* [gentoo-commits] proj/R_overlay:gsoc13/next commit in: config/simple-deprules.d/
@ 2013-07-08 22:47 André Erdmann
0 siblings, 0 replies; 6+ messages in thread
From: André Erdmann @ 2013-07-08 22:47 UTC (permalink / raw
To: gentoo-commits
commit: 86103e27ab2b4d6c8df1ce238b0b24ae74fd9d2a
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Jul 8 19:52:13 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Jul 8 19:52:13 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=86103e27
config/dependency rules: mark selfdeps as selfdeps
---
config/simple-deprules.d/selfdeps | 2 +-
config/simple-deprules.d/sys | 2 ++
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/config/simple-deprules.d/selfdeps b/config/simple-deprules.d/selfdeps
index 6a8bf17..2037de2 100644
--- a/config/simple-deprules.d/selfdeps
+++ b/config/simple-deprules.d/selfdeps
@@ -1,4 +1,4 @@
-#deptype pkg
+#deptype pkg,selfdep
# FIXME: this may be incorrect
~sci-R/BSgenome {
diff --git a/config/simple-deprules.d/sys b/config/simple-deprules.d/sys
index 482c0e6..5b899db 100644
--- a/config/simple-deprules.d/sys
+++ b/config/simple-deprules.d/sys
@@ -20,11 +20,13 @@ sys-libs/zlib :: zlib (optional)
}
# Some packages list Rcpp in system dependencies
+@selfdep
~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
+@selfdep
sci-R/rJava :: JRI
~app-text/pandoc :: Pandoc (http://johnmacfarlane.net/pandoc) forexporting markdown files to other formats.
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/R_overlay:gsoc13/next commit in: config/simple-deprules.d/
@ 2013-07-08 22:47 André Erdmann
0 siblings, 0 replies; 6+ messages in thread
From: André Erdmann @ 2013-07-08 22:47 UTC (permalink / raw
To: gentoo-commits
commit: 2a1f9641b2e5aa34e524865fe3fb050236bbc2a0
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Jul 8 19:52:45 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Jul 8 19:52:45 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=2a1f9641
config/dep rules: mark dot_remap for removal
This file should no longer be necessary.
(package-)Dependencies that are unresolvable due to dot issues are bugs (at
least in most cases).
---
config/simple-deprules.d/dot_remap | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/config/simple-deprules.d/dot_remap b/config/simple-deprules.d/dot_remap
index 9b53f32..03aa2f4 100644
--- a/config/simple-deprules.d/dot_remap
+++ b/config/simple-deprules.d/dot_remap
@@ -1,4 +1,10 @@
-#deptype pkg
+#! NOPARSE
+#
+# !!! This file should no longer be necessary
+# (the dynamic selfdep pool is able to remap dots automatically)
+#
+
+#deptype pkg,selfdep
~sci-R/aroma_affymetrix :: aroma.affymetrix
~sci-R/aroma_apd :: aroma.apd
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/R_overlay:gsoc13/next commit in: config/simple-deprules.d/
@ 2013-07-10 15:10 André Erdmann
2013-07-10 16:16 ` [gentoo-commits] proj/R_overlay:master " André Erdmann
0 siblings, 1 reply; 6+ messages in thread
From: André Erdmann @ 2013-07-10 15:10 UTC (permalink / raw
To: gentoo-commits
commit: 509b653311036616423e7cdf70f9bc8cb16a37dd
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Wed Jul 10 14:29:07 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Wed Jul 10 14:29:07 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=509b6533
config/simple-deprules.d: add SLOTted jdk rule
---
config/simple-deprules.d/dev | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index 9c256e8..fe3f41c 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -35,6 +35,17 @@ dev-util/cmake {
cmake (http://www.cmake.org)
}
+# resolve "java 5", "java 1.5" ... as 'virtual/jdk:1.5'
+~virtual/jdk:slotparts=i1.5:restrict=1.5,5.0 {
+ java
+ Java 1.4 or later
+ Java version
+ java runtime
+}
+
+# slot-relative rules take precedence
+# TODO: slot-restricted rules should get a lower priority
+# than "catch-all" slot rules
~virtual/jdk {
java
Java 1.4 or later
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
2013-07-10 15:10 [gentoo-commits] proj/R_overlay:gsoc13/next commit in: config/simple-deprules.d/ André Erdmann
@ 2013-07-10 16:16 ` André Erdmann
0 siblings, 0 replies; 6+ messages in thread
From: André Erdmann @ 2013-07-10 16:16 UTC (permalink / raw
To: gentoo-commits
commit: 509b653311036616423e7cdf70f9bc8cb16a37dd
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Wed Jul 10 14:29:07 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Wed Jul 10 14:29:07 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=509b6533
config/simple-deprules.d: add SLOTted jdk rule
---
config/simple-deprules.d/dev | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index 9c256e8..fe3f41c 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -35,6 +35,17 @@ dev-util/cmake {
cmake (http://www.cmake.org)
}
+# resolve "java 5", "java 1.5" ... as 'virtual/jdk:1.5'
+~virtual/jdk:slotparts=i1.5:restrict=1.5,5.0 {
+ java
+ Java 1.4 or later
+ Java version
+ java runtime
+}
+
+# slot-relative rules take precedence
+# TODO: slot-restricted rules should get a lower priority
+# than "catch-all" slot rules
~virtual/jdk {
java
Java 1.4 or later
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/R_overlay:gsoc13/next commit in: config/simple-deprules.d/
2013-07-16 16:36 [gentoo-commits] proj/R_overlay:master " André Erdmann
@ 2013-07-15 22:31 ` André Erdmann
0 siblings, 0 replies; 6+ messages in thread
From: André Erdmann @ 2013-07-15 22:31 UTC (permalink / raw
To: gentoo-commits
commit: b1717d8475559af7f95250b0cf26034f2ef46ec1
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Jul 15 22:28:03 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Jul 15 22:28:03 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=b1717d84
dependency rules #1
---
config/simple-deprules.d/R | 1 +
config/simple-deprules.d/app-text | 1 +
config/simple-deprules.d/compound_deps | 4 ++++
config/simple-deprules.d/dev | 16 +++++++++++++++-
config/simple-deprules.d/dev-libs | 14 +++++++++++++-
config/simple-deprules.d/ignored_text | 22 ++++++++++++++++++++++
config/simple-deprules.d/media | 8 ++++++++
config/simple-deprules.d/net | 2 ++
config/simple-deprules.d/nvidia | 4 ++++
config/simple-deprules.d/sci | 14 ++++++++++++++
config/simple-deprules.d/sci-libs | 7 ++++++-
config/simple-deprules.d/system.set | 5 +++--
config/simple-deprules.d/x11 | 4 +++-
13 files changed, 96 insertions(+), 6 deletions(-)
diff --git a/config/simple-deprules.d/R b/config/simple-deprules.d/R
index c6fd193..ecb78fd 100644
--- a/config/simple-deprules.d/R
+++ b/config/simple-deprules.d/R
@@ -60,6 +60,7 @@ dev-lang/R[tk] {
! {
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
+ R must be compiled with --enable-R-shlibif the server 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 object.
diff --git a/config/simple-deprules.d/app-text b/config/simple-deprules.d/app-text
index 3d1a579..3edb48f 100644
--- a/config/simple-deprules.d/app-text
+++ b/config/simple-deprules.d/app-text
@@ -16,5 +16,6 @@ app-text/poppler {
# 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 (http://www.latex-project.org/) with'pdfpages' package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs.
(PDF)LaTeX for saveLatex()
}
diff --git a/config/simple-deprules.d/compound_deps b/config/simple-deprules.d/compound_deps
index 2cc54cb..963ee0f 100644
--- a/config/simple-deprules.d/compound_deps
+++ b/config/simple-deprules.d/compound_deps
@@ -45,3 +45,7 @@
|| ( media-libs/tiff virtual/jpeg ) {
libtiff and/or libjpeg
}
+
+( virtual/blas virtual/lapack ) {
+ BLAS/LAPACK libraries
+}
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index fe3f41c..b53100e 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -20,8 +20,22 @@ dev-db/unixODBC {
dev-java/ant :: ant
dev-java/jdbc-postgresql:: PostgreSQL JDBCdriver
+
+# try to slot-match dev-lang/python, but use known slots only
+~dev-lang/python:slotparts=2:restrict=2.5,2.6,2.7,3.1,3.2,3.3 {
+ python
+ python headers
+}
+# else fall back to fuzzy
+~dev-lang/python {
+ python
+}
# lowest python version in portage: 2.5
-~dev-lang/python :: python
+>=dev-lang/python-2.5 {
+ Python (>= 2.4) to run Asciidoc(http://www.python.org/)
+}
+
+
dev-lang/lua :: lua version>= 5.1.4
~dev-lang/lua :: lua
diff --git a/config/simple-deprules.d/dev-libs b/config/simple-deprules.d/dev-libs
index 0303be7..c475a6b 100644
--- a/config/simple-deprules.d/dev-libs
+++ b/config/simple-deprules.d/dev-libs
@@ -14,6 +14,7 @@ dev-libs/boost {
Boost libraryfrom http://www.boost.org
boost headers for smart pointers
The Boost 'program_options' library(http://boost.org) is required.
+ Boost (or the BoostHeaders package)
}
~dev-libs/glib {
@@ -34,7 +35,10 @@ dev-libs/boost {
~dev-libs/libffi :: libffi
-~dev-libs/libpcre :: libpcre
+~dev-libs/libpcre {
+ libpcre
+ pcre
+}
~dev-libs/libxml2 {
xml
@@ -70,3 +74,11 @@ dev-libs/quantlib {
xerces-c
libxerces-c
}
+
+~sys-devel/clang {
+ clang
+}
+
+dev-libs/geoip {
+ GeoIP from MaxMinds
+}
diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text
index d6effd6..b46d7b6 100644
--- a/config/simple-deprules.d/ignored_text
+++ b/config/simple-deprules.d/ignored_text
@@ -35,11 +35,33 @@
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
+ A valid copy of the Csound library must present.Csound can be downloaded Thelibrary is included in the Windows
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
+ Mac
+ Mac OS X
+ Mac OS X binaries
+ Mac.Parallel HDF5
+ Linux/64bit
+ sources are included for other OSes.
+ see readme.txt
+ so for instance on Debian
+ so for instance onDebian
+ Ubuntu you would need the "libcsound64-dev" package.See the package web site for more guidance on setup andconfiguration.
+ Ubuntuyou would need the "libcsound64-dev" package.
+ which is included with standard Mac
+ which requires the free
+ drivers.
+ License
+ its development files
}
+% :: Linux
+
+# how to dependend on ARCHes? -- ignoring it
+! :: Little Endian
+
! :: None
! {
diff --git a/config/simple-deprules.d/media b/config/simple-deprules.d/media
index 86790ab..7e09871 100644
--- a/config/simple-deprules.d/media
+++ b/config/simple-deprules.d/media
@@ -1,6 +1,10 @@
#deptype sys
~media-sound/csound :: csound
+media-sound/csound {
+ open source software synthesizerCsound
+ Windowsinstallations of Csound. Some Linux distributions package thelibrary file separately from the executible
+}
~media-gfx/imagemagick {
imagemagick
@@ -25,3 +29,7 @@ virtual/ffmpeg {
}
media-gfx/dcraw :: dcraw(for reading RAW images).
+
+media-libs/fontconfig {
+ fontconfig
+}
diff --git a/config/simple-deprules.d/net b/config/simple-deprules.d/net
index b739b80..54e8044 100644
--- a/config/simple-deprules.d/net
+++ b/config/simple-deprules.d/net
@@ -8,10 +8,12 @@ net-misc/curl {
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
+ you will oftenhave to explicitly install libcurl-devel to have theheader files
}
~net-misc/curl {
curl
libcurl
+ the libcurl library.
}
# FIXME
diff --git a/config/simple-deprules.d/nvidia b/config/simple-deprules.d/nvidia
index 3ed7ed6..88db79e 100644
--- a/config/simple-deprules.d/nvidia
+++ b/config/simple-deprules.d/nvidia
@@ -27,6 +27,10 @@ dev-util/nvidia-cuda-toolkit {
Nvidia's CUDA toolkit (>= release 4.5)
}
+~dev-util/nvidia-cuda-toolkit {
+ CUDA SDK
+}
+
>=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 40db728..a7d4615 100644
--- a/config/simple-deprules.d/sci
+++ b/config/simple-deprules.d/sci
@@ -39,6 +39,16 @@ sci-mathematics/yacas {
yacas (>= 1.0.63) # instructions on home page
}
+#deptype all
+
+# some packages have glpk in "pkg" deps
+# (FIXME: does glpk in that context refer to an R package?)
+~sci-mathematics/glpk {
+ glpk
+}
+
+#deptype sys
+
# == misc ==
# FIXME: correct?
@@ -56,3 +66,7 @@ sci-physics/root {
~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.
+
+sci-visualization/gnuplot {
+ gnuplot
+}
diff --git a/config/simple-deprules.d/sci-libs b/config/simple-deprules.d/sci-libs
index ea1f25f..abd31d7 100644
--- a/config/simple-deprules.d/sci-libs
+++ b/config/simple-deprules.d/sci-libs
@@ -17,8 +17,12 @@
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
+ for building from source: GDAL
}
-~sci-libs/gdal :: gdal
~sci-libs/geos {
geos
@@ -64,6 +68,7 @@ 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/)
+>=sci-libs/proj-4.4.9 :: PROJ.4(proj >= 4.4.9)
# FIXME, portage version is 2.1.21
diff --git a/config/simple-deprules.d/system.set b/config/simple-deprules.d/system.set
index 7ee9fdc..dc535b1 100644
--- a/config/simple-deprules.d/system.set
+++ b/config/simple-deprules.d/system.set
@@ -13,6 +13,9 @@
<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).
+#sys-devel/gcc[cxx] :: g++ or Microsoft VC++
+! :: g++ or Microsoft VC++
+
# always provided? (except for Gentoo/*BSD)
! {
@@ -26,5 +29,3 @@
POSIX-compliant OS (essentially anything butWindows)
Unix
}
-
-
diff --git a/config/simple-deprules.d/x11 b/config/simple-deprules.d/x11
index bb78ed7..795052a 100644
--- a/config/simple-deprules.d/x11
+++ b/config/simple-deprules.d/x11
@@ -7,10 +7,12 @@ x11-libs/cairo :: cairo (>= 1.2 http://www.cairographics.org/)
~x11-libs/pango :: pango
-x11-libs/qt-core {
+# qt has its own category now
+dev-qt/qtcore {
qt
Qt4 libraries and headers (http://qt.nokia.com)
}
+! :: headers (http://qt.nokia.com)
x11-misc/xclip {
xclip (Linux)
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/R_overlay:gsoc13/next commit in: config/simple-deprules.d/
2013-07-16 16:36 André Erdmann
@ 2013-07-16 16:35 ` André Erdmann
0 siblings, 0 replies; 6+ messages in thread
From: André Erdmann @ 2013-07-16 16:35 UTC (permalink / raw
To: gentoo-commits
commit: d08f6944edc0aacdc2bb19218dd640d0e3d2ee2f
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Tue Jul 16 16:34:25 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Tue Jul 16 16:34:25 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=d08f6944
dependency rules #2
---
config/simple-deprules.d/app-text | 4 ++++
config/simple-deprules.d/dev | 6 +++++-
config/simple-deprules.d/dev-libs | 4 ++++
config/simple-deprules.d/ignored_text | 11 +++++++++++
config/simple-deprules.d/media | 4 ++++
config/simple-deprules.d/media-libs | 8 +++++++-
config/simple-deprules.d/misc | 7 +++++++
config/simple-deprules.d/missing | 13 +------------
config/simple-deprules.d/nvidia | 7 ++++++-
config/simple-deprules.d/sci | 27 +++++++++++++++++++++++++++
config/simple-deprules.d/sys | 10 +++++++++-
config/simple-deprules.d/system.set | 3 +++
config/simple-deprules.d/x11 | 1 +
13 files changed, 89 insertions(+), 16 deletions(-)
diff --git a/config/simple-deprules.d/app-text b/config/simple-deprules.d/app-text
index 3edb48f..d88fb1e 100644
--- a/config/simple-deprules.d/app-text
+++ b/config/simple-deprules.d/app-text
@@ -19,3 +19,7 @@ app-text/texlive {
(PDF)LaTeX (http://www.latex-project.org/) with'pdfpages' package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs.
(PDF)LaTeX for saveLatex()
}
+
+app-text/poppler {
+ pdfinfo
+}
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index b53100e..01603a1 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -41,7 +41,11 @@ dev-lang/lua :: lua version>= 5.1.4
~dev-tex/pgf :: pgf
-dev-tcltk/bwidget :: bwidget
+~dev-tcltk/bwidget {
+ bwidget
+ Tcl/Tk extensions BWidget
+}
+
~dev-tcltk/tktable :: tktable
dev-util/cmake {
diff --git a/config/simple-deprules.d/dev-libs b/config/simple-deprules.d/dev-libs
index c475a6b..b378a9b 100644
--- a/config/simple-deprules.d/dev-libs
+++ b/config/simple-deprules.d/dev-libs
@@ -70,6 +70,10 @@ dev-libs/quantlib {
QuantLib library from http://quantlib.org
}
+~dev-libs/quantlib {
+ QuantLib library
+}
+
~dev-libs/xerces-c {
xerces-c
libxerces-c
diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text
index b46d7b6..a2567e2 100644
--- a/config/simple-deprules.d/ignored_text
+++ b/config/simple-deprules.d/ignored_text
@@ -55,10 +55,21 @@
drivers.
License
its development files
+ library (version2.2.0 or later)
+ libraries(See README.REQ)
}
% :: Linux
+# ignore "Windows" in dependency fields:
+# (a) there's OS_Type for OS restrictions
+# (b) it's a filler word sometimes ("xyz on Solaris, Linux and Windows")
+# (c) windows-only packages usually have more specific windows-only deps
+#
+# That said, add windows-only packages to a "do-not-process" package rule
+#
+! :: Windows
+
# how to dependend on ARCHes? -- ignoring it
! :: Little Endian
diff --git a/config/simple-deprules.d/media b/config/simple-deprules.d/media
index 7e09871..365455f 100644
--- a/config/simple-deprules.d/media
+++ b/config/simple-deprules.d/media
@@ -33,3 +33,7 @@ media-gfx/dcraw :: dcraw(for reading RAW images).
media-libs/fontconfig {
fontconfig
}
+
+media-fonts/corefonts {
+ msttcorefonts
+}
diff --git a/config/simple-deprules.d/media-libs b/config/simple-deprules.d/media-libs
index 6558f40..8b7ba10 100644
--- a/config/simple-deprules.d/media-libs
+++ b/config/simple-deprules.d/media-libs
@@ -29,7 +29,12 @@ media-libs/libpng {
media-libs/raptor :: libraptor2 (>= 2.0.0 http://librdf.org/raptor/)
-media-libs/tiff :: linux: libtiff (and libtiff-devel)
+media-libs/tiff {
+ linux: libtiff (and libtiff-devel)
+ optional libtiff
+ optionally libtiff
+}
+
~media-libs/tiff {
tiff
libtiff
@@ -39,4 +44,5 @@ media-libs/tiff :: linux: libtiff (and libtiff-devel)
virtual/jpeg {
libjpeg
jpeg
+ jpeg libraries
}
diff --git a/config/simple-deprules.d/misc b/config/simple-deprules.d/misc
new file mode 100644
index 0000000..9a1bae1
--- /dev/null
+++ b/config/simple-deprules.d/misc
@@ -0,0 +1,7 @@
+dev-vcs/git {
+ git
+}
+
+>=app-emulation/wine-1.5.26 {
+ wine (>= wine-1.5.26)
+}
diff --git a/config/simple-deprules.d/missing b/config/simple-deprules.d/missing
index 9674bba..ad66be2 100644
--- a/config/simple-deprules.d/missing
+++ b/config/simple-deprules.d/missing
@@ -1,17 +1,6 @@
#! 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?
-
+# this file is out of date
# === missing ===
ALL
diff --git a/config/simple-deprules.d/nvidia b/config/simple-deprules.d/nvidia
index 88db79e..ed77098 100644
--- a/config/simple-deprules.d/nvidia
+++ b/config/simple-deprules.d/nvidia
@@ -1,12 +1,17 @@
#deptype sys
-# lowest cuda version in portage is 3.2
+# lowest cuda version in portage is 4.2.9
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
NVIDIA CUDAtoolkit
+ NVIDIA CUDA Toolkit (>= release 4.0)
+}
+
+>=dev-util/nvidia-cuda-toolkit-5.0 {
+ Nvidia's CUDA toolkit (>= release 5.0)
}
# FIXME cuda-toolkit or sdk?
diff --git a/config/simple-deprules.d/sci b/config/simple-deprules.d/sci
index a7d4615..4e5363a 100644
--- a/config/simple-deprules.d/sci
+++ b/config/simple-deprules.d/sci
@@ -17,6 +17,10 @@
~sci-mathematics/jags :: jags
sci-mathematics/jags :: jags (see http://mcmc-jags.sourceforge.net)
+sci-mathematics/jags {
+ JAGS (>= 3.2.0) (or WinBUGS (>= 1.4) or OpenBUGS(>= 3.2.2))
+}
+
# lowest octave version in portage is 3.4
sci-mathematics/octave {
Octave (>= 3.2.4) and its development files
@@ -39,6 +43,29 @@ sci-mathematics/yacas {
yacas (>= 1.0.63) # instructions on home page
}
+sci-mathematics/octave {
+ Octave (>= 3.2.4)
+}
+
+sci-libs/netcdf {
+ NetCDF4 (4.1 or later) libraries.
+}
+
+# there's also sci-biology/clustalw-mpi
+#
+sci-biology/clustalw {
+ clustalw
+}
+
+sci-biology/ncbi-tools++ {
+ ncbi-blast+
+ ncbi-tools++
+}
+
+sci-mathematics/glpk {
+ libglpk-dev onDebian/Ubuntu)
+}
+
#deptype all
# some packages have glpk in "pkg" deps
diff --git a/config/simple-deprules.d/sys b/config/simple-deprules.d/sys
index 5b899db..b2fa9bd 100644
--- a/config/simple-deprules.d/sys
+++ b/config/simple-deprules.d/sys
@@ -10,9 +10,17 @@
sys-libs/zlib :: zlib (optional)
# => sys-cluster/
-~virtual/mpi {
+virtual/mpi {
LamMPI(>= 6.5.9) or MPICH2(>= 1.0.2) or OpenMPI ()
LamMpi(>= 6.5.9) or Mpich2(>= 1.0.2)
+ OpenMPI (>= 1.5.4) on Linux
+ OpenMPI or MPICH2
+}
+
+# the "... on Windows" line could probably be ignored
+virtual/mpi {
+ MPI2
+ MPICH2 (>=1.4.1p1) on Windows
}
! {
diff --git a/config/simple-deprules.d/system.set b/config/simple-deprules.d/system.set
index dc535b1..828d995 100644
--- a/config/simple-deprules.d/system.set
+++ b/config/simple-deprules.d/system.set
@@ -29,3 +29,6 @@
POSIX-compliant OS (essentially anything butWindows)
Unix
}
+
+# rpcgen is part of glibc
+! :: rpcgen
diff --git a/config/simple-deprules.d/x11 b/config/simple-deprules.d/x11
index 795052a..2858ddd 100644
--- a/config/simple-deprules.d/x11
+++ b/config/simple-deprules.d/x11
@@ -11,6 +11,7 @@ x11-libs/cairo :: cairo (>= 1.2 http://www.cairographics.org/)
dev-qt/qtcore {
qt
Qt4 libraries and headers (http://qt.nokia.com)
+ Qt4 libraries
}
! :: headers (http://qt.nokia.com)
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