linux distributions package thelibrary file separately from the executible
+	playitbyr creates sound using the csound package
+	which requires the free and open source software synthesizerCsound
+	A valid copy of the Csound library must present.Csound can be downloaded Thelibrary is included in the Windows and Mac OS X binaries
+	binary Linux distributions often package the library separatelyfrom the executible file
+	so for instance on Debian and Ubuntuyou would need the "libcsound64-dev" package.
+	For the MERLIN wrapper
 }
 
 ! :: None
diff --git a/config/simple-deprules.d/media b/config/simple-deprules.d/media
index 5692eac..86790ab 100644
--- a/config/simple-deprules.d/media
+++ b/config/simple-deprules.d/media
@@ -2,7 +2,10 @@
 
 ~media-sound/csound :: csound
 
-~media-gfx/imagemagick :: imagemagick
+~media-gfx/imagemagick {
+	imagemagick
+	Image Magick (for reading non PPM format)
+}
 
 media-gfx/graphviz :: dot from graphviz
 ~media-gfx/graphviz {
@@ -20,3 +23,5 @@ virtual/ffmpeg {
 	FFmpeg(http://ffmpeg.org) for saveVideo()
 	ffmpeg
 }
+
+media-gfx/dcraw :: dcraw(for reading RAW images).
diff --git a/config/simple-deprules.d/nvidia b/config/simple-deprules.d/nvidia
index a508e1b..3ed7ed6 100644
--- a/config/simple-deprules.d/nvidia
+++ b/config/simple-deprules.d/nvidia
@@ -6,6 +6,7 @@ dev-util/nvidia-cuda-toolkit {
 	Nvidia CUDAToolkit (>= release 3.0)
 	Nvidia's CUDA toolkit (>= release 2.3)
 	NVIDIA CUDA Toolkit 3.1 or above
+	NVIDIA CUDAtoolkit
 }
 
 # FIXME cuda-toolkit or sdk?
@@ -22,6 +23,10 @@ dev-util/nvidia-cuda-toolkit {
 	Nvidia's CUDA toolkit (release >= 4.1)
 }
 
+>=dev-util/nvidia-cuda-toolkit-4.5 {
+	Nvidia's CUDA toolkit (>= release 4.5)
+}
+
 >=x11-drivers/nvidia-drivers-270 {
 	Nvidia CUDA driver (>= 270.xx.xx)
 }
diff --git a/config/simple-deprules.d/sci b/config/simple-deprules.d/sci
index 4728a8d..40db728 100644
--- a/config/simple-deprules.d/sci
+++ b/config/simple-deprules.d/sci
@@ -9,7 +9,10 @@
 
 # == math ==
 
-~sci-mathematics/glpk :: glpk
+~sci-mathematics/glpk {
+	glpk
+	GLPK library package (e.g.
+}
 
 ~sci-mathematics/jags :: jags
 sci-mathematics/jags :: jags (see http://mcmc-jags.sourceforge.net)
@@ -51,3 +54,5 @@ sci-physics/root {
 # == visualization ==
 
 ~sci-visualization/ggobi :: ggobi
+
+sci-biology/merlin :: MERLIN(www.sph.umich.edu/csg/abecasis/merlin) must be installed andpointed to in the PATH environment variable.
diff --git a/config/simple-deprules.d/sci-libs b/config/simple-deprules.d/sci-libs
index cb48d04..ea1f25f 100644
--- a/config/simple-deprules.d/sci-libs
+++ b/config/simple-deprules.d/sci-libs
@@ -20,7 +20,7 @@ sci-libs/gdal {
 }
 ~sci-libs/gdal :: gdal
 
-~sci-libs/geos :: {
+~sci-libs/geos {
 	geos
 	for building from source: GEOS
 }
diff --git a/config/simple-deprules.d/selfdeps b/config/simple-deprules.d/selfdeps
index f4e77c7..6a8bf17 100644
--- a/config/simple-deprules.d/selfdeps
+++ b/config/simple-deprules.d/selfdeps
@@ -38,7 +38,7 @@ sci-R/quadprog :: portfolio.optim needs package quadprog
 
 sci-R/rgl :: rgl packages for rendering
 
-~sci-R/sgeostat :: {
+~sci-R/sgeostat {
 	sgeostat.
 	geostat.
 }
@@ -53,3 +53,5 @@ sci-R/xgobi {
 	xgobi must be installed additionally
 	xgobi & xgvis programs: http://www.research.att.com/areas/stat/xgobi/
 }
+
+~sci-R/BayesFactor :: BayesFactorPCL
diff --git a/config/simple-deprules.d/sys b/config/simple-deprules.d/sys
index df2ad0c..482c0e6 100644
--- a/config/simple-deprules.d/sys
+++ b/config/simple-deprules.d/sys
@@ -18,3 +18,21 @@ sys-libs/zlib :: zlib (optional)
 ! {
 	rgl packages for rendering
 }
+
+# Some packages list Rcpp in system dependencies
+~sci-R/Rcpp :: Rcpp
+
+# Split across multiple lines, next line adds Linux and Mac
+>=sys-cluster/openmpi-1.5.4 :: OpenMPI (>= 1.5.4) on Solaris
+
+sci-R/rJava :: JRI
+
+~app-text/pandoc :: Pandoc (http://johnmacfarlane.net/pandoc) forexporting markdown files to other formats.
+
+>=dev-tcltk/tktable-2.9 :: Tktable (>= 2.9
+
+>=app-text/aspell-0.60 :: aspell (>= 0.60
+
+dev-libs/openssl :: OpenSSL library
+
+~app-crypt/dieharder :: DieHarder library