* [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; 17+ 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] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2018-05-28 8:28 Benda XU
0 siblings, 0 replies; 17+ messages in thread
From: Benda XU @ 2018-05-28 8:28 UTC (permalink / raw
To: gentoo-commits
commit: daa3c7277f25c71620679fb439c763a0426ab7e7
Author: Benda Xu <heroxbd <AT> gentoo <DOT> org>
AuthorDate: Mon May 28 08:26:46 2018 +0000
Commit: Benda XU <heroxbd <AT> gentoo <DOT> org>
CommitDate: Mon May 28 08:26:46 2018 +0000
URL: https://gitweb.gentoo.org/proj/R_overlay.git/commit/?id=daa3c727
Update default deprules.
config/simple-deprules.d/R | 19 -------------------
config/simple-deprules.d/app-text | 10 ++++++++++
config/simple-deprules.d/dev | 5 +++++
config/simple-deprules.d/dev-libs | 7 +++++++
config/simple-deprules.d/ignored_text | 6 ++++++
config/simple-deprules.d/net | 4 ++++
config/simple-deprules.d/sci-libs | 6 ++++++
config/simple-deprules.d/system.set | 12 +++++++++++-
config/simple-deprules.d/unknown | 2 ++
config/simple-deprules.d/virtual | 15 +++++++++++++++
10 files changed, 66 insertions(+), 20 deletions(-)
diff --git a/config/simple-deprules.d/R b/config/simple-deprules.d/R
index bf46e87..9106deb 100644
--- a/config/simple-deprules.d/R
+++ b/config/simple-deprules.d/R
@@ -32,25 +32,6 @@ dev-lang/R[tk] {
utils
}
-# recommended packages
-dev-lang/R[-minimal] {
- boot
- class
- cluster
- codetools
- foreign
- KernSmooth
- lattice
- MASS
- Matrix
- mgcv
- nlme
- nnet
- rpart
- spatial
- survival
-}
-
# FIXME, seems to be provided too
% {
stepfun
diff --git a/config/simple-deprules.d/app-text b/config/simple-deprules.d/app-text
index d88fb1e..6e4cdd4 100644
--- a/config/simple-deprules.d/app-text
+++ b/config/simple-deprules.d/app-text
@@ -3,6 +3,7 @@
app-text/antiword {
Antiword (http://www.winfield.demon.nl/) forreading MS Word files
antiword for reading MS Word files
+ Antiword (<http://www.winfield.demon.nl/>) forreading MS Word files
}
~app-text/ghostscript-gpl :: ghostscript
@@ -23,3 +24,12 @@ app-text/texlive {
app-text/poppler {
pdfinfo
}
+
+
+~app-text/pandoc :: pandoc
+app-text/pandoc {
+ pandoc (>= 1.12.3) -http://johnmacfarlane.net/pandoc
+ pandoc with https support
+ Package vignettes based on R Markdown v2 requirePandoc (http://pandoc.org). The function rst2pdf() andvignettes based on reStructuredText require rst2pdf(https://github.com/rst2pdf/rst2pdf).
+}
+
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index 891f264..89759fc 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -33,6 +33,7 @@ dev-java/jdbc-postgresql :: PostgreSQL JDBCdriver
# lowest python version in portage: 2.7 (2.6 masked)
dev-lang/python {
Python (>= 2.4) to run Asciidoc(http://www.python.org/)
+ Python 2.7.x or Python 3.2.x-3.4.x
}
@@ -59,6 +60,10 @@ dev-util/cmake {
cmake (http://www.cmake.org)
}
+~dev-python/numpy {
+ numpy
+}
+
# FIXME: the jdk rules are not quite correct,
# virtual/jdk:1.7 (probably) works for some packages, too
#
diff --git a/config/simple-deprules.d/dev-libs b/config/simple-deprules.d/dev-libs
index b378a9b..b46d2a6 100644
--- a/config/simple-deprules.d/dev-libs
+++ b/config/simple-deprules.d/dev-libs
@@ -2,6 +2,8 @@
~dev-libs/atk :: ATK
+~dev-libs/openssl :: OpenSSL
+
~dev-libs/boost {
boost library
boost
@@ -86,3 +88,8 @@ dev-libs/quantlib {
dev-libs/geoip {
GeoIP from MaxMinds
}
+
+dev-libs/icu {
+ ICU4C (>= 50
+ ICU4C (>= 52
+}
diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text
index bd4e8ae..097f004 100644
--- a/config/simple-deprules.d/ignored_text
+++ b/config/simple-deprules.d/ignored_text
@@ -22,8 +22,10 @@
your mileage may vary)
optional)
heavily suggested)
+ and Windows
hence Windows or Linux
$distributions package thelibrary file separately from the executible
+ libraries(See the INSTALL file)
or INSTALL.windows under Windows
standard unix tools (e.g.
rgdal OSX binary packages are also available at the samesite.
@@ -40,6 +42,7 @@
so for instance on Debian and Ubuntuyou would need the "libcsound64-dev" package.
For the MERLIN wrapper
Mac
+ Mac OSX
Mac OS X
Mac OS X binaries
Mac.Parallel HDF5
@@ -62,6 +65,8 @@
writing some graphicformats
available athttp://www.monetdb.org
it is used in the demos too).
+ headers
+ OpenCSW.
}
# that's a hardware requirement
@@ -87,6 +92,7 @@
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)
+ SYMPHONY libraries
}
# ignore OSX recommendations
diff --git a/config/simple-deprules.d/net b/config/simple-deprules.d/net
index e99087e..ab87ea8 100644
--- a/config/simple-deprules.d/net
+++ b/config/simple-deprules.d/net
@@ -20,6 +20,10 @@ net-misc/curl {
# FIXME
net-libs/czmq :: libzmq
+net-libs/zeromq {
+ or ZeroMQ library >=4.0.4. Solaris 10 needs ZeroMQ library 4.0.7
+}
+
net-misc/s3cmd :: s3cmd
virtual/ssh {
diff --git a/config/simple-deprules.d/sci-libs b/config/simple-deprules.d/sci-libs
index abd31d7..14da6a3 100644
--- a/config/simple-deprules.d/sci-libs
+++ b/config/simple-deprules.d/sci-libs
@@ -45,6 +45,12 @@ sci-libs/gsl {
}
~sci-libs/hdf5 :: hdf5
+sci-libs/hdf5[cxx] {
+ libhdf5 (>= 1.8.x) with C++ interface(--enable-cxx=yes)
+ libhdf5 (>= 1.8.12) with C++ interface(--enable-cxx=yes)
+}
+# remnant of hdf5
+! :: v18 API enabled
~sci-libs/itpp {
itpp
diff --git a/config/simple-deprules.d/system.set b/config/simple-deprules.d/system.set
index 78ae160..54fc6a5 100644
--- a/config/simple-deprules.d/system.set
+++ b/config/simple-deprules.d/system.set
@@ -2,6 +2,7 @@
# @system
! {
+ GNU make
GNU Make
GNU Make forexternalization
andg++ GNU compiler (a nvcc-compatible version of g++ is needed
@@ -16,10 +17,18 @@
#sys-devel/gcc[cxx] :: g++ or Microsoft VC++
! :: g++ or Microsoft VC++
-
+! {
+ g++-4.6.* or later should be sufficient
+ g++-4.9.* or lateris preferred.
+ gcc (release >= 4.5).
+ C++11
+ C++11 (supporting at least std=c++0x)
+ A C++11 compiler. Version 4.6.* of g++ (ascurrently in Rtools) is insufficient
+}
# always provided? (except for Gentoo/*BSD)
! {
+ Linux operating system
Linux operating system.
Linuxoperationg system
}
@@ -29,6 +38,7 @@
POSIX-compliant OS (essentially anything butWindows
POSIX-compliant OS (essentially anything butWindows)
Unix
+ A 64-bit POSIX OS such as Linux or OS X with IANAtime zone data in /usr/share/zoneinfo as well as a C++11compiler.
}
# rpcgen is part of glibc
diff --git a/config/simple-deprules.d/unknown b/config/simple-deprules.d/unknown
index 939c77d..8d1549d 100644
--- a/config/simple-deprules.d/unknown
+++ b/config/simple-deprules.d/unknown
@@ -3,4 +3,6 @@
# FIXME: which library is meant?
! {
A C library with the fesetround/fegetroundfunctions.
+ library.
+ library
}
diff --git a/config/simple-deprules.d/virtual b/config/simple-deprules.d/virtual
new file mode 100644
index 0000000..33f0d74
--- /dev/null
+++ b/config/simple-deprules.d/virtual
@@ -0,0 +1,15 @@
+virtual/boot :: boot
+virtual/class :: class
+virtual/cluster :: cluster
+virtual/codetools :: codetools
+virtual/foreign :: foreign
+virtual/KernSmooth :: KernSmooth
+virtual/lattice :: lattice
+virtual/MASS :: MASS
+virtual/Matrix :: Matrix
+virtual/mgcv :: mgcv
+virtual/nlme :: nlme
+virtual/nnet :: nnet
+virtual/rpart :: rpart
+virtual/spatial :: spatial
+virtual/survival :: survival
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2015-11-06 1:03 Benda XU
0 siblings, 0 replies; 17+ messages in thread
From: Benda XU @ 2015-11-06 1:03 UTC (permalink / raw
To: gentoo-commits
commit: 8353fa3eae0021da37e807bb7ec04ed1789438fc
Author: Benda Xu <heroxbd <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 6 01:00:28 2015 +0000
Commit: Benda XU <heroxbd <AT> gentoo <DOT> org>
CommitDate: Fri Nov 6 01:00:28 2015 +0000
URL: https://gitweb.gentoo.org/proj/R_overlay.git/commit/?id=8353fa3e
config/simple-deprules.d/R: recommended packages into dev-lang/R[-minimal]
Split default R package list into "base" and "recommended", because R with
USE minimal disables recommended packages and base packages are always
available.
config/simple-deprules.d/R | 34 +++++++++++++++++++---------------
1 file changed, 19 insertions(+), 15 deletions(-)
diff --git a/config/simple-deprules.d/R b/config/simple-deprules.d/R
index ceb82da..bf46e87 100644
--- a/config/simple-deprules.d/R
+++ b/config/simple-deprules.d/R
@@ -14,39 +14,43 @@ dev-lang/R[tk] {
tcltk (but only for the GUI
}
-# always assumed to be provided by dev-lang/R (taken from generate_ebuild)
+# base packages that always assumed to be provided by dev-lang/R (taken from generate_ebuild)
% {
base
- boot
- class
- cluster
- codetools
compiler
datasets
- foreign
graphics
grDevices
grid
+ methods
+ parallel
+ splines
+ stats
+ stats4
+ tcltk
+ tools
+ utils
+}
+
+# recommended packages
+dev-lang/R[-minimal] {
+ boot
+ class
+ cluster
+ codetools
+ foreign
KernSmooth
lattice
- libR
MASS
Matrix
- methods
mgcv
nlme
nnet
- parallel
rpart
spatial
- splines
- stats
- stats4
survival
- tcltk
- tools
- utils
}
+
# FIXME, seems to be provided too
% {
stepfun
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2015-11-05 5:52 Benda XU
0 siblings, 0 replies; 17+ messages in thread
From: Benda XU @ 2015-11-05 5:52 UTC (permalink / raw
To: gentoo-commits
commit: 9b5289f2357ed2c06039e1cd03d3eb1fc98129f0
Author: Benda Xu <heroxbd <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 5 05:52:43 2015 +0000
Commit: Benda XU <heroxbd <AT> gentoo <DOT> org>
CommitDate: Thu Nov 5 05:52:43 2015 +0000
URL: https://gitweb.gentoo.org/proj/R_overlay.git/commit/?id=9b5289f2
config/simple-deprules.d/net: parse dependency for sci-CRAN/curl.
config/simple-deprules.d/net | 1 +
1 file changed, 1 insertion(+)
diff --git a/config/simple-deprules.d/net b/config/simple-deprules.d/net
index 54e8044..e99087e 100644
--- a/config/simple-deprules.d/net
+++ b/config/simple-deprules.d/net
@@ -9,6 +9,7 @@ net-misc/curl {
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
+ libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb).
}
~net-misc/curl {
curl
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2014-06-24 21:38 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2014-06-24 21:38 UTC (permalink / raw
To: gentoo-commits
commit: a751fd20c3c2a14bcd7d9b9b01d026e807c58634
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Jun 23 19:14:01 2014 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Jun 23 19:14:01 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=a751fd20
deprules: remove dev-lang/python:{2.5,2.6,3.1}
... rules, which cause roverlay to create unsatisfiable slot-relative
dependencies (python 2.5, 3.1 not in the main tree; 2.6 masked for removal)
workaround, see previous commit
---
config/simple-deprules.d/dev | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index 8430cc1..891f264 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -22,7 +22,7 @@ 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 {
+~dev-lang/python:slotparts=2:restrict=2.7,3.2,3.3,3.4 {
python
python headers
}
@@ -30,8 +30,8 @@ dev-java/jdbc-postgresql :: PostgreSQL JDBCdriver
~dev-lang/python {
python
}
-# lowest python version in portage: 2.5
->=dev-lang/python-2.5 {
+# lowest python version in portage: 2.7 (2.6 masked)
+dev-lang/python {
Python (>= 2.4) to run Asciidoc(http://www.python.org/)
}
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2014-06-24 21:38 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2014-06-24 21:38 UTC (permalink / raw
To: gentoo-commits
commit: ff166920df39e19771367ff785d35cb120716486
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Jun 23 18:28:41 2014 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Jun 23 19:13:15 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=ff166920
deprules: remove virtual/jdk:1.5 rule (workaround)
SLOT-relative dependency rules do not take the version operator (<, >, ==, !=,
<=, >=) into account, which is a logic/design error because dep strings like
"Java (>= 5.0)" can be interpreted as
(a) any version within the 5.0 release series
(b) any version greater or equal than 5.0, e.g. 7.0
SLOT rules always assume (a), but (b) is equally possible - depending on
the R package in question as well as the respective rule.
This commit is a *workaround* for a single dep rule.
It removes the SLOT rule for virtual/jdk:1.5, which is not available in
the main tree and some packages affected by this rule (RWeka, RWekajars) have
been confirmed to work with more recent java releases.
Effectively, this means that all "Java <somehow> 5.0" dep strings get resolved
as ">=virtual/jdk-1.5" now, which breaks packages that really depend on java
1.5 (should be solvable by installing it manually).
All other SLOT rules (=3) are affected by this issue, too.
Needs to be fixed code-wise.
Reported-By: Randall Wald <rdwald <AT> gmail.com>
---
config/simple-deprules.d/dev | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index 36f9a93..8430cc1 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -60,17 +60,8 @@ dev-util/cmake {
}
# FIXME: the jdk rules are not quite correct,
-# virtual/jdk:1.6 (probably) works for some packages, too
+# virtual/jdk:1.7 (probably) works for some packages, too
#
-# 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 1.5 or higher
- Java version
- java runtime
-}
-
~virtual/jdk:slotparts=i1.6:restrict=1.6,6.0 {
java
Java version
@@ -89,6 +80,7 @@ dev-util/cmake {
~virtual/jdk {
java
Java 1.4 or later
+ Java 1.5 or higher
Java version
java runtime
}
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2014-06-05 22:09 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2014-06-05 22:09 UTC (permalink / raw
To: gentoo-commits
commit: e583b134a6cdf2dc0043d8aafa5c2b0fc4190148
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Wed May 7 01:23:27 2014 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Wed May 7 01:23:27 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=e583b134
fix deprule
---
config/simple-deprules.d/dev | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index 9e3fe55..36f9a93 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -18,7 +18,7 @@ dev-db/unixODBC {
}
dev-java/ant :: ant
-dev-java/jdbc-postgresql:: PostgreSQL JDBCdriver
+dev-java/jdbc-postgresql :: PostgreSQL JDBCdriver
# try to slot-match dev-lang/python, but use known slots only
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-09-03 14:32 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2013-09-03 14:32 UTC (permalink / raw
To: gentoo-commits
commit: 434aec3c8178b9a0233d8efd338d5043fc9779d0
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Tue Sep 3 14:31:27 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Tue Sep 3 14:31:27 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=434aec3c
SLOTted dependency rules for jdk 1.6/1.7
---
config/simple-deprules.d/dev | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index bed0153..9e3fe55 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -71,6 +71,18 @@ dev-util/cmake {
java runtime
}
+~virtual/jdk:slotparts=i1.6:restrict=1.6,6.0 {
+ java
+ Java version
+ java runtime
+}
+
+~virtual/jdk:slotparts=i1.7:restrict=1.7,7.0 {
+ java
+ Java version
+ java runtime
+}
+
# slot-relative rules take precedence
# TODO: slot-restricted rules should get a lower priority
# than "catch-all" slot rules
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-08-27 16:08 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2013-08-27 16:08 UTC (permalink / raw
To: gentoo-commits
commit: 92dde02e08880b42d92e542ca8f448bfdb89e98f
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Tue Aug 27 16:07:23 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Tue Aug 27 16:07:23 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=92dde02e
add new "missing" dep rule file
---
config/simple-deprules.d/missing | 555 +++++++++++++++++++++++++++++++++++++++
1 file changed, 555 insertions(+)
diff --git a/config/simple-deprules.d/missing b/config/simple-deprules.d/missing
new file mode 100644
index 0000000..f7ecf3e
--- /dev/null
+++ b/config/simple-deprules.d/missing
@@ -0,0 +1,555 @@
+#! NOPARSE
+# ------------------------------------
+# FORMAT
+#
+# <dependency string>
+# {<dependency string>}
+# {<upstream url>}
+# {[<notes>}
+# {package: <name> <version> from <repo> [-- optional|mandatory]}
+# {[<notes>}
+#
+# ------------------------------------
+
+<= 1.0.3(http://hadoop.apache.org/core/) or CDH3(http://www.cloudera.com)
+ package: hive 0.1.15 from CRAN
+
+ABCtoolbox
+ http://www.cmpg.iee.unibe.ch/content/softwares__services/computer_programs/abctoolbox/index_eng.html
+ package: abctools 0.2 from CRAN
+
+ADMB version 11 (http://admb-project.org/) foruse.admb=TRUE
+ http://admb-project.org/
+ package: marked 1.0.9 from CRAN
+ package: marked 1.1.2 from CRAN
+
+An ODBC3 driver manager
+ package: RODBC 1.3.6 from CRAN
+ package: RODBC 1.3.7 from CRAN
+ dev-db/unixODBC, dev-db/sqliteodbc, dev-db/myodbc, dev-db/psqlodbc, ...?
+
+asreml
+asreml-R
+asreml-R 3.x
+ http://www.vsni.co.uk/software/asreml
+ package: dlmap 1.12 from CRAN
+ package: dlmap 1.13 from CRAN
+ package: mpMap 1.14 from CRAN
+ package: nadiv 2.8 from R-Forge
+ package: nadiv 2.9 from CRAN
+ package: nadiv 2.11 from CRAN
+ package: nadiv 2.12 from CRAN
+ package: wgaim 1.2 from CRAN
+ package: wgaim 1.3.0 from CRAN
+ package: wgaim 1.4.0 from CRAN
+
+Bayescan 2.1. See README.
+ http://cmpg.unibe.ch/software/bayescan/
+ package: AFLPsim 0.1.3 from CRAN
+ package: AFLPsim 0.1.4 from CRAN
+
+bio3d
+ http://thegrantlab.org/bio3d/index.html
+ package: Rknots 1.2.1 from CRAN -- optional
+
+boxshade
+ http://sourceforge.net/projects/boxshade/
+ http://gpo.zugaina.org/sci-biology/boxshade-bin
+ package: BioTools 0.0.1 from R-Forge
+
+calibayesR
+ package: basisR 0.1.5 from R-Forge -- optional
+
+CnaStruct
+ package: jointSeg 0.3.11 from R-Forge -- optional
+
+cudaMatrixOps
+ package: LargeRegression 1.0 from CRAN -- optional
+
+Cytoscape (>= 2.8.0) (if used for visualization ofresults
+CytoscapeRPC plugin (>= 1.8)
+ http://www.cytoscape.org/download.html
+ * clicking "Proceed to Download" works even if nothing filled out
+ package: categoryCompare 1.0.0
+ package: categoryCompare 1.0.2
+
+Debian or Ubuntu system with access to Goto Blas
+ needs to be checked whether virtual/blas would suffice
+ package: gcbd 0.2.4 from CRAN
+
+DESeq2 (>= 1.0.17)
+ http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
+ "in BIOC since 2.12"
+ package: metaRNASeq 0.3 from R-Forge
+
+DSA
+ package: tmle 1.2.0.1 from CRAN -- optional
+ Theres a newer version available, tmle 1.2.0.3, which does no longer suggest
+ DSA.
+
+fCalendar
+ package: FinTS 0.4.4 from R-Forge -- optional
+ fCalendar is available in CRAN-Archive
+
+FEAR
+ http://www.clemson.edu/economics/faculty/wilson/software/fear/fear.html
+ seems to have its own license!
+
+ 6. You are prohibited from the following activities, unless specifically permitted by OWNER:
+ [...]
+ ii. distributing, selling, sub-licensing, or otherwise making the software available for use by a third party; and
+
+ package: Benchmarking 0.20 from CRAN -- optional
+ package: Benchmarking 0.21 from CRAN -- optional
+ package: Benchmarking 0.22 from CRAN -- optional
+ package: Benchmarking 0.23 from CRAN -- optional
+
+Fedora: poppler-glib-devel]
+ app-text/poppler?
+ package: Rpoppler 0.0.0 from CRAN -- mandatory
+ package: Rpoppler 0.0.1 from CRAN -- mandatory
+
+fUtilities
+ CRAN-Archive
+ package: FinTS 0.4.4 from R-Forge -- optional
+
+GAPS-JAGS (==1.0.2)
+ *** TODO, cannot access upstream site currently ***
+ package: CoGAPS 1.6.0
+
+glcoxph
+ http://datamining.dongguk.ac.kr/Rlib/index.html
+ http://datamining.dongguk.ac.kr/Rlib/glcoxph/
+ package: plsRcox 0.7.0 from CRAN -- optional
+ package: plsRcox 0.9 from CRAN -- optional
+
+Hadoop core >= 0.19.1
+Hadoop core >= 0.20.3(http://hadoop.apache.org/core/)
+ http://hadoop.apache.org/
+ package: hive 0.1.15 from R-Forge -- mandatory
+ package: RHive 0.0.6 from CRAN -- mandatory
+ package: RHive 0.0.7 from CRAN -- mandatory
+
+happy.hbrem
+ http://www.well.ox.ac.uk/happy/happyR.shtml
+ package: mpMap 1.14 from CRAN -- optional
+
+Hive >= 0.8(http://hive.apache.org/)
+ http://hive.apache.org/
+ package: RHive 0.0.6 from CRAN -- mandatory
+ package: RHive 0.0.7 from CRAN -- mandatory
+
+IBGEPesq
+ *** TODO ***
+ package: dicionariosIBGE 1.1.1 from CRAN -- optional
+
+IBM ILOG CPLEX (>= 12.1)
+ http://www-03.ibm.com/software/products/us/en/ibmilogcpleoptistud/
+ $$
+ package: cplexAPI 1.2.3 from CRAN -- mandatory
+ package: cplexAPI 1.2.2 from CRAN -- mandatory
+ package: cplexAPI 1.2.9 from CRAN -- mandatory
+
+INLA
+ http://www.r-inla.org/download
+ package: abn 0.83 from CRAN
+ package: diseasemapping 0.6 from CRAN
+ package: diseasemapping 0.7 from R-Forge
+ package: inlaDevel 0.001 from R-Forge
+ package: lgcp 0.9.7 from CRAN
+ package: lgcp 1.3.2 from CRAN
+
+Internal files Xba.CQV
+ nothing useful found.
+ package: RLMM 1.18.0 from BIOC -- mandatory
+
+KEGGREST
+ http://bioconductor.org/packages/2.12/bioc/html/KEGGREST.html
+ "in BIOC since 2.12"
+ package: opm 0.10.22 from R-Forge
+ package: opm 0.10.32 from R-Forge
+
+kinship
+kinship (>= 1.1.0-9)
+ CRAN-Archive
+ package: multic 0.3.2 -- optional
+ package: pbatR 2.2.9 from CRAN -- optional
+
+Komodo Edit (http://www.openkomodo.com)
+ http://www.openkomodo.com/
+ http://www.activestate.com/komodo-edit
+ package: svKomodo 0.9.58 from R-Forge -- mandatory
+ package: svKomodo 0.9.59 from CRAN -- mandatory
+ package: svKomodo 0.9.60 from R-Forge -- mandatory
+
+kopls
+ http://kopls.sourceforge.net/
+ package: Metabonomic 3.5 from CRAN
+
+libapparmor-dev
+ sys-libs/libapparmor is available in hardened-dev
+ http://git.overlays.gentoo.org/gitweb/?p=proj/hardened-dev.git;a=summary
+ package: RAppArmor 0.8.3 from CRAN
+ !!! Older versions (0.5.0, 0.6.0) do not declare any apparmor dependency.
+
+libraries(<http://poppler.freedesktop.org/>) [Debian/Ubuntu:libpoppler-glib-dev
+ see "Fedora: poppler-glib-devel]" // app-text/poppler?
+
+libsbml (>=3.0.3)
+ http://sbml.org/Software/libSBML
+ http://sourceforge.net/projects/sbml/files/libsbml/
+ package: rsbml 2.14.4 -- mandatory
+
+LINDO API 8.0
+ http://www.lindo.com/index.php?option=com_content&view=article&id=1..
+ package: rLindo 8.0.1 from CRAN -- mandatory
+
+lodplot
+ CRAN-Archive
+ package: quantsmooth 1.22.0 -- mandatory
+
+MAGMA library
+MAGMA shared libraries (== release 0.2)
+MAGMA shared libraries (== release 1.3.0)
+ http://icl.cs.utk.edu/magma/
+ http://icl.cs.utk.edu/magma/software/index.html
+ package: HiPLARM 0.1 from CRAN
+ package: magma 0.2.2.1 from CRAN
+ package: magma 1.3.0.2 from CRAN
+
+mark.exe (>= 6.2) (or mark32.exe andmark64.exe)
+ name implies windows-only
+ upstream site http://www.phidot.org/software/mark/download/ is dead.
+ package: RMark 2.1.3 from CRAN -- mandatory
+ package: RMark 2.1.5 from CRAN -- mandatory
+ package: RMark 2.1.6.1 from CRAN -- mandatory
+
+MERLIN fromurl{www.sph.umich.edu/csg/abecasis/merlin} must be installedand pointed to in the PATH environment variable.
+ www.sph.umich.edu/csg/abecasis/merlin
+ http://www.sph.umich.edu/csg/abecasis/merlin/download/
+ packages: paramlink * from CRAN
+
+MonetDB installation
+ http://www.monetdb.org/
+ http://dev.monetdb.org/downloads/sources/Latest/
+ package: MonetDB_R 0.7.9 from R-Forge
+ package: MonetDB_R 0.7.5 from R-Forge
+ package: MonetDB_R 0.7.10 from R-Forge
+ package: MonetDB_R 0.7.3 from R-Forge
+ package: MonetDB_R 0.7.4 from R-Forge
+ package: MonetDB_R 0.7.8 from R-Forge
+ package: MonetDB_R 0.7 from R-Forge
+
+MOSEK
+MOSEK (http://www.mosek.com)
+MOSEK License
+MOSEK License foruse of Rmosek.
+MOSEK Optimization Software
+ package: REBayes 0.40 from CRAN
+ package: Rmosek 1.2.3 from CRAN
+ package: Rmosek 1.2.5 from R-Forge
+ package: REBayes 0.32 from CRAN
+ package: Rmosek 1.2.4 from CRAN
+
+notepad.exe
+ explicit windows dependency (->mark.exe, ...)
+ package: RMark 2.1.3 from CRAN
+ package: RMark 2.1.5 from CRAN
+ package: RMark 2.1.6.1 from CRAN
+
+NW RFC SDK downloaded
+ SAP software?
+ package: RSAP 0.9 from CRAN
+
+OpenBugs
+OpenBUGS (>= 3.2.2)
+OpenBUGS (>=3.2.2)
+OpenBUGS (http://www.openbugs.info/w/Downloads)
+ http://www.openbugs.info/w/
+ http://www.openbugs.info/w/Downloads
+ package: BTSPAS 2012.0217 from CRAN
+ package: rbugs 0.5.9 from CRAN
+ package: rbugs 0.5.6 from CRAN
+ package: BTSPAS 2012.0219 from CRAN
+ package: R2OpenBUGS 3.2.2.2 from CRAN
+ package: BRugs 0.8.3 from CRAN
+ package: R2OpenBUGS 3.2.2.1 from CRAN
+ package: BRugs 0.8.1 from CRAN
+ package: BRugs 0.8.0 from CRAN
+ package: rriskBayes 2.3 from CRAN
+ package: rriskBayes 2.2 from CRAN
+
+OpenMx
+ http://openmx.psyc.virginia.edu/
+ http://gitorious.org/openmx/openmx.git
+ package: MBESS 3.3.2 from CRAN
+ package: simsem 0.5.3 from CRAN
+ package: MBESS 3.3.3 from CRAN
+ package: semTools 0.4.0 from CRAN
+
+OPIOctopus900
+ http://people.eng.unimelb.edu.au/aturpin/opi/octo900.html
+ package: OPI 1.2 from R-Forge -- optional
+ package: OPI 1.2.2 from R-Forge -- optional
+ package: OPI 1.6 from R-Forge -- optional
+ package: OPI 1.2.1 from R-Forge -- optional
+ package: OPI 1.5 from R-Forge -- optional
+ package: OPI 1.4 from CRAN -- optional
+ package: OPI 1.1 from CRAN -- optional
+
+optionally qacct)
+ http://en.wikipedia.org/wiki/Sun_Grid_Engine
+ http://www.oracle.com/technetwork/oem/grid-engine-166852.html
+ package: Rsge 0.6.3 from CRAN
+
+Oracle client
+ dev-db/oracle-instantclient-basic?
+ package: ora 2.0.0 from CRAN
+
+Oracle Instant Client or Oracle Database Client
+ dev-db/oracle-instantclient-basic?
+ package: ROracle 1.1.10 from CRAN
+ package: ROracle 1.1.3 from CRAN
+ package: ROracle 1.1.5 from CRAN
+
+pdf2
+ http://r-forge.r-project.org/projects/pdf2/
+ https://r-forge.r-project.org/R/?group_id=193
+ R-Forge: "failed to build"
+ package: SGP 0.9.9.0 from CRAN
+
+PLASMA library
+ kde-base/plasma-runtime?
+ kde-base/libplasmagenericshell?
+ package: HiPLARM 0.1 from CRAN
+
+ply2ascii(http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries/)
+ ?
+
+polynomial
+ built-in "poly"?
+ package list not correct due to false positives
+ package: sqlsurvey 0.6.7 from R-Forge
+ package: glmBfp 0.0.26 from R-Forge
+ package: lava_nlin 0.2.4 from R-Forge
+ package: glmBfp 0.0.35 from R-Forge
+ package: smoothtest 2.0.3 from R-Forge
+ package: sqlsurvey 0.4.2 from R-Forge
+ package: nFDR 0.0.1 from CRAN
+ package: epr 1.0 from CRAN
+ package: polspline 1.1.5 from CRAN
+ package: CompetingRiskFrailty 2.0
+ package: ptw 1.0.5 from CRAN
+ package: simPH 0.7.2 from CRAN
+ package: multipol 1.0.6 from CRAN
+ package: polspline 1.1.8 from CRAN
+ package: polydect 0.1.2 from CRAN
+ package: lpint 1.0 from CRAN
+ package: gaussquad 1.0.1 from CRAN
+ package: quantchem 0.13 from CRAN
+ package: PoMoS 1.1.1 from CRAN
+ package: orthopolynom 1.0.5 from CRAN
+ package: locpol 0.4.0 from CRAN
+ package: mfp 1.4.9 from CRAN
+ package: NonpModelCheck 1.0 from CRAN
+ package: polynom 1.3.6 from CRAN
+ package: locpol 0.5.0 from CRAN
+ package: nsga2R 1.0 from CRAN
+ package: mirt 0.8.0 from CRAN
+ package: locpol 0.6.0 from CRAN
+ package: gptk 1.05 from CRAN
+ package: ptw 1.0.4 from CRAN
+ package: mirt 0.2.6 from CRAN
+ package: orthopolynom 1.0.3 from CRAN
+ package: gaussquad 1.0.2 from CRAN
+ package: PolynomF 0.94 from CRAN
+ package: mpoly 0.0.3 from CRAN
+ package: multipol 1.0.5 from CRAN
+ package: MonoPoly 0.2.7 from CRAN
+ package: EQL 1.0.0 from CRAN
+ package: BayesNI 0.1 from CRAN
+ package: bfp 0.0.25 from R-Forge
+ package: TwoWaySurvival 2.2
+ package: Lmoments 1.1.5 from CRAN
+ package: DPpackage 1.1.5 from CRAN
+ package: epr 2.0 from CRAN
+ package: DPpackage 1.1.6 from CRAN
+ package: RSA 0.7.1 from CRAN
+ package: mirt 0.4.0 from CRAN
+ package: marelac 2.1.2 from R-Forge
+ package: bdynsys 1.0 from CRAN
+ package: quantchem 0.12.1 from CRAN
+ package: boolfun 0.2.7 from CRAN
+ package: gptk 1.06 from CRAN
+ package: genlasso 1.0 from CRAN
+ package: boolfun 0.2.8 from CRAN
+ package: tmg 0.1 from CRAN
+ package: wombsoft 2.0 from CRAN
+ package: mpoly 0.0.1 from CRAN
+ package: ptw 1.0.3 from CRAN
+ package: widenet 0.1.2 from CRAN
+
+Poppler Glib interface headers
+ app-text/poppler?
+ package: Rpoppler 0.0.1 from CRAN
+ package: Rpoppler 0.0.0 from CRAN
+
+PostgreSQL JDBCdriver
+ dev-java/jdbc-postgresql?
+
+Protocol Buffer compiler (to create C++ header andsource files from .proto descriptions)
+ ?
+
+qsarr
+ https://r-forge.r-project.org/projects/qsarr/
+ R-Forge: "failed to build"
+ package: qsarm 1.1 from R-Forge
+
+qstat
+ http://en.wikipedia.org/wiki/Sun_Grid_Engine
+ http://www.oracle.com/technetwork/oem/grid-engine-166852.html
+ or CAN BE RESOLVED: games-util/qstat?
+ package: IsoGeneGUI 1.11.0 from R-Forge
+ package: IsoGeneGUI 1.12.0
+ package: Rsge 0.6.3 from CRAN
+
+R-Forge build/check environment(http://R-Forge.R-project.org)
+ ?
+ package: RForgeTools 0.4.13
+ package: rfTools 0.5.8.0
+ package: rfTools 0.5.8.2
+ package: rfTools 0.5.8.5
+ package: rfTools 0.5.8.6
+
+rayproject
+ http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries/sources/
+ package: Morpho 0.24.1 from CRAN
+ package: Morpho 0.25 from CRAN
+ package: Morpho 0.25.1 from CRAN
+
+RdbiPgSQL
+ in BIOC 1.6, 1.7
+ package: RForgeTools 0.4.13 from R-Forge -- optional
+
+rdp-classifier
+ http://sourceforge.net/projects/rdp-classifier/?
+ package: BioTools 0.0.1 from R-Forge -- mandatory
+
+rel_32.exe (see README.txt)
+ windows only
+ package: RMark 2.1.3 from CRAN
+ package: RMark 2.1.5 from CRAN
+ package: RMark 2.1.6.1 from CRAN
+
+Requires SGE (qsub
+ http://en.wikipedia.org/wiki/Sun_Grid_Engine
+ http://www.oracle.com/technetwork/oem/grid-engine-166852.html
+ package: Rsge 0.6.3 from CRAN
+
+retistruct (>= 0.4.10)
+retistruct (>= 0.5.7)
+ https://r-forge.r-project.org/R/?group_id=1436
+ "failed to build"
+ package: retistructgui 0.5.8 from R-Forge
+ package: retistructdemos 0.5.8 from R-Forge
+
+revoIPC(>= 1.0-1)
+ CRAN Archive
+ package: doSMP 1.0.3 from R-Forge
+
+Rlsf
+ CRAN Archive
+ package: MSToolkit 3.0.3 from R-Forge
+ package: MSToolkit 2.0 from CRAN
+
+RNMImport
+ ?
+ package: MSToolkit 3.2.1 from R-Forge -- optional
+ package: MSToolkit 3.0.3 from R-Forge -- optional
+ package: MSToolkit 3.2.0 from R-Forge -- optional
+
+rpvm
+ CRAN Archive
+ package: snow 0.3.10 from CRAN
+ package: snow 0.3.12 from CRAN
+ package: snowFT 1.2.0 from CRAN
+ package: varSelRF 0.7.3 from CRAN
+ package: race 0.1.59 from CRAN
+
+rtreebase
+ treebase from CRAN?
+ package: PhyloOrchard 0.1 from R-Forge
+
+SAGA GIS (2.0.4 - 2.0.8)
+SAGA GIS (2.0.4 - 2.1.0)
+ http://www.saga-gis.org/en/index.html
+ http://sourceforge.net/projects/saga-gis/
+ package: RSAGA 0.93.2.1 from CRAN
+ package: RSAGA 0.93.1 from CRAN
+ package: RSAGA 0.93.6 from CRAN
+
+SciViews-K(http://www.sciviews.org/SciViews-K)
+ http://www.sciviews.org/SciViews-K/
+ package: svKomodo 0.9.58
+ package: svKomodo 0.9.59
+ package: svKomodo 0.9.60
+
+The standalone program xgobi must be installedadditionally
+xgobi must be installed additionally
+ http://www2.research.att.com/areas/stat/xgobi/
+ package: xgobi 1.2.14
+ package: xgobi 1.2.15
+
+TODO!!!
+ cannot be resolved.
+ package: svDialogs 0.9.53 from R-Forge
+ package: svDialogs 0.9.52 from CRAN
+ package: svDialogs 0.9.54 from R-Forge
+
+traceR
+ ?
+ nlmeU 0.70.3 does no longer suggest this package
+ package: nlmeU 0.60.14 from R-Forge -- optional
+
+trimesh_project
+ http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries/sources/ ?
+ package: Morpho 0.24.1 from CRAN
+ package: Morpho 0.25 from CRAN
+ package: Morpho 0.25.1 from CRAN
+
+twMisc
+ R-Forge, failed to build
+ package: twMiscRgl 0.5.1 from R-Forge
+ package: twSnowfall 0.8.81 from R-Forge
+
+Ubigraph (http://ubietylab.net/ubigraph/index.html)
+ http://ubietylab.net/ubigraph/index.html
+ package: RUbigraph 0.1.1 -- mandatory
+
+WinBUGS (>= 1.4)
+WinBUGS 1.4
+ http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/contents.shtml
+ seems to be windows-only
+ TOOD: check if the listed packages "really" need WinBUGS
+ package: dclone 2.0.0 from R-Forge
+ package: JMbayes 0.4.1 from CRAN
+ package: dclone 1.8.1 from R-Forge
+ package: dclone 1.8.0 from R-Forge
+ package: JMbayes 0.2.0 from CRAN
+ package: R2WinBUGS 2.1.19 from CRAN
+ package: R2WinBUGS 2.1.18 from CRAN
+
+WNdb-3.0.tar.gz fromwordnet.princeton.edu
+ http://wordnet.princeton.edu/wordnet/download/current-version/
+ http://wordnetcode.princeton.edu/3.0/WNdb-3.0.tar.gz
+ package: wordnet 0.1.9
+ package: wordnet 0.1.8
+
+Xba.regions (or otherregions file)
+ *** see "Internal files Xba.CQV" above // nothing found ***
+
+ypaddon
+ https://bitbucket.org/remkoduursma/ypaddon
+ https://bitbucket.org/remkoduursma/ypaddon/downloads
+ package: YplantQMC 0.5 from CRAN
+ package: YplantQMC 0.5.2 from R-Forge
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-08-27 16:08 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2013-08-27 16:08 UTC (permalink / raw
To: gentoo-commits
commit: d015768fc975f3abfac9ce91d5c0ff3c1c30ca79
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Tue Aug 27 16:05:48 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Tue Aug 27 16:05:48 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=d015768f
move config/simple-deprules.d/missing{,.old}
---
config/simple-deprules.d/{missing => missing.old} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/config/simple-deprules.d/missing b/config/simple-deprules.d/missing.old
similarity index 100%
rename from config/simple-deprules.d/missing
rename to config/simple-deprules.d/missing.old
^ permalink raw reply [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-08-27 15:39 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2013-08-27 15:39 UTC (permalink / raw
To: gentoo-commits
commit: f08ec4d99dd1534efe8b8743fae4ace5ae9d9957
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Tue Aug 27 15:38:46 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Tue Aug 27 15:38:46 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=f08ec4d9
more dependency rules
---
config/simple-deprules.d/R | 1 +
config/simple-deprules.d/dev | 12 +++++++++++-
config/simple-deprules.d/ignored_text | 8 ++++++++
config/simple-deprules.d/media | 10 +++++++++-
config/simple-deprules.d/misc | 9 +++++++++
config/simple-deprules.d/sci | 9 +++++++++
config/simple-deprules.d/system.set | 1 +
7 files changed, 48 insertions(+), 2 deletions(-)
diff --git a/config/simple-deprules.d/R b/config/simple-deprules.d/R
index ecb78fd..ceb82da 100644
--- a/config/simple-deprules.d/R
+++ b/config/simple-deprules.d/R
@@ -29,6 +29,7 @@ dev-lang/R[tk] {
grid
KernSmooth
lattice
+ libR
MASS
Matrix
methods
diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
index 01603a1..bed0153 100644
--- a/config/simple-deprules.d/dev
+++ b/config/simple-deprules.d/dev
@@ -39,7 +39,13 @@ dev-java/jdbc-postgresql:: PostgreSQL JDBCdriver
dev-lang/lua :: lua version>= 5.1.4
~dev-lang/lua :: lua
-~dev-tex/pgf :: pgf
+~dev-tex/pgf {
+ pgf
+}
+
+>=dev-tex/pgf-2.10 {
+ pgf (>=2.10) (http://sourceforge.net/projects/pgf/)for the vignette
+}
~dev-tcltk/bwidget {
bwidget
@@ -53,10 +59,14 @@ dev-util/cmake {
cmake (http://www.cmake.org)
}
+# FIXME: the jdk rules are not quite correct,
+# virtual/jdk:1.6 (probably) works for some packages, too
+#
# 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 1.5 or higher
Java version
java runtime
}
diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text
index a2567e2..bd4e8ae 100644
--- a/config/simple-deprules.d/ignored_text
+++ b/config/simple-deprules.d/ignored_text
@@ -57,8 +57,16 @@
its development files
library (version2.2.0 or later)
libraries(See README.REQ)
+ Google Chrome for Windows
+ for externalization
+ writing some graphicformats
+ available athttp://www.monetdb.org
+ it is used in the demos too).
}
+# that's a hardware requirement
+! :: double-precision AMD or Nvidia GPU
+
% :: Linux
# ignore "Windows" in dependency fields:
diff --git a/config/simple-deprules.d/media b/config/simple-deprules.d/media
index 365455f..41d8a03 100644
--- a/config/simple-deprules.d/media
+++ b/config/simple-deprules.d/media
@@ -8,8 +8,13 @@ media-sound/csound {
~media-gfx/imagemagick {
imagemagick
+}
+
+#deptype all
+media-gfx/imagemagick {
Image Magick (for reading non PPM format)
}
+#deptype sys
media-gfx/graphviz :: dot from graphviz
~media-gfx/graphviz {
@@ -28,7 +33,10 @@ virtual/ffmpeg {
ffmpeg
}
-media-gfx/dcraw :: dcraw(for reading RAW images).
+media-gfx/dcraw {
+ dcraw(for reading RAW images).
+ dcraw (for readingRAW images).
+}
media-libs/fontconfig {
fontconfig
diff --git a/config/simple-deprules.d/misc b/config/simple-deprules.d/misc
index 9a1bae1..9157f64 100644
--- a/config/simple-deprules.d/misc
+++ b/config/simple-deprules.d/misc
@@ -5,3 +5,12 @@ dev-vcs/git {
>=app-emulation/wine-1.5.26 {
wine (>= wine-1.5.26)
}
+
+
+# spGoogle 0.1.2 from CRAN wants "Google Chrome" or "Firefox"
+# TODO: check whether this dep can be dropped/ignored or other browsers
+# would suffice, too
+#
+|| ( www-client/google-chrome www-client/firefox www-client/firefox-bin ) {
+ Linux users orFirefox just for Linux users.
+}
diff --git a/config/simple-deprules.d/sci b/config/simple-deprules.d/sci
index 4e5363a..70521d9 100644
--- a/config/simple-deprules.d/sci
+++ b/config/simple-deprules.d/sci
@@ -62,6 +62,10 @@ sci-biology/ncbi-tools++ {
ncbi-tools++
}
+sci-biology/kalign {
+ kalign
+}
+
sci-mathematics/glpk {
libglpk-dev onDebian/Ubuntu)
}
@@ -74,6 +78,11 @@ sci-mathematics/glpk {
glpk
}
+#deptype pkg
+sci-mathematics/rstudio {
+ manipulate
+}
+
#deptype sys
# == misc ==
diff --git a/config/simple-deprules.d/system.set b/config/simple-deprules.d/system.set
index 828d995..78ae160 100644
--- a/config/simple-deprules.d/system.set
+++ b/config/simple-deprules.d/system.set
@@ -3,6 +3,7 @@
# @system
! {
GNU Make
+ GNU Make forexternalization
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)
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-07-16 16:36 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2013-07-16 16:36 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)
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-07-16 16:36 André Erdmann
0 siblings, 0 replies; 17+ messages in thread
From: André Erdmann @ 2013-07-16 16:36 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] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-01-27 20:12 Denis Dupeyron
0 siblings, 0 replies; 17+ messages in thread
From: Denis Dupeyron @ 2013-01-27 20:12 UTC (permalink / raw
To: gentoo-commits
commit: b662d144fda85060e932f5bd7a4c4984fa9f652c
Author: Denis Dupeyron <calchan <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 27 20:11:57 2013 +0000
Commit: Denis Dupeyron <calchan <AT> gentoo <DOT> org>
CommitDate: Sun Jan 27 20:11:57 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=b662d144
More rules added
---
config/simple-deprules.d/dev-libs | 5 ++++-
config/simple-deprules.d/ignored_text | 9 +++++++++
config/simple-deprules.d/media | 7 ++++++-
config/simple-deprules.d/nvidia | 5 +++++
config/simple-deprules.d/sci | 7 ++++++-
config/simple-deprules.d/sci-libs | 2 +-
config/simple-deprules.d/selfdeps | 4 +++-
config/simple-deprules.d/sys | 18 ++++++++++++++++++
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
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-01-27 8:29 Denis Dupeyron
0 siblings, 0 replies; 17+ messages in thread
From: Denis Dupeyron @ 2013-01-27 8:29 UTC (permalink / raw
To: gentoo-commits
commit: 39d21926cf61ed4d303ac86e2e7e1d11dbbedf92
Author: Denis Dupeyron <calchan <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 27 08:29:26 2013 +0000
Commit: Denis Dupeyron <calchan <AT> gentoo <DOT> org>
CommitDate: Sun Jan 27 08:29:26 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=39d21926
Add a bunch of deprules
---
config/simple-deprules.d/dot_remap | 56 +++++++++++++++++++++++++++++++++
config/simple-deprules.d/ignored_text | 3 ++
config/simple-deprules.d/missing | 20 ------------
config/simple-deprules.d/sci-libs | 3 ++
config/simple-deprules.d/sys | 4 ++
5 files changed, 66 insertions(+), 20 deletions(-)
diff --git a/config/simple-deprules.d/dot_remap b/config/simple-deprules.d/dot_remap
index 57d65b1..9b53f32 100644
--- a/config/simple-deprules.d/dot_remap
+++ b/config/simple-deprules.d/dot_remap
@@ -49,6 +49,27 @@
~sci-R/oro_dicom :: oro.dicom
~sci-R/oro_nifti :: oro.nifti
+~sci-R/org_Ag_eg_db :: org.Ag.eg.db
+~sci-R/org_At_tair_db :: org.At.tair.db
+~sci-R/org_Bt_eg_db :: org.Bt.eg.db
+~sci-R/org_Ce_eg_db :: org.Ce.eg.db
+~sci-R/org_Cf_eg_db :: org.Cf.eg.db
+~sci-R/org_Dm_eg_db :: org.Dm.eg.db
+~sci-R/org_Dr_eg_db :: org.Dr.eg.db
+~sci-R/org_EcK12_eg_db :: org.EcK12.eg.db
+~sci-R/org_EcSakai_eg_db :: org.EcSakai.eg.db
+~sci-R/org_Gg_eg_db :: org.Gg.eg.db
+~sci-R/org_Hs_eg_db :: org.Hs.eg.db
+~sci-R/org_Mm_eg_db :: org.Mm.eg.db
+~sci-R/org_Mmu_eg_db :: org.Mmu.eg.db
+~sci-R/org_Pf_plasmo_db :: org.Pf.plasmo.db
+~sci-R/org_Pt_eg_db :: org.Pt.eg.db
+~sci-R/org_Rn_eg_db :: org.Rn.eg.db
+~sci-R/org_Sc_sgd_db :: org.Sc.sgd.db
+~sci-R/org_Sco_eg_db :: org.Sco.eg.db
+~sci-R/org_Ss_eg_db :: org.Ss.eg.db
+~sci-R/org_Xl_eg_db :: org.Xl.eg.db
+
~sci-R/R_cache :: R.cache
~sci-R/RcmdrPlugin_IPSUR :: RcmdrPlugin.IPSUR
~sci-R/R_devices :: R.devices
@@ -70,3 +91,38 @@
~sci-R/survJamda_data :: survJamda.data
~sci-R/tawny_types :: tawny.types
+
+~sci-R/DO_db :: DO.db
+~sci-R/IlluminaHumanMethylation27k_db :: IlluminaHumanMethylation27k.db
+~sci-R/IlluminaHumanMethylation450k_db :: IlluminaHumanMethylation450k.db
+~sci-R/KEGG_db :: KEGG.db
+~sci-R/SNPlocs_Hsapiens_dbSNP_20090506 :: SNPlocs.Hsapiens.dbSNP.20090506
+~sci-R/SNPlocs_Hsapiens_dbSNP_20100427 :: SNPlocs.Hsapiens.dbSNP.20100427
+~sci-R/SNPlocs_Hsapiens_dbSNP_20101109 :: SNPlocs.Hsapiens.dbSNP.20101109
+~sci-R/gahgu133plus2_db :: gahgu133plus2.db
+~sci-R/hgfocus_db :: hgfocus.db
+~sci-R/hgu133a_db :: hgu133a.db
+~sci-R/hgu133plus2_db :: hgu133plus2.db
+~sci-R/hgu95a_db :: hgu95a.db
+~sci-R/hgu95av2_db :: hgu95av2.db
+~sci-R/hgug4112a_db :: hgug4112a.db
+~sci-R/hu6800_db :: hu6800.db
+~sci-R/illuminaHumanv1_db :: illuminaHumanv1.db
+~sci-R/nutshell_bbdb :: nutshell.bbdb
+~sci-R/reactome_db :: reactome.db
+
+~sci-R/RmiR_Hs_miRNA :: RmiR.Hs.miRNA
+~sci-R/TxDb_Hsapiens_UCSC_hg18_knownGene :: TxDb.Hsapiens.UCSC.hg18.knownGene
+~sci-R/TxDb_Hsapiens_UCSC_hg19_knownGene :: TxDb.Hsapiens.UCSC.hg19.knownGene
+~sci-R/bigmemory_sri :: bigmemory.sri
+~sci-R/gamlss_add :: gamlss.add
+~sci-R/gemtc_jar :: gemtc.jar
+~sci-R/haplo_stats :: haplo.stats
+~sci-R/nutshell_audioscrobbler :: nutshell.audioscrobbler
+~sci-R/pd_charm_hg18_example :: pd.charm.hg18.example
+~sci-R/pd_mapping250k_nsp :: pd.mapping250k.nsp
+~sci-R/pd_mapping250k_sty :: pd.mapping250k.sty
+~sci-R/pd_mapping50k_hind240 :: pd.mapping50k.hind240
+~sci-R/pd_mapping50k_xba240 :: pd.mapping50k.xba240
+~sci-R/simdat_base :: simdat.base
+
diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text
index 31871e3..34f11eb 100644
--- a/config/simple-deprules.d/ignored_text
+++ b/config/simple-deprules.d/ignored_text
@@ -57,3 +57,6 @@
windows: Tiff(libtiff3.dll)
zlib1.dll and jpeg62.dll
}
+
+# typo, and glibc is always built with pthreads nowadays
+! :: lippthread
diff --git a/config/simple-deprules.d/missing b/config/simple-deprules.d/missing
index 0cf60b4..9674bba 100644
--- a/config/simple-deprules.d/missing
+++ b/config/simple-deprules.d/missing
@@ -243,26 +243,6 @@ 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,
diff --git a/config/simple-deprules.d/sci-libs b/config/simple-deprules.d/sci-libs
index 8e20c5b..cb48d04 100644
--- a/config/simple-deprules.d/sci-libs
+++ b/config/simple-deprules.d/sci-libs
@@ -74,3 +74,6 @@ sci-libs/udunits :: udunits (>= 1.11.7) or udunits2(>= 2.1.22)
}
virtual/blas :: blas
+
+# In the science overlay
+~sci-libs/coinor-clp :: COIN-OR Clp
diff --git a/config/simple-deprules.d/sys b/config/simple-deprules.d/sys
index 3b793d0..df2ad0c 100644
--- a/config/simple-deprules.d/sys
+++ b/config/simple-deprules.d/sys
@@ -14,3 +14,7 @@ sys-libs/zlib :: zlib (optional)
LamMPI(>= 6.5.9) or MPICH2(>= 1.0.2) or OpenMPI ()
LamMpi(>= 6.5.9) or Mpich2(>= 1.0.2)
}
+
+! {
+ rgl packages for rendering
+}
^ permalink raw reply related [flat|nested] 17+ messages in thread* [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/
@ 2013-01-25 17:49 Denis Dupeyron
0 siblings, 0 replies; 17+ messages in thread
From: Denis Dupeyron @ 2013-01-25 17:49 UTC (permalink / raw
To: gentoo-commits
commit: aeb5147e7651d57e72e4bdf8c441827a311e9d9d
Author: Denis Dupeyron <calchan <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 25 17:49:02 2013 +0000
Commit: Denis Dupeyron <calchan <AT> gentoo <DOT> org>
CommitDate: Fri Jan 25 17:49:02 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=aeb5147e
Fix dependency on fftw3 in seewave (and maybe others)
---
config/simple-deprules.d/sci-libs | 3 +++
1 files changed, 3 insertions(+), 0 deletions(-)
diff --git a/config/simple-deprules.d/sci-libs b/config/simple-deprules.d/sci-libs
index 7fade76..8e20c5b 100644
--- a/config/simple-deprules.d/sci-libs
+++ b/config/simple-deprules.d/sci-libs
@@ -5,11 +5,14 @@
~sci-libs/cddlib :: cddlib
# lowest fftw-3 version in portage is 3.2.2
+# Use slot when the resolver can deal with them properly
>=sci-libs/fftw-3 {
fftw3
fftw3 (optional)
}
~sci-libs/fftw :: fftw
+# Use slot when the resolver can deal with them properly
+~sci-libs/fftw :: fftw3
sci-libs/gdal {
GDAL library from http://www.gdal.org/download.html
^ permalink raw reply related [flat|nested] 17+ messages in thread
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