[gentoo-commits] proj/R_overlay:master commit in: simple-deprules.d/

[André Erdmann]

commit:     e5fc16a751755b9de646d1a2b5b1a7d8016c6e4a
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Jul 30 08:48:31 2012 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Jul 30 08:48:31 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=e5fc16a7

dependency rules

---
 simple-deprules.d/R             |   51 +++++++-
 simple-deprules.d/app           |   12 ++
 simple-deprules.d/app-text      |   20 +++
 simple-deprules.d/compound_deps |   49 +++++++
 simple-deprules.d/dev           |   43 ++++++
 simple-deprules.d/dev-libs      |   57 ++++++++
 simple-deprules.d/dot_remap     |   72 ++++++++++
 simple-deprules.d/gnome         |    5 +
 simple-deprules.d/ignored_text  |   58 ++++++++
 simple-deprules.d/media         |   22 +++
 simple-deprules.d/media-libs    |   42 ++++++
 simple-deprules.d/missing       |  296 +++++++++++++++++++++++++++++++++++++++
 simple-deprules.d/net           |   24 +++
 simple-deprules.d/nvidia        |   27 ++++
 simple-deprules.d/other         |    1 -
 simple-deprules.d/perl          |   12 ++
 simple-deprules.d/sci           |   53 +++++++
 simple-deprules.d/sci-libs      |   73 ++++++++++
 simple-deprules.d/selfdeps      |   60 +++++++-
 simple-deprules.d/sys           |   16 ++
 simple-deprules.d/system.set    |   30 ++++
 simple-deprules.d/unknown       |    6 +
 simple-deprules.d/x11           |   25 ++++
 23 files changed, 1043 insertions(+), 11 deletions(-)

diff --git a/simple-deprules.d/R b/simple-deprules.d/R
index 0bdba02..ac8c3d4 100644
--- a/simple-deprules.d/R
+++ b/simple-deprules.d/R
@@ -1,8 +1,55 @@
+#deptype all
+
 # R versions available in portage:
 #  2.10.1, 2.14.1, 2.14.2, 2.15.0, 2.15.1
 
-# R is always compiled with '--enabled-R-shlib'; from: 'Rserve_0.6.8'
-! :: R must be compiled with --enable-R-shlib if the server is to be built
+#deptype all
 
 # using fuzzy dep matches
 ~dev-lang/R :: R
+
+dev-lang/R[tk] {
+	tcl/tk 8.5
+	Tcl/Tk (>= 8.5)
+	tcltk (but only for the GUI
+}
+
+# always assumed to be provided by dev-lang/R (taken from generate_ebuild)
+% {
+	base
+	compiler
+	datasets
+	graphics
+	grDevices
+	grid
+	methods
+	parallel
+	splines
+	stats
+	stats4
+	tcltk
+	tools
+	utils
+}
+# FIXME, seems to be provided too
+% {
+	stepfun
+	ts
+	package ts
+	package ts (included in the R release)
+}
+# modreg is in stats, according to https://stat.ethz.ch/pipermail/bioconductor/2010-June/034197.html
+! :: modreg
+
+# R is always compiled with '--enabled-R-shlib'
+! {
+	R must be compiled with --enable-R-shlib if the server is to be built
+	R must be compiled with --enable-R-shlib if theserver is to be built
+	Download regular shlib (420 KB) from externalsource ('xls.getshlib()' or manually)
+	R built as a shared object
+	R built as a shared or static (R >= 2.7.0) library
+	R built as a shared orstatic library
+	R-0.64 or later
+	Regular shlib must be obtained from an externalsource (use 'xls.getshlib()' or dl manually).
+	dl regular shlib with 'xls.getshlib()'or manually (~420 KB)
+}

diff --git a/simple-deprules.d/app b/simple-deprules.d/app
new file mode 100644
index 0000000..99ba3c3
--- /dev/null
+++ b/simple-deprules.d/app
@@ -0,0 +1,12 @@
+#deptype sys
+
+app-admin/ec2-api-tools :: ec2-api-tools
+
+# FIXME zip or unzip?
+app-arch/zip :: zip
+
+# FIXME: this is not satisfiable, latest dieharder version in portage is 2.28.1
+app-crypt/dieharder {
+	DieHarder library (>= 2.8.1) fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php
+	DieHarder library (>= 3.31.1) fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php
+}

diff --git a/simple-deprules.d/app-text b/simple-deprules.d/app-text
new file mode 100644
index 0000000..3d1a579
--- /dev/null
+++ b/simple-deprules.d/app-text
@@ -0,0 +1,20 @@
+#deptype sys
+
+app-text/antiword {
+	Antiword (http://www.winfield.demon.nl/) forreading MS Word files
+	antiword for reading MS Word files
+}
+
+~app-text/ghostscript-gpl :: ghostscript
+
+app-text/poppler {
+	pdfinfo andpdftotext for reading PDF
+	pdfinfo and pdftotext from Poppler(http://poppler.freedesktop.org/) for reading PDF
+	pdftotext from Poppler(http://poppler.freedesktop.org/) for reading PDF
+}
+
+# pdflatex?
+app-text/texlive {
+	(PDF)LaTeX (http://www.latex-project.org/) withpdfpages package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs.
+	(PDF)LaTeX for saveLatex()
+}

diff --git a/simple-deprules.d/compound_deps b/simple-deprules.d/compound_deps
new file mode 100644
index 0000000..fa88ae7
--- /dev/null
+++ b/simple-deprules.d/compound_deps
@@ -0,0 +1,49 @@
+#deptype sys
+
+( media-libs/fontconfig media-fonts/corefonts ) {
+	fontconfig and msttcorefonts
+	fontconfig and msttcorefonts recommended)
+}
+
+( net-libs/liboauth net-misc/curl ) {
+	liboauth (>= 0.9.4) liboauth.sourceforge.net andlibcurl http://curl.haxx.se
+}
+
+# FIXME
+( sci-libs/blas-atlas dev-util/nvidia-cuda-toolkit ) {
+	Atlas development build as well as a Nvidia GPU withCUDA support
+}
+
+|| ( dev-libs/libxml2 dev-libs/expat ) {
+	Daniel Veillard's libxml(ftp://ftp.gnome.org/pub/GNOME/sources/libxml/)and/orJim Clark's expat (http://www.jclark.com/xml)
+	Daniel Veillard's libxml(ftp://ftp.gnome.org/pub/GNOME/stable/sources/libxml/)and/orJim Clark's expat (http://www.jclark.com/xml)
+}
+
+( media-libs/tiff >=sci-libs/fftw-3  ) {
+	optional libtiff and fftw3
+}
+
+( sci-libs/gdal sci-libs/proj ) {
+	for building from source: GDAL >= 1.3.1 && GDAL < 1.6.0 (until tested) library from http://www.gdal.org/download.html and PROJ.4 (proj >= 4.4.9) from http://proj.maptools.org/
+	for building from source: GDAL >= 1.3.1 library from http://trac.osgeo.org/gdal/wiki/DownloadSource and PROJ.4 (proj >= 4.4.9) from http://trac.osgeo.org/proj/
+	for building from source: GDAL >= 1.3.1 libraryfrom http://trac.osgeo.org/gdal/wiki/DownloadSource and PROJ.4(proj >= 4.4.9) from http://trac.osgeo.org/proj/
+	for building from source: GDAL >= 1.3.1 library from http://www.gdal.org/download.html and PROJ.4 (proj >= 4.4.9) from http://proj.maptools.org/
+	for building from source: GDAL >= 1.3.1 library from http://www.gdal.org/download.html and PROJ.4 (proj >= 4.4.9) from http://www.remotesensing.org/proj/
+	for building from source: GDAL >= 1.6.0 libraryfrom http://trac.osgeo.org/gdal/wiki/DownloadSource and PROJ.4(proj >= 4.4.9) from http://trac.osgeo.org/proj/
+}
+
+( dev-libs/mpfr dev-libs/gmp ) {
+	http://mpfr.org/) and GMP (GNU Multiple Precision library
+}
+
+|| ( media-gfx/imagemagick media-gfx/graphicsmagick ) {
+	ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) for saveGIF()
+}
+
+|| ( media-gfx/imagemagick media-gfx/graphicsmagick app-office/lyx ) {
+	ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) or LyX(http://www.lyx.org) for saveGIF()
+}
+
+|| ( media-libs/tiff virtual/jpeg ) {
+	libtiff and/or libjpeg
+}

diff --git a/simple-deprules.d/dev b/simple-deprules.d/dev
new file mode 100644
index 0000000..9c256e8
--- /dev/null
+++ b/simple-deprules.d/dev
@@ -0,0 +1,43 @@
+#deptype sys
+
+dev-cpp/gtkmm :: gtkmm-2.4
+
+~dev-db/mongodb :: mongodb
+
+# FIXME: dev-db/postgresql-server ?
+~dev-db/postgresql-base {
+	PostgreSql
+}
+
+# FIXME
+dev-db/unixODBC {
+	An ODBC driver manager and drivers. See README.
+	An ODBC3 driver manager and drivers.
+	An ODBC3 driver manager and drivers. See README.
+	ODBC support and a back end database
+}
+
+dev-java/ant :: ant
+dev-java/jdbc-postgresql:: PostgreSQL JDBCdriver
+
+# lowest python version in portage: 2.5
+~dev-lang/python :: python
+dev-lang/lua :: lua version>= 5.1.4
+~dev-lang/lua :: lua
+
+~dev-tex/pgf :: pgf
+
+dev-tcltk/bwidget :: bwidget
+~dev-tcltk/tktable :: tktable
+
+dev-util/cmake {
+	cmake
+	cmake (http://www.cmake.org)
+}
+
+~virtual/jdk {
+	java
+	Java 1.4 or later
+	Java version
+	java runtime
+}

diff --git a/simple-deprules.d/dev-libs b/simple-deprules.d/dev-libs
new file mode 100644
index 0000000..fadc63b
--- /dev/null
+++ b/simple-deprules.d/dev-libs
@@ -0,0 +1,57 @@
+#deptype sys
+
+~dev-libs/atk :: ATK
+
+dev-libs/boost {
+	Boost
+	Boost C++ libraries (1.31 or greater)
+	Boost library (>= 1.34.0) from http://www.boost.org
+	Boost library (>= 1.34.0) fromhttp://www.boost.org
+	Boost library from http://www.boost.org
+	Boost libraryfrom http://www.boost.org
+	boost headers for smart pointers
+	The Boost 'program_options' library(http://boost.org) is required.
+}
+
+~dev-libs/glib :: glib
+
+~dev-libs/gmp {
+	libgmp
+	gmp
+}
+~dev-libs/gmp {
+	GMP (GNU MP bignum library from http://gmplib.org/)
+	GMP (GNU MP bignum library)
+	GMP (GNU Multiple Precision library
+	http://gmplib.org/)
+}
+
+~dev-libs/libxml2 :: libxml2
+
+~dev-libs/libxslt :: libxslt
+
+dev-libs/mpc {
+	and MPC (Multiple Precision ComplexLibrary
+	http://www.multiprecision.org/)
+}
+
+~dev-libs/mpfr {
+	MPFR (MP Floating-Point Reliable Library
+	mpfr
+	http://mpfr.org/)
+}
+# FIXME versions -> fuzzy
+dev-libs/quantlib {
+	QuantLib libraries must be installed
+	QuantLib library (>= 0.8.1) from http://quantlib.org
+	QuantLib library (>= 0.9.0) from http://quantlib.org
+	QuantLib library (>= 0.9.7) from http://quantlib.org
+	QuantLib library (>= 0.9.7) fromhttp://quantlib.org
+	QuantLib library (>= 0.9.9) fromhttp://quantlib.org
+	QuantLib library from http://quantlib.org
+}
+
+~dev-libs/xerces-c {
+	xerces-c
+	libxerces-c
+}

diff --git a/simple-deprules.d/dot_remap b/simple-deprules.d/dot_remap
new file mode 100644
index 0000000..57d65b1
--- /dev/null
+++ b/simple-deprules.d/dot_remap
@@ -0,0 +1,72 @@
+#deptype pkg
+
+~sci-R/aroma_affymetrix :: aroma.affymetrix
+~sci-R/aroma_apd :: aroma.apd
+~sci-R/aroma_core :: aroma.core
+~sci-R/aroma_light :: aroma.light
+
+~sci-R/bio_infer :: bio.infer
+
+~sci-R/Ckmeans_1d_dp :: Ckmeans.1d.dp
+~sci-R/clim_pact :: clim.pact
+~sci-R/compute_es :: compute.es
+~sci-R/conf_design :: conf.design
+
+~sci-R/data_table :: data.table
+~sci-R/DoE_base :: DoE.base
+~sci-R/DoE_wrapper :: DoE.wrapper
+
+~sci-R/ergm_userterms :: ergm.userterms
+
+~sci-R/FrF2_catlg128 :: FrF2.catlg128
+~sci-R/FunciSNP :: FunciSNP.data
+~sci-R/futile_any :: futile.any
+~sci-R/futile_logger :: futile.logger
+~sci-R/futile_matrix :: futile.matrix
+~sci-R/futile_options :: futile.options
+~sci-R/futile_paradigm :: futile.paradigm
+
+~sci-R/gamlss_data :: gamlss.data
+~sci-R/gamlss_dist :: gamlss.dist
+~sci-R/gamlss_nl :: gamlss.nl
+~sci-R/gamlss_tr :: gamlss.tr
+~sci-R/gamlss_util :: gamlss.util
+~sci-R/GO_db :: GO.db
+
+~sci-R/haplo_score :: haplo_score
+~sci-R/haplo_stats :: haplo_stats
+~sci-R/heapmap_plus :: heatmap.plus
+
+~sci-R/lava_tobit :: lava.tobit
+
+~sci-R/minpack_lm :: minpack.lm
+
+~sci-R/opencpu_encode :: opencpu.encode
+~sci-R/openNLPmodels_en :: openNLPmodels.en
+~sci-R/openNLPmodels_es :: openNLPmodels.es
+~sci-R/operator_tools :: operator.tools
+~sci-R/orloca_es :: orloca.es
+~sci-R/oro_dicom :: oro.dicom
+~sci-R/oro_nifti :: oro.nifti
+
+~sci-R/R_cache :: R.cache
+~sci-R/RcmdrPlugin_IPSUR :: RcmdrPlugin.IPSUR
+~sci-R/R_devices :: R.devices
+~sci-R/R_filesets :: R.filesets
+~sci-R/R_huge :: R.huge
+~sci-R/R_matlab :: R.matlab
+~sci-R/R_methodsS3 :: R.methodsS3
+~sci-R/ROI_plugin_glpk :: ROI.plugin.glpk
+~sci-R/ROI_plugin_quadprog :: ROI.plugin.quadprog
+~sci-R/ROI_plugin_symphony :: ROI.plugin.symphony
+~sci-R/R_oo :: R.oo
+~sci-R/rpart_plot :: rpart.plot
+~sci-R/R_rsp :: R.rsp
+~sci-R/RSQLite_extfuns :: RSQLite.extfuns
+~sci-R/R_utils :: R.utils
+
+~sci-R/Sim_DiffProc :: Sim.DiffProc
+~sci-R/SNPMaP_cdm :: SNPMaP.cdm
+~sci-R/survJamda_data :: survJamda.data
+
+~sci-R/tawny_types :: tawny.types

diff --git a/simple-deprules.d/gnome b/simple-deprules.d/gnome
new file mode 100644
index 0000000..1e85243
--- /dev/null
+++ b/simple-deprules.d/gnome
@@ -0,0 +1,5 @@
+#deptype sys
+
+~gnome-base/libglade :: libglade
+
+gnome-base/libgnome :: GNOME development libraries

diff --git a/simple-deprules.d/ignored_text b/simple-deprules.d/ignored_text
new file mode 100644
index 0000000..909e028
--- /dev/null
+++ b/simple-deprules.d/ignored_text
@@ -0,0 +1,58 @@
+#deptype all
+
+# ignored text
+! {
+	available at <http://csound.sourceforge.net/>. See<http://playitbyr.org/csound.html> for more guidance on settingup Csound.
+	available at<http://csound.sourceforge.net/>. This package uses the sharedlibrary file
+	becauseBRugs does not support other platforms/OS right now.
+	binary Linux distributions often package thelibrary separately from the executible file
+	it is an extension for the R package tcltk that consists of Tclscripts. See README file.
+	all other functions are stand alone)
+	see also the topic 'SoPhy' in the documentation
+	see also the topic'SoPhy' in the documentation
+	see file README
+	see README
+	see README.
+	see ./README.
+	see the cloudRmpi manual (vignette)for details.
+	see topic SoPhy below
+	so for instance onDebian and Ubuntu you would need the "libcsound64-dev" package.See the package web site for more guidance on setup andconfiguration.
+	so for instance onDebian and Ubuntu you would need the "libcsound64-dev" package.See the web site below for more guidance on setup.
+	some Windows variants are supported experimentally
+	your mileage may vary)
+	optional)
+	heavily suggested)
+	hence Windows or Linux
+	$distributions package thelibrary file separately from the executible
+	or INSTALL.windows under Windows
+	standard unix tools (e.g.
+	rgdal OSX binary packages are also available at the samesite.
+	rgdal OSX binary packages are also available at the same site.
+}
+
+! :: None
+
+! {
+	Will use djmrgl or rgl packages for rendering ifpresent
+	Will use djmrgl or rgl packages for rendering if present
+	SYMPHONY for Windows (sources included for otherOSes)
+}
+
+# ignore OSX recommendations
+! {
+	GDAL OSX frameworks built by William Kyngesburye at http://www.kyngchaos.com/ may be used for source installs on OSX
+	GDAL OSXframeworks built by William Kyngesburye athttp://www.kyngchaos.com/ may be used for source installs onOSX
+	GDAL OSXframeworks built by William Kyngesburye athttp://www.kyngchaos.com/ may be used for source installs onOSX.
+}
+
+! {
+	GEOS OSX frameworks built byWilliam Kyngesburye at http://www.kyngchaos.com/ may be usedfor source installs on OSX.
+}
+
+# SoPhy splits its Depends field into windows and linux
+! {
+	windows:Tiff for windows
+	windows: Tiff (libtiff3.dll)
+	windows: Tiff(libtiff3.dll)
+	zlib1.dll and jpeg62.dll
+}

diff --git a/simple-deprules.d/media b/simple-deprules.d/media
new file mode 100644
index 0000000..5692eac
--- /dev/null
+++ b/simple-deprules.d/media
@@ -0,0 +1,22 @@
+#deptype sys
+
+~media-sound/csound :: csound
+
+~media-gfx/imagemagick :: imagemagick
+
+media-gfx/graphviz :: dot from graphviz
+~media-gfx/graphviz {
+	graphviz
+	graphviz version
+}
+
+media-gfx/swftools {
+	SWF Tools (http://swftools.org) forsaveSWF()
+	SWF Tools (http://swftools.org) for saveSWF()
+}
+
+virtual/ffmpeg {
+	FFmpeg (http://ffmpeg.org) for saveVideo()
+	FFmpeg(http://ffmpeg.org) for saveVideo()
+	ffmpeg
+}

diff --git a/simple-deprules.d/media-libs b/simple-deprules.d/media-libs
new file mode 100644
index 0000000..6558f40
--- /dev/null
+++ b/simple-deprules.d/media-libs
@@ -0,0 +1,42 @@
+#deptype sys
+
+~media-libs/flac :: flac
+
+# FIXME: some packages write optional deps into SystemRequirements (e.g. rgl from CRAN)
+media-libs/freetype :: FreeType (optional)
+~media-libs/freetype :: freetype
+media-libs/freetype:2 :: recommended: freetype2
+
+media-libs/gd {
+	libgd (>= 2.0.28 http://www.boutell.com/gd/)
+	libgd (>= 2.0.29 http://www.boutell.com/gd/)
+	libgd (freetype2
+}
+
+media-libs/libpng {
+	libpng(>=1.2.9
+	libpng (optional)
+	libpng(optional)
+}
+~media-libs/libpng {
+	png
+	libpng
+}
+
+~media-libs/libsndfile :: libsndfile
+
+~media-libs/netpbm :: netpbm
+
+media-libs/raptor :: libraptor2 (>= 2.0.0 http://librdf.org/raptor/)
+
+media-libs/tiff :: linux: libtiff (and libtiff-devel)
+~media-libs/tiff {
+	tiff
+	libtiff
+	libtiff-devel
+}
+
+virtual/jpeg {
+	libjpeg
+	jpeg
+}

diff --git a/simple-deprules.d/missing b/simple-deprules.d/missing
new file mode 100644
index 0000000..0cf60b4
--- /dev/null
+++ b/simple-deprules.d/missing
@@ -0,0 +1,296 @@
+#! NOPARSE
+
+# === Notes ===
+
+* BIOC experimental -> these packages could also be included in BIOC-2.10;
+-> solution: try BIOC-2.10 (next test run)
+
+* some packages have multiple 'Depends' fields which results in
+  dep strings like 'R (>= 2.3.0)Depends: tcltk' - fix this
+
+* maybe add dev-lang/R with specific USE flags to deps like lapack
+
+* omegahat?
+
+
+# === missing ===
+ALL
+ALLMLL
+ActiveTcl
+AffymetrixDataTestFiles -- BIOC experimental
+AmpAffyExample -- BIOC experimental
+ArcGIS -- seems to be some proprietary software for windows (which implies that a packages has incorrect OS_type set when reching depres)
+BLACS -- not in portage, http://www.netlib.org/blacs/
+CCl4 -- BIOC experimental
+CLL -- BIOC experimental
+Currently only MS-WIndows OS is supported.* -- result of missing/incorrect OS_type in an R package
+COIN-OR Clp -- not in portage, http://www.coin-or.org/projects/
+CodeDepends -- http://www.omegahat.org/CodeDepends/
+Concorde -- http://www.tsp.gatech.edu/concorde/
+Cytoscape -- http://www.cytoscape.org/, LPGL but wants some information from downloaders
+DLBCL -- BIOC experimental
+Do.db -- BIOC experimental
+DSA -- partDSA from CRAN?
+Goto Blas -- http://www.csar.cfs.ac.uk/user_information/software/maths/goto.shtml?
+EatonEtAlChIPseq -- BIOC 2.10
+Windows -- see Currently...
+Excel --
+FDb.UCSC.tRNAs -- BIOC 2.10
+FEAR -- suggested by Benchmarking from CRAN
+File::Basename; File::Glob -- what's the correct perl dependency?
+MERLIN -- http://www.sph.umich.edu/csg/abecasis/merlin/
+GAPS-JAGS -- described in http://www.rits.onc.jhmi.edu/dbb/custom/A6/Software/CoGAPSDistribution_v1_0/CoGAPSUsersManual.pdf
+GGdata -- BIOC 2.10
+GO -- dev-lang/go, sys-devel/gcc[go], sci-R/GO_db, ...?
+GSVAdata -- BIOC 2.10
+HEEBOdata -- BIOC 2.10
+HaarSeg -- http://webee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm
+Hadoop -- http://hadoop.apache.org/core/
+Hive -- http://hive.apache.org/
+HuExExonProbesetLocation -- BIOC 2.10
+IBGEPesq -- ?
+IBM ILOG CPLEX -- http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/
+ITALICSData -- BIOC
+IlluminaHumanMethylation** -- BIOC
+Img -- (tcl/tk related?)
+Internal files Xba.CQV -- ?
+JRI -- java-related? (deducer from CRAN, openstreetmap from CRAN)
+KEGG -- BIOC
+Komodo Edit -- http://www.openkomodo.com
+LAM MPI -- ?
+MPI2 -- ?
+Linux/64bit -- KEYWORD, not DEPEND!!
+MAGMA shared libraries -- http://icl.cs.utk.edu/magma/software/index.html
+MAQCsubset -- BIOC
+MEEBOdata -- BIOC
+MOSEK -- http://mosek.com/products/mosek/
+Mac OS X -- see Windows / Currently only Windows..
+MoExExonProbesetLocation -- BIOC
+NMMAPSdata -- http://www.ihapss.jhsph.edu/data/NMMAPS/R/ ?
+OpenBUGS -- http://www.openbugs.info/w/
+Oracle Instant Client or Oracle Database Client, Oracle client -- sys-libs/db
+PREDAsampledata -- BIOC
+PVM -- http://www.csm.ornl.gov/pvm/
+PWMEnrich.Dmelanogaster.background -- BIOC
+Platform LSF development libraries -- ?
+PolyPhen.Hsapiens.dbSNP131 -- BIOC
+Protocol Buffer compiler (to create C++ header andsource files from .proto descriptions) and library (version2.2.0 or later) -- dev-libs/protobuf
+RDCOMClient -- http://www.omegahat.org/RDCOMClient/ ==> maybe add omegahat as repo?
+RGTK -- http://www.omegahat.org/RGtk/
+RaExExonProbesetLocation -- BIOC
+Rcompression -- OmegaHat
+Rcpp as sysdep (pcaMethods from BIOC) -- ?
+"TODO!!!" -- sysdeps for svDialogs from CRAN; solution: deps unknown -> fail at ebuild creation
+Win 32-bit -- Windows
+affycompData -- BIOC
+affydata -- BIOC
+SPRNG -- http://sprng.cs.fsu.edu/
+asreml[-R] -- http://www.vsni.co.uk/downloads/asreml
+beadarrayExampleData -- BIOC
+bio3d -- http://mccammon.ucsd.edu/~bgrant/bio3d/download/download.html
+bladderbatch -- BIOC
+we expect to support Linux in future releases -- that's great, but why is it in DEPEND?
+weexpect to support Linux in future releases -- ^
+XMLRPC -- what's the correct dep here?
+breastCancerMAINZ,
+breastCancerNKI,
+breastCancerTRANSBIG,
+breastCancerUNT,
+breastCancerUPP,
+breastCancerVDX -- BIOC
+golubEsets -- BIOC
+genomewidesnp5Crlmm -- BIOC
+hgfocuscdf,
+hgu133acdf,
+hgu133afrmavecs,
+hgu133aprobe,
+hgu133atagcdf,
+hgu133atagprobe,
+hgu133plus2cdf,
+hgu133plus2.db,
+hgu133plus2probe,
+hgu95acdf,
+hgu95av2,
+hgu95av2cdf,
+hgu95av2cdf (>= 2.0.0),
+hgu95av2.db,
+hgu95av2.db (>= 1.13.0),
+hgu95av2probe,
+hgu95av2probe (>= 2.0.0),
+hu6800,
+hu6800.db,
+hu6800.db (>= 1.8.1),
+human370v1cCrlmm,
+human610quadv1bCrlmm,
+humanCHRLOC,
+humanStemCell,
+illuminaHumanv1.db,
+illuminaHumanv3.db,
+iontreeData -- BIOC
+WinBUGS -- Windows only?
+WinEdit -- ^
+tensor -- ?
+expectile -- ? (required for aroma.core et al)
+estrogen -- BIOC
+ecolicdf,
+ecoliLeucine,
+faahKO -- BIOC
+fEcofin -- "could" be in CRAN, to check; https://www.rmetrics.org/
+libsbml -- in portage?; http://sbml.org/Software/libSBML
+ppiData -- BIOC
+polynomial -- polynom?
+Sxslt -- omegahat
+yeastCC,
+yeastExpData,
+yeastNagalakshmi,
+yeastRNASeq -- BIOC
+statconnDCOM -- http://rcom.univie.ac.at/download.html#statconnDCOM
+stdjudem -- BIOC
+survnnet -- ?
+SVGAnnotation -- omegahat
+SuperCurve --  http://bioinformatics.mdanderson.org/Software/supercurve/ or OOMPA repo
+gada - R-Forge?
+gageData -- BIOC
+mpcbs -- R-Forge
+msdata -- BIOC
+bsseqData,
+charmData,
+cMap,
+cnvGSAdata,
+colonCA -- BIOC
+coefplot2 -- R-Forge
+cudaMatrixOps -- cuda-toolkit?
+dChipIO -- ?
+hapmap100kxba,
+hapmapsnp5,
+hapmapsnp6 -- BIOC
+iWidgets -- R-forge?
+kopls -- http://kopls.sourceforge.net/
+pasillaBamSubset, pasilla -- BIOC
+plasmodiumanophelescdf -- BIOC
+rmutil -- http://www.commanster.eu/rcode.html
+Vennerable -- R-Forge
+test3cdf,
+tweeDEseqCountData,
+synapterdata,
+SpikeInSubset,
+snpMatrix,
+simpIntLists,
+serumStimulation,
+RnaSeqTutorial,
+rheumaticConditionWOLLBOLD,
+rae230aprobe,
+rat2302.db,
+pumadata,
+TargetSearchData -- BIOC
+UScensus2000blk -- ?
+spacemakeR -- R-Forge
+sfit -- R package, but where to get?
+ScaLAPACK -- http://www.netlib.org/scalapack/
+SAGA, SAGA-GIS -- http://www.saga-gis.org/en/index.html
+rpcgen -- not in portage
+SGE ?~ (qsub, qstat, optionally qacct) --
+reposTools -- BIOC
+Rdonlp2 -- R-Forge
+pdf2 -- ?
+pairseqsim -- BIOC
+oligoData -- BIOC
+manipulate -- ?
+drosgenome1.db,
+drosophila2probe,
+dyebiasexamples,
+ffpeExampleData,
+fibroEset,
+flowWorkspaceData,
+frmaExampleData,
+gatingMLData,
+gcspikelite,
+geneLenDataBase,
+leeBamViews,
+lumiBarnes,
+lumiHumanIDMapping,
+lungExpression,
+maqcExpression4plex,
+minfiData,
+moe430a,
+mosaicsExample,
+mouse4302.db,
+mvoutData -- BIOC
+lippthread -- ?
+nwPro -- ? http://nws-r.sourceforge.net/
+nlcv -- BIOC?
+miRNATarget -- http://www.microrna.org/microrna/getDownloads.do?
+lqs -- ?
+gmmExtra -- R-Forge?
+glcoxph -- http://datamining.dongguk.ac.kr/R/glcoxph/src/
+notepad.exe -- probably unsatisfiable
+WNdb-3.0.tar.gz -- wordnet.princeton.edu
+"mark.exe (>= 6.2) (or mark32.exe andmark64.exe) and rel_32.exe (see README.txt),
+mark.exe and rel_32.exe (seeREADME.txt)" -- ^notepad.exe
+happy.hbrem -- unknown
+hgu133a.db,
+hgug4112a.db,
+hom.Dm.inp.db,
+hom.Hs.inp.db,
+hom.Mm.inp.db,
+hom.Rn.inp.db,
+hom.Sc.inp.db,
+hugene10sttranscriptcluster.db,
+human.db0,
+lumiHumanAll.db,
+mirbase.db,
+moe430a.db,
+mogene10sttranscriptcluster.db,
+mouse.db0 -- BIOC
+"mSQL-2.0.8 (http://www.Hughes.com.au), mSQL-2.0.8 (http://www.Hughes.com.au) or higher" --
+org.Ag.eg.db,
+org.At.tair.db,
+org.Bt.eg.db,
+org.Ce.eg.db,
+org.Cf.eg.db,
+org.Dm.eg.db,
+org.Dr.eg.db,
+org.EcK12.eg.db,
+org.EcSakai.eg.db,
+org.Gg.eg.db,
+org.Hs.eg.db,
+org.Hs.ipi.db,
+org.Mm.eg.db,
+org.Mmu.eg.db,
+org.Pf.plasmo.db,
+org.Pt.eg.db,
+org.Rn.eg.db,
+org.Sco.eg.db,
+org.Sc.sgd.db,
+org.Ss.eg.db,
+org.Xl.eg.db -- BIOC
+pcaGoPromoter.Hs.hg19,
+pcaGoPromoter.Mm.mm9,
+pcaGoPromoter.Rn.rn4,
+pd.genomewidesnp.5,
+pd.genomewidesnp.6,
+pd.hg18.60mer.expr,
+pd.huex.1.0.st.v2,
+pd.hugene.1.0.st.v1,
+pd.mapping250k.nsp,
+pd.mapping250k.sty,
+pd.mapping50k.hind240,
+pd.mapping50k.xba240,
+rae230a.db,
+ragene10sttranscriptcluster.db,
+rat.db0,
+reactome.db -- BIOC
+TxDb.Dmelanogaster.UCSC.dm3.ensGene,
+TxDb.Hsapiens.UCSC.hg18.knownGene,
+TxDb.Hsapiens.UCSC.hg19.knownGene,
+TxDb.Mmusculus.UCSC.mm9.knownGene -- BIOC
+targetscan.Hs.eg.db,
+targetscan.Mm.eg.db -- BIOC
+seqnames.db,
+SIFT.Hsapiens.dbSNP132 -- BIOC
+SNPlocs.Hsapiens.dbSNP.20100427,
+SNPlocs.Hsapiens.dbSNP.20110815,
+SNPlocs.Hsapiens.dbSNP.20111119 -- BIOC
+RmiR.Hs.miRNA -- BIOC
+SciViews-K -- http://www.sciviews.org/SciViews-K
+Xba.regions -- ?

diff --git a/simple-deprules.d/net b/simple-deprules.d/net
new file mode 100644
index 0000000..b739b80
--- /dev/null
+++ b/simple-deprules.d/net
@@ -0,0 +1,24 @@
+#deptype sys
+
+net-misc/curl {
+	curl (version 7.12.0) http://curl.haxx.se
+	curl (version 7.12.0 or higher)<http://curl.haxx.se>
+	curl (version 7.12.0 or higher) http://curl.haxx.se
+	curl (version 7.12.0 or higher) <http://curl.haxx.se>
+	curl (version 7.14.0 or higher) http://curl.haxx.se
+	you will often have toexplicitly install libcurl-devel to have the header files andthe libcurl library.
+	libcurl (version 7.14.0 or higher)http://curl.haxx.se. On Linux systems
+}
+~net-misc/curl {
+	curl
+	libcurl
+}
+
+# FIXME
+net-libs/czmq :: libzmq
+
+net-misc/s3cmd :: s3cmd
+
+virtual/ssh {
+	ssh daemon on the server side only:see the rreval manual (vignette) for details.
+}

diff --git a/simple-deprules.d/nvidia b/simple-deprules.d/nvidia
new file mode 100644
index 0000000..a508e1b
--- /dev/null
+++ b/simple-deprules.d/nvidia
@@ -0,0 +1,27 @@
+#deptype sys
+
+# lowest cuda version in portage is 3.2
+dev-util/nvidia-cuda-toolkit {
+	NVIDIA CUDA Toolkit (>= release 3.0)
+	Nvidia CUDAToolkit (>= release 3.0)
+	Nvidia's CUDA toolkit (>= release 2.3)
+	NVIDIA CUDA Toolkit 3.1 or above
+}
+
+# FIXME cuda-toolkit or sdk?
+dev-util/nvidia-cuda-toolkit {
+	nvcc (>= release 2.1)
+	nvcc (>= release 2.1) nVidia GPU (compute number >=1.3)
+	nvcc (release 2.3) NVIDIA Cuda Compiler driver
+	nvcc (release 3.0) NVIDIA Cuda Compiler driver
+	nvcc (release >= 3.1) (NVIDIA Cuda Compilerdriver)
+	nvcc release 3.1 (NVIDIA Cuda Compiler driver)
+}
+
+>=dev-util/nvidia-cuda-toolkit-4.1 {
+	Nvidia's CUDA toolkit (release >= 4.1)
+}
+
+>=x11-drivers/nvidia-drivers-270 {
+	Nvidia CUDA driver (>= 270.xx.xx)
+}

diff --git a/simple-deprules.d/other b/simple-deprules.d/other
deleted file mode 100644
index 8b13789..0000000
--- a/simple-deprules.d/other
+++ /dev/null
@@ -1 +0,0 @@
-

diff --git a/simple-deprules.d/perl b/simple-deprules.d/perl
new file mode 100644
index 0000000..c4e460b
--- /dev/null
+++ b/simple-deprules.d/perl
@@ -0,0 +1,12 @@
+#deptype sys
+
+# lowest perl version in portage: 5.8 (masked) -> 5.12
+~dev-lang/perl :: perl
+
+dev-perl/OLE-StorageLite :: OLE::Storage_Lite
+dev-perl/Parse-RecDescent :: Parse::RecDescent
+dev-perl/Spreadsheet-WriteExcel :: Spreadsheet::WriteExcel
+dev-perl/Text-CSV_XS :: Text::CSV_XS
+
+# FIXME: this is very specific, required by WriteXLS from CRAN
+virtual/perl-Encode :: Encode

diff --git a/simple-deprules.d/sci b/simple-deprules.d/sci
new file mode 100644
index 0000000..4728a8d
--- /dev/null
+++ b/simple-deprules.d/sci
@@ -0,0 +1,53 @@
+#deptype sys
+
+# == geo ==
+~sci-geosciences/gmt {
+	libgmt
+	gmt
+}
+~sci-geosciences/grass :: grass
+
+# == math ==
+
+~sci-mathematics/glpk :: glpk
+
+~sci-mathematics/jags :: jags
+sci-mathematics/jags :: jags (see http://mcmc-jags.sourceforge.net)
+
+# lowest octave version in portage is 3.4
+sci-mathematics/octave {
+	Octave (>= 3.2.4) and its development files
+}
+
+# lowest version in portage is 2.3.4-r1
+sci-mathematics/pari {
+	PARI/GP >= 2.3.0 [strongly recommended for logkda()]
+	PARI/GP >= 2.3.0 [strongly recommended forlogkda()]
+	pari/gp
+}
+
+sci-mathematics/singular {
+	Singular (http://www.singular.uni-kl.de) for exactcalculation of the MFR for graphs without splitting edges (onlyfor Unix systems).
+}
+
+~sci-mathematics/yacas :: yacas
+sci-mathematics/yacas {
+	yacas (= 1.0.63) # instructions on home page
+	yacas (>= 1.0.63) # instructions on home page
+}
+
+# == misc ==
+
+# FIXME: correct?
+~sci-misc/netlogo-bin :: NetLogo
+
+# == physics ==
+
+# lowest sci-physics/root version in portage is 5.32.03
+sci-physics/root {
+	root_v5.32.01 <http://root.cern.ch> - See READMEfile for installation instructions.
+}
+
+# == visualization ==
+
+~sci-visualization/ggobi :: ggobi

diff --git a/simple-deprules.d/sci-libs b/simple-deprules.d/sci-libs
new file mode 100644
index 0000000..1b2b1d7
--- /dev/null
+++ b/simple-deprules.d/sci-libs
@@ -0,0 +1,73 @@
+#deptype sys
+
+~sci-libs/armadillo :: armadillo
+
+~sci-libs/cddlib :: cddlib
+
+# lowest fftw-3 version in portage is 3.2.2
+>=sci-libs/fftw-3 {
+	fftw3
+	fftw3 (optional)
+}
+~sci-libs/fftw :: fftw
+
+sci-libs/gdal {
+	GDAL library from http://www.gdal.org/download.html
+	GDAL library from http://www.remotesensing.org/gdal/download.html
+}
+~sci-libs/gdal :: gdal
+
+sci-libs/geos {
+	for building from source: GEOS fromhttp://trac.osgeo.org/geos/
+	for building from source: GEOSfrom http://trac.osgeo.org/geos/
+}
+~sci-libs/geos :: geos
+
+sci-libs/gsl {
+	gsl. Note: users should have GSL installed. Windowsusers: 'consult the README file available in the inst directoryof the source distribution for necessary configurationinstructions'.
+	gsl (with development libraries)
+}
+~sci-libs/gsl {
+	GNU GSL
+	gsl
+	libgsl
+	libgslcblas
+	GNU GSL for the GSL random-number generators
+	GNU GSL forthe GSL random-number generators
+	GNU Scientific Library (GSL)
+}
+
+~sci-libs/hdf5 :: hdf5
+
+~sci-libs/itpp {
+	itpp
+	libitpp
+}
+
+# FIXME: dev-lang/R[lapack]?
+virtual/lapack {
+	LAPACK sharedlibrary
+	LAPACKshared library
+}
+
+sci-libs/lapack-atlas :: lapack_atlas
+
+#FIXME
+sci-libs/libsvm :: SVMlight
+
+~sci-libs/mkl :: Intel MKL
+
+sci-libs/netcdf :: netcdf library version 4.1 or later
+~sci-libs/netcdf :: netcdf
+
+sci-libs/proj :: proj 4.4.6 or higher (http://proj.maptools.org/)
+
+
+# FIXME, portage version is 2.1.21
+sci-libs/udunits :: udunits (>= 1.11.7) or udunits2(>= 2.1.22)
+~sci-libs/udunits {
+	udunits
+	udunits-2
+}
+
+virtual/blas :: blas

diff --git a/simple-deprules.d/selfdeps b/simple-deprules.d/selfdeps
index d3306ad..7350593 100644
--- a/simple-deprules.d/selfdeps
+++ b/simple-deprules.d/selfdeps
@@ -1,8 +1,52 @@
-~fftw
-~sound
-~audio
-~rgl
-~rpanel
-~tuneR
-~flac
-~tcltk
+#deptype pkg
+
+# FIXME: this may be incorrect
+~sci-R/BSgenome {
+	BSgenome.Celegans.UCSC.ce2
+	BSgenome.Dmelanogaster.UCSC.dm3
+	BSgenome.Ecoli.NCBI.20080805
+	BSgenome.Hsapiens.UCSC.hg18
+	BSgenome.Hsapiens.UCSC.hg19
+	BSgenome.Mmusculus.UCSC.mm9
+	BSgenome.Rnorvegicus.UCSC.rn4
+	BSgenome.Scerevisiae.UCSC.sacCer2
+}
+
+sci-R/chron :: get.hist.quote needs packagechron.
+
+# FIXME: correct?
+~sci-R/CoCo {
+	CoCoCore
+	CoCoObjects
+	CoCoRaw
+}
+
+sci-R/csound {
+	A valid copy of the Csound library must be present.Csound can be downloaded from http://www.csounds.com. Thelibrary is included in the default Windows and Mac OS Xdistributions
+	playitbyr creates sound using the csound package
+	which requires the free and open source software synthesizerCsound
+}
+
+~sci-R/mimR :: mim
+
+sci-R/MVA {
+	white.test needs packagemva
+	white.test needs package mva
+}
+
+sci-R/quadprog :: portfolio.optim needs package quadprog
+
+sci-R/rgl :: rgl packages for rendering
+
+~sci-R/sgeostat :: geostat.
+
+sci-R/survival4 :: survival4 if survival models are to be used.
+~sci-R/survival5 :: survival5 for some examples
+sci-R/survival5 :: survival5 if survival models are to be used.
+
+~sci-R/VhayuR :: Vhayu
+
+sci-R/xgobi {
+	xgobi must be installed additionally
+	xgobi & xgvis programs: http://www.research.att.com/areas/stat/xgobi/
+}

diff --git a/simple-deprules.d/sys b/simple-deprules.d/sys
new file mode 100644
index 0000000..3b793d0
--- /dev/null
+++ b/simple-deprules.d/sys
@@ -0,0 +1,16 @@
+#deptype sys
+
+~sys-libs/db {
+	BerkelyDB
+	BerkeleyDB
+	Oracle Berkeley DB 11gR2
+}
+
+~sys-libs/zlib :: zlib
+sys-libs/zlib :: zlib (optional)
+
+# => sys-cluster/
+~virtual/mpi {
+	LamMPI(>= 6.5.9) or MPICH2(>= 1.0.2) or OpenMPI ()
+	LamMpi(>= 6.5.9) or Mpich2(>= 1.0.2)
+}

diff --git a/simple-deprules.d/system.set b/simple-deprules.d/system.set
new file mode 100644
index 0000000..7ee9fdc
--- /dev/null
+++ b/simple-deprules.d/system.set
@@ -0,0 +1,30 @@
+#deptype sys
+
+# @system
+! {
+	GNU Make
+	andg++ GNU compiler (a nvcc-compatible version of g++ is needed
+	andg++ GNU compiler version 3.4 (version 4.4 is not yet compatiblewith nvcc).
+	chmod)
+}
+
+% :: gcc
+# FIXME: newer gcc versions could work, too
+<sys-devel/gcc-4.4 :: gcc/g++ version 4.4 is not yet compatible with nvcc).
+<=sys-devel/gcc-4.5 :: gcc (release <= 4.5).
+
+
+# always provided? (except for Gentoo/*BSD)
+! {
+	Linux operating system.
+	Linuxoperationg system
+}
+# always provided
+! {
+	POSIX-compliant OS (essentially anything but Windows)
+	POSIX-compliant OS (essentially anything butWindows
+	POSIX-compliant OS (essentially anything butWindows)
+	Unix
+}
+
+

diff --git a/simple-deprules.d/unknown b/simple-deprules.d/unknown
new file mode 100644
index 0000000..939c77d
--- /dev/null
+++ b/simple-deprules.d/unknown
@@ -0,0 +1,6 @@
+#deptype sys
+
+# FIXME: which library is meant?
+! {
+	A C library with the fesetround/fegetroundfunctions.
+}

diff --git a/simple-deprules.d/x11 b/simple-deprules.d/x11
new file mode 100644
index 0000000..bb78ed7
--- /dev/null
+++ b/simple-deprules.d/x11
@@ -0,0 +1,25 @@
+#deptype sys
+
+x11-libs/cairo :: cairo (>= 1.2 http://www.cairographics.org/)
+~x11-libs/cairo :: cairo
+
+~x11-libs/gtk+ :: gtk+
+
+~x11-libs/pango :: pango
+
+x11-libs/qt-core {
+	qt
+	Qt4 libraries and headers (http://qt.nokia.com)
+}
+
+x11-misc/xclip {
+	xclip (Linux)
+}
+
+virtual/opencl {
+	OpenCL library
+	OpenCl
+}
+
+~virtual/glu :: GLU Library
+virtual/opengl :: opengl