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

2018-05-29 Thread Benda XU 
commit: 3f7c507a97b62ef814517adf3e9fae935db4ad04
Author: Benda Xu  gentoo  org>
AuthorDate: Wed May 30 05:25:20 2018 +
Commit: Benda XU  gentoo  org>
CommitDate: Wed May 30 05:25:20 2018 +
URL:https://gitweb.gentoo.org/proj/R_overlay.git/commit/?id=3f7c507a

Use regex in dep string matches.

  Ignore rules should come later than positive rules.

Closes: https://bugs.gentoo.org/653694

 config/simple-deprules.d/R |  66 ++--
 config/simple-deprules.d/app   |   7 +-
 config/simple-deprules.d/app-text  |  29 +-
 config/simple-deprules.d/compound_deps |  25 ++---
 config/simple-deprules.d/dev   |  58 ++-
 config/simple-deprules.d/dev-libs  |  73 +++---
 config/simple-deprules.d/dot_remap | 134 -
 config/simple-deprules.d/ignored_text  | 103 ++-
 config/simple-deprules.d/media |  20 +---
 config/simple-deprules.d/media-libs|  30 ++
 config/simple-deprules.d/misc  |   6 +-
 config/simple-deprules.d/net   |  21 +---
 config/simple-deprules.d/nvidia|  22 ++--
 config/simple-deprules.d/sci   |  34 +++
 config/simple-deprules.d/sci-libs  |  35 ++-
 config/simple-deprules.d/selfdeps  |  22 
 config/simple-deprules.d/selfdeps.d/sci-CRAN   |  23 ++---
 config/simple-deprules.d/sys   |  32 +++---
 config/simple-deprules.d/system.set|  39 ++-
 config/simple-deprules.d/unknown   |   5 +-
 config/simple-deprules.d/x11   |  12 +--
 roverlay/depres/simpledeprule/abstractrules.py |  10 +-
 roverlay/depres/simpledeprule/rules.py |   6 +-
 23 files changed, 195 insertions(+), 617 deletions(-)

diff --git a/config/simple-deprules.d/R b/config/simple-deprules.d/R
index 9106deb..8edf111 100644
--- a/config/simple-deprules.d/R
+++ b/config/simple-deprules.d/R
@@ -6,53 +6,43 @@
 #deptype all
 
 # using fuzzy dep matches
-~dev-lang/R :: R
+~dev-lang/R :: ^R$
 
 dev-lang/R[tk] {
-   tcl/tk 8.5
-   Tcl/Tk (>= 8.5)
-   tcltk (but only for the GUI
-}
-
-# base packages that always assumed to be provided by dev-lang/R (taken from 
generate_ebuild)
-% {
-   base
-   compiler
-   datasets
-   graphics
-   grDevices
-   grid
-   methods
-   parallel
-   splines
-   stats
-   stats4
+   tcl/tk
tcltk
-   tools
-   utils
 }
 
-# FIXME, seems to be provided too
-% {
-   stepfun
-   ts
-   package ts
-   package ts (included in the R release)
-}
 # modreg is in stats, according to 
https://stat.ethz.ch/pipermail/bioconductor/2010-June/034197.html
 ! :: modreg
 
 # R is always compiled with '--enabled-R-shlib'
 ! {
-   R must be compiled with --enable-R-shlib if the server is to be built
-   R must be compiled with --enable-R-shlib if theserver is to be built
-   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.
-   R built as a shared or static (R >= 2.7.0) library
-   R built as a shared orstatic library
+--enable-R-shlib
+xls.getshlib
+   R built as a shared
R-0.64 or later
-   Regular shlib must be obtained from an externalsource (use 
'xls.getshlib()' or dl manually).
-   dl regular shlib with 'xls.getshlib()'or manually (~420 KB)
+}
+
+# base packages that always assumed to be provided by dev-lang/R (taken from 
generate_ebuild)
+% {
+   ^base$
+   ^compiler$
+   ^datasets$
+   ^graphics$
+   ^grDevices$
+   ^grid$
+   ^methods$
+   ^parallel$
+   ^splines$
+   ^stats4?
+^tools$
+^utils$
+}
+
+# FIXME, seems to be provided too
+% {
+   ^stepfun$
+   ^ts$
+   package.*ts
 }

diff --git a/config/simple-deprules.d/app b/config/simple-deprules.d/app
index 99ba3c3..6c086c4 100644
--- a/config/simple-deprules.d/app
+++ b/config/simple-deprules.d/app
@@ -3,10 +3,7 @@
 app-admin/ec2-api-tools :: ec2-api-tools
 
 # FIXME zip or unzip?
-app-arch/zip :: zip
+app-arch/zip :: ^zip$
 
 # FIXME: this is not satisfiable, latest dieharder version in portage is 2.28.1
-app-crypt/dieharder {
-   DieHarder library (>= 2.8.1) 
fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php
-   DieHarder library (>= 3.31.1) 
fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php
-}
+app-crypt/dieharder :: DieHarder
\ No newline at end of file

diff --git a/config/simple-deprules.d/app-text 
b/config/simple-deprules.d/app-text
index 6e4cdd4..810178c 100644
--- a/config/simple-deprules.d/app-text
+++ b/config/simple-deprules.d/app-text
@@ -1,35 +1,16 @@
 #deptype sys
 
-app-text/antiw

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

2018-05-28 Thread Benda XU 
commit: daa3c7277f25c71620679fb439c763a0426ab7e7
Author: Benda Xu  gentoo  org>
AuthorDate: Mon May 28 08:26:46 2018 +
Commit: Benda XU  gentoo  org>
CommitDate: Mon May 28 08:26:46 2018 +
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 () 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
@@

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

2015-11-05 Thread Benda XU 
commit: 8353fa3eae0021da37e807bb7ec04ed1789438fc
Author: Benda Xu  gentoo  org>
AuthorDate: Fri Nov  6 01:00:28 2015 +
Commit: Benda XU  gentoo  org>
CommitDate: Fri Nov  6 01:00:28 2015 +
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

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

2015-11-04 Thread Benda XU 
commit: 9b5289f2357ed2c06039e1cd03d3eb1fc98129f0
Author: Benda Xu  gentoo  org>
AuthorDate: Thu Nov  5 05:52:43 2015 +
Commit: Benda XU  gentoo  org>
CommitDate: Thu Nov  5 05:52:43 2015 +
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

[gentoo-commits] proj/R_overlay:master commit in: config/

2014-07-16 Thread André Erdmann 
commit: f4531ed9e7d9086f4bb391d93274d276f313aea2
Author: André Erdmann  mailerd  de>
AuthorDate: Mon Jul 14 00:00:14 2014 +
Commit: André Erdmann  mailerd  de>
CommitDate: Mon Jul 14 00:00:17 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=f4531ed9

config/: update license map file

---
 config/license.map | 5 +
 1 file changed, 5 insertions(+)

diff --git a/config/license.map b/config/license.map
index db4c855..deb8ca6 100644
--- a/config/license.map
+++ b/config/license.map
@@ -164,6 +164,11 @@ GPL-2+ {
bsd|gpl|apachelicense
 }
 
+# FIXME: non-versioned
+|| ( GPL-2+ Apache-2.0 ) {
+   gpl|apachelicense2.0
+}
+
 || ( GPL-3+ BSD ) {
gpl|bsd
 }

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

2014-06-24 Thread André Erdmann 
commit: a751fd20c3c2a14bcd7d9b9b01d026e807c58634
Author: André Erdmann  mailerd  de>
AuthorDate: Mon Jun 23 19:14:01 2014 +
Commit: André Erdmann  mailerd  de>
CommitDate: Mon Jun 23 19:14:01 2014 +
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/)
 }

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

2014-06-24 Thread André Erdmann 
commit: ff166920df39e19771367ff785d35cb120716486
Author: André Erdmann  mailerd  de>
AuthorDate: Mon Jun 23 18:28:41 2014 +
Commit: André Erdmann  mailerd  de>
CommitDate: Mon Jun 23 19:13:15 2014 +
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  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  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
 }

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

2014-06-05 Thread André Erdmann 
commit: e583b134a6cdf2dc0043d8aafa5c2b0fc4190148
Author: André Erdmann  mailerd  de>
AuthorDate: Wed May  7 01:23:27 2014 +
Commit: André Erdmann  mailerd  de>
CommitDate: Wed May  7 01:23:27 2014 +
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