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

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

[André Erdmann]

commit:     bc9a0e2d728f266611d5fd625d96480988b604b4
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Jul  9 16:29:40 2012 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Jul  9 16:29:40 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=bc9a0e2d

add --overlay-name to config/R-overlay.conf

---
 config/R-overlay.conf |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/config/R-overlay.conf b/config/R-overlay.conf
index dd160b3..5276520 100644
--- a/config/R-overlay.conf
+++ b/config/R-overlay.conf
@@ -68,7 +68,7 @@
 # This is a listing of options to consider
 #
 # options that are required:
-#  OVERLAY_NAME,
+#  OVERLAY_NAME,      (or use --overlay-name <name>)
 #  OVERLAY_DIR,       (or use --overlay <OVERLAY>)
 #  DISTFILES,         (or use --distroot <DISTROOT>)
 #  REPO_CONFIG,       (or use --repo-config <file>) # FIXME: required?

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

[André Erdmann]

commit:     9462b6268f8bc4b1d8bd50a59ef2b8df55dd562a
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Wed Jul 10 08:24:15 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Wed Jul 10 08:24:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=9462b626

config/: license map file, update field-def

The license map file is neither complete nor 100% correct, but it roughly works.

Added/Enabled '[License]' in description_fields.conf so that the description
reader parses this field.

---
 config/description_fields.conf |  30 ++++---
 config/license.map             | 194 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 214 insertions(+), 10 deletions(-)

diff --git a/config/description_fields.conf b/config/description_fields.conf
index 0705798..b0d355d 100644
--- a/config/description_fields.conf
+++ b/config/description_fields.conf
@@ -25,7 +25,7 @@
 #                            whitelist and adds <some value> to this list.
 #
 #  allowed_values = <some values>
-#                        -- same as allowed_value but witj multiple values
+#                        -- same as allowed_value but with multiple values
 #
 #  alias_withcase = <aliases>,
 #  alias = <aliases>
@@ -55,6 +55,11 @@
 #  isWhitespaceList
 #         -- declares that the field's value is a list
 #             separated by whitespace. Has no effect if 'isList' is set.
+#
+#  isLicense
+#         -- use hardcoded 'License' field parsing
+#             configuration for this flag is done in the main config file
+#
 #  mandatory
 #         -- declares that this field has to have an value that evaluates
 #             to True (value is set and not empty).
@@ -71,6 +76,12 @@
 #
 # ----------------------------------------------------------------------------
 
+## Useful docs:
+##
+## http://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file
+##
+## http://en.wikipedia.org/wiki/Commonly_misspelled_words
+##  has some links to other sites as well
 
 [Description]
 joinValues
@@ -85,10 +96,11 @@ joinValues
 ignore
 
 [License]
-isList
+alias_nocase = License, Licence, Lisence
+
+# use hardcoded field handling
+isLicense
 
-# not used
-ignore
 
 [Version]
 joinValues
@@ -122,6 +134,10 @@ isList
 alias_nocase = OS_TYPE
 allowed_values = unix
 
+[Homepage]
+alias_nocase = Homepage, URL, Webpage
+ignore
+
 [Author]
 ignore
 
@@ -146,12 +162,6 @@ ignore
 [Type]
 ignore
 
-[URL]
-ignore
-
-[Webpage]
-ignore
-
 [ZipData]
 ignore
 

diff --git a/config/license.map b/config/license.map
new file mode 100644
index 0000000..bcaf168
--- /dev/null
+++ b/config/license.map
@@ -0,0 +1,194 @@
+# freedist, as-is, ...?
+! {
+   unlimited
+}
+
+# freestyle text
+! {
+   foo
+   freeforresearchpurpose.
+   whatlicenseisitunder?
+}
+
+
+AGPL-3 :: agpl
+
+AGPL-3 {
+   agpl3
+   agpl>3
+}
+
+Apache-2.0 {
+   apachelicense2.0
+}
+
+Artistic {
+   artistic-1.0
+}
+
+Artistic-2 {
+   artistic-2.0
+   artistic2.0#modifyasdesired
+   artisticlicense2.0
+   theartisticlicense2.0
+}
+
+Boost-1.0 {
+   bsl
+   bsl-1.0
+}
+
+BSD {
+   freebsd
+}
+
+CC0-1.0 {
+   cc0
+}
+
+CC-BY-SA-3.0 {
+   ccby-sa3.0us
+}
+CC-BY-SA-2.0 {
+   ccbysa2.0
+}
+
+|| ( CC-BY-SA-3.0 CC-BY-NC-SA-3.0 ) {
+   ccbysa3.0us|ccbyncsa3.0
+}
+
+CeCILL-C :: cecill
+CeCILL-2 :: cecill2
+
+# ?
+CPL-0.5 {
+   cpl
+   commonpubliclicense1.0
+}
+
+EPL-1.0 {
+   epl
+}
+
+EUPL-1.1 {
+   eupl
+}
+
+GPL-2 {
+   gnugeneralpubliclicense2
+   gpl2
+   gpl2.0
+}
+
+GPL-2 :: gpl2forrpackage;researchonlylicenseforemdl1
+
+GPL-2+ {
+   gpl>2
+   gpl>2.0
+   gpl>2.15.1
+   gpl2.1ornewer
+   gpl2orlater
+   gpl2orlater.
+   gpl2ornewer
+   gpl2ornewercopying.
+   gpl2ornewer.thetermsofthislicenseareinafilecalledcopyingwhichisprovidedwithr.
+}
+
+|| ( GPL-2 Artistic-2 ) {
+   gpl2|artistic2.0
+}
+
+|| ( GPL-2+ BSD ) {
+   gpl>2|bsd
+   gpl>2|freebsd
+}
+
+GPL-3 {
+   gpl3
+   gpl3.0
+}
+
+GPL-3+ {
+   gpl>3
+   gpl>3.0
+}
+
+# gpl licenses without version:
+GPL-3+ {
+   gnugeneralpubliclicense
+   gnugeneralpubliclicensegpl
+   gnugpl
+   gpl
+   gpl.
+}
+
+|| ( GPL-3+ BSD ) {
+   gpl|bsd
+}
+
+|| ( GPL-3+ LGPL-3+ ) {
+   gpl|lgpl
+}
+
+|| ( GPL-2 GPL-3 ) {
+   gpl2|gpl3
+}
+
+LGPL-2 {
+   lgpl2
+}
+
+LGPL-2+ {
+   lgpl>2
+   lgpl>2.0
+   lgpl2ornewer
+}
+
+LGPL-2.1 {
+   lgpl2.1
+}
+
+LGPL-2.1+ {
+   lgpl>2.1
+}
+
+LGPL-3 {
+   lgpl3
+}
+
+LGPL-3+ {
+   lgpl>3
+}
+
+LGPL-3+ {
+   lgpl
+}
+
+MIT {
+   mitlicense
+}
+
+# x11 is MIT?
+MIT :: x11
+
+|| ( MIT GPL-2 ) {
+   mit|gpl2
+}
+
+MPL-1.1 {
+   mozillapubliclicense1.1
+   mpl1.1
+}
+
+MPL-2.0 {
+   mozillapubliclicense
+   mpl2.0
+}
+
+public-domain {
+   publicdomain
+}
+
+ZLIB {
+   zliblicense
+}

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

[André Erdmann]

commit:     5c268a97c1f99fe43a6edbd933fca9551eaee0e7
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Wed Jul 10 14:03:19 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Wed Jul 10 14:03:19 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=5c268a97

config/repo.list: disable CRAN-Archive

---
 config/repo.list | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/config/repo.list b/config/repo.list
index 0d52013..4d8f25d 100644
--- a/config/repo.list
+++ b/config/repo.list
@@ -4,12 +4,12 @@ rsync_uri        = cran.r-project.org::CRAN/src/contrib
 src_uri          = http://cran.r-project.org/src/contrib
 extra_rsync_opts = --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
 
-[CRAN-Archive]
-type             = rsync
-rsync_uri        = cran.r-project.org::CRAN/src/contrib/Archive
-src_uri          = http://cran.r-project.org/src/contrib/Archive
-extra_rsync_opts = --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
-recursive = yes
+#[CRAN-Archive]
+#type             = rsync
+#rsync_uri        = cran.r-project.org::CRAN/src/contrib/Archive
+#src_uri          = http://cran.r-project.org/src/contrib/Archive
+#extra_rsync_opts = --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
+#recursive = yes
 
 [BIOC-2.10/bioc]
 type             = rsync

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

[André Erdmann]

commit:     759e51525d4f8840031492f9f538d4b91ddb678f
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Fri Jul 12 13:56:31 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Fri Jul 12 13:56:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=759e5152

update R-overlay.conf.install

---
 config/R-overlay.conf.install | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/R-overlay.conf.install b/config/R-overlay.conf.install
index 9f4fb53..5285bc7 100644
--- a/config/R-overlay.conf.install
+++ b/config/R-overlay.conf.install
@@ -13,7 +13,7 @@ OVERLAY_DIR="~/roverlay/overlay"
 
 # this is the directory where hard/symbolic links to all package files
 #  will be created (during Manifest file creation)
-DISTDIR="~/roverlay/distdir"
+DISTDIR="~/roverlay/mirror"
 
 LOG_FILE="~/roverlay/log/roverlay.log"
 

[gentoo-commits] proj/R_overlay:gsoc13/next commit in: config/

[André Erdmann]

commit:     8b2eaf23dace19a99848fdde00b95901c4658f2f
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Tue Jul 23 07:50:05 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Tue Jul 23 07:50:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=8b2eaf23

update config/package_rules

Removed the doc section from this file and added a few examples.

---
 config/package_rules | 191 ++++++---------------------------------------------
 1 file changed, 21 insertions(+), 170 deletions(-)

diff --git a/config/package_rules b/config/package_rules
index 560d4d0..ee56bf2 100644
--- a/config/package_rules
+++ b/config/package_rules
@@ -1,190 +1,41 @@
-# roverlay package rules reference
+# package rules file
 #
-# !!! draft / todo
+#  This file lists a few examples.
+#  Refer to "Package Rules" in the usage guide (doc/rst/usage.rst or
+#  doc/html/usage.html).
 #
-# (Concrete examples: scroll down)
 #
-#
-# ========================
-# Package Rule File Syntax
-# ========================
-#
-# Each rule consists of a match- and an action block
-#
-# The basic syntax is <<<
+# set KEYWORDS to "-x86 amd64" for all packages from CRAN that have "x86_64"
+# or "amd64" in their name
 #
 # MATCH:
-#    <match statement 1>
-#    <match statement 2>
-#    ...
-#    <match statement n>
+#    repo == CRAN
+#    or
+#    * package ~ x86_64
+#    * package ~ amd64
 # ACTION:
-#    <action statement 1>
-#    <action statement 2>
-#    ...
-#    <action statement n>
+#    keywords "-x86 amd64"
 # END;
 #
-# >>>
-#
-# As usual, leading whitespace is optional and will be ignored.
-#
-# ------------
-# Match blocks
-# ------------
-#
-# A match block consists of one or more conditions ("match statements")
-# under which a rule applies its actions to a package.
-# It can also contain nested blocks representing a boolean function
-# (AND, OR, NOR, XOR1; syntax: see below)
-# Such "boolean blocks" will _not_ be optimized, so (as usual) be careful
-# with adding unnecessary blocks.
-# The top-level logic for a match block is AND.
-#
-# << copy-paste from roverlay/packagerules/abstract/acceptors.py >>
-# Note:
-#  There's no Acceptor_NOT class.
-#  How would you define a multi-input function "not :: [Acceptor] -> Bool"?
-#  In most cases, you want "none of the listed Acceptors should match",
-#  which is exactly the definition of Acceptor_NOR.
-# << end c-p >>
-#
-# Match statement syntax
-# ----------------------
-#
-# Nested match statements / boolean blocks:
-#
-# <boolean function>
-# * <match statement 1>
-# * <match statement 2>
-# * ...
-# * <match statement n>
-#
-# The leading asterisk chars '*' are important and indicate the match depth.
-# For a match depth > 1 they have to be combined into a single string, e.g.
-# "**" for a match depth of 2.
-# As an alternative to the asterisk char, dash chars '-' can also be used
-# (they're interchangeable).
-#
-# A less abstract example that realizes
-#
-#  f :: (<match statement>^4) -> <match statement>
-#  f (a,b,c,d) := XOR1 ( c, OR ( a, b, AND ( c, d ) ), NOR ( a, d ), b )
-#
-# is <<<
-#
-# xor1
-# * c
-# * or
-# ** a
-# ** b
-# ** and
-# *** c
-# *** d
-# ** nor
-# *** a
-# *** d
-# * b
-#
-# >>>
 #
-# boolean expressions: keywords
-#
-# +======+===============+
-# | func | keywords      |
-# +======+===============+
-# | AND  | and, all, &&  |
-# +------+---------------+
-# | OR   | or,  ||       |
-# +------+---------------+
-# | XOR1 | xor1, xor, ^^ |
-# +------+---------------+
-# | NOR  | nor, none     |
-# +------+---------------+
-#
-# * these keywords are case sensitive
-#
-#
-# "normal" match statements:
-#
-#  A normal match statement consists of a keyword, an operator (optional) and
-#  a value ("argv for the keyword").
-#
-# +===============+=============+====================================+
-# | operator name | operator(s) | description                        |
-# +===============+=============+====================================+
-# | exact-string  | == =        | exact string match                 |
-# +---------------+-------------+------------------------------------+
-# | nocase-string | ,= =,       | case-insensitive string match      |
-# +---------------+-------------+------------------------------------+
-# | exact-regex   | ~= =~       | exact regex match (^<expression>$) |
-# +---------------+-------------+------------------------------------+
-# | regex         | ~~ ~        | partial regex match                |
-# +---------------+-------------+------------------------------------+
-#
-#
-# +==============+==================+================================+
-# | keyword      | default operator | description                    |
-# +==============+==================+================================+
-# | repo         | nocase-string    | alias to repo_name             |
-# +--------------+------------------+--------------------------------+
-# | repo_name    | nocase-string    | name of the repo, e.g. 'CRAN'  |
-# +--------------+------------------+--------------------------------+
-# | package      | implicit         | package name + version         |
-# +--------------+------------------+--------------------------------+
-# | package_name | implicit         | the package name (package file |
-# |              |                  | name without version and file  |
-# |              |                  | extension)                     |
-# +--------------+------------------+--------------------------------+
-# | name         | implicit         | alias to package_name          |
-# +--------------+------------------+--------------------------------+
-#
-# implicit operator: exact-regex if any wildcard char ('?','*') in string
-#                     else exact-string (wildcards will be replaced when
-#                     using the implicit op.)
-#
-#
-# -------------
-# Action blocks
-# -------------
-#
-# action keywords
-# +================+============+==========================+
-# | keyword        | has value? | description              |
-# +================+============+==========================+
-# | ignore         | no         | ignore package           |
-# +----------------+------------+--------------------------+
-# | do-not-process | no         | ignore package           |
-# +----------------+------------+--------------------------+
-# | keywords       | yes        | set per-package KEYWORDS |
-# +----------------+------------+--------------------------+
-#
-# TODO;
-#
-#
-# ========
-# Examples
-# ========
-#
-# ignore all packages starting with R <<<
+# move packages from CRAN and its archive to the sci-CRAN category
+# and prefix their source files with "cran_"
 #
 # MATCH:
-#    package_name R*
+#   or
+#   * repo CRAN
+#   * repo CRAN-Archive
 # ACTION:
-#    ignore
+#    set category sci-CRAN
+#    rename destfile s/^/cran_/
 # END;
 #
-# >>>
 #
-# set KEYWORDS to "-x86 amd64" for all packages from CRAN that have "x86_64"
-# or "amd64" in their name
+# move packages from the bioc repos (BIOC/*) to the sci-BIOC category
 #
 # MATCH:
-#    repo == CRAN
-#    or
-#    * package ~ x86_64
-#    * package ~ amd64
+#    repo ~ ^BIOC
 # ACTION:
-#    keywords "-x86 amd64"
+#    set category sci-BIOC
 # END;
 #

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

[André Erdmann]

commit:     8b2eaf23dace19a99848fdde00b95901c4658f2f
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Tue Jul 23 07:50:05 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Tue Jul 23 07:50:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=8b2eaf23

update config/package_rules

Removed the doc section from this file and added a few examples.

---
 config/package_rules | 191 ++++++---------------------------------------------
 1 file changed, 21 insertions(+), 170 deletions(-)

diff --git a/config/package_rules b/config/package_rules
index 560d4d0..ee56bf2 100644
--- a/config/package_rules
+++ b/config/package_rules
@@ -1,190 +1,41 @@
-# roverlay package rules reference
+# package rules file
 #
-# !!! draft / todo
+#  This file lists a few examples.
+#  Refer to "Package Rules" in the usage guide (doc/rst/usage.rst or
+#  doc/html/usage.html).
 #
-# (Concrete examples: scroll down)
 #
-#
-# ========================
-# Package Rule File Syntax
-# ========================
-#
-# Each rule consists of a match- and an action block
-#
-# The basic syntax is <<<
+# set KEYWORDS to "-x86 amd64" for all packages from CRAN that have "x86_64"
+# or "amd64" in their name
 #
 # MATCH:
-#    <match statement 1>
-#    <match statement 2>
-#    ...
-#    <match statement n>
+#    repo == CRAN
+#    or
+#    * package ~ x86_64
+#    * package ~ amd64
 # ACTION:
-#    <action statement 1>
-#    <action statement 2>
-#    ...
-#    <action statement n>
+#    keywords "-x86 amd64"
 # END;
 #
-# >>>
-#
-# As usual, leading whitespace is optional and will be ignored.
-#
-# ------------
-# Match blocks
-# ------------
-#
-# A match block consists of one or more conditions ("match statements")
-# under which a rule applies its actions to a package.
-# It can also contain nested blocks representing a boolean function
-# (AND, OR, NOR, XOR1; syntax: see below)
-# Such "boolean blocks" will _not_ be optimized, so (as usual) be careful
-# with adding unnecessary blocks.
-# The top-level logic for a match block is AND.
-#
-# << copy-paste from roverlay/packagerules/abstract/acceptors.py >>
-# Note:
-#  There's no Acceptor_NOT class.
-#  How would you define a multi-input function "not :: [Acceptor] -> Bool"?
-#  In most cases, you want "none of the listed Acceptors should match",
-#  which is exactly the definition of Acceptor_NOR.
-# << end c-p >>
-#
-# Match statement syntax
-# ----------------------
-#
-# Nested match statements / boolean blocks:
-#
-# <boolean function>
-# * <match statement 1>
-# * <match statement 2>
-# * ...
-# * <match statement n>
-#
-# The leading asterisk chars '*' are important and indicate the match depth.
-# For a match depth > 1 they have to be combined into a single string, e.g.
-# "**" for a match depth of 2.
-# As an alternative to the asterisk char, dash chars '-' can also be used
-# (they're interchangeable).
-#
-# A less abstract example that realizes
-#
-#  f :: (<match statement>^4) -> <match statement>
-#  f (a,b,c,d) := XOR1 ( c, OR ( a, b, AND ( c, d ) ), NOR ( a, d ), b )
-#
-# is <<<
-#
-# xor1
-# * c
-# * or
-# ** a
-# ** b
-# ** and
-# *** c
-# *** d
-# ** nor
-# *** a
-# *** d
-# * b
-#
-# >>>
 #
-# boolean expressions: keywords
-#
-# +======+===============+
-# | func | keywords      |
-# +======+===============+
-# | AND  | and, all, &&  |
-# +------+---------------+
-# | OR   | or,  ||       |
-# +------+---------------+
-# | XOR1 | xor1, xor, ^^ |
-# +------+---------------+
-# | NOR  | nor, none     |
-# +------+---------------+
-#
-# * these keywords are case sensitive
-#
-#
-# "normal" match statements:
-#
-#  A normal match statement consists of a keyword, an operator (optional) and
-#  a value ("argv for the keyword").
-#
-# +===============+=============+====================================+
-# | operator name | operator(s) | description                        |
-# +===============+=============+====================================+
-# | exact-string  | == =        | exact string match                 |
-# +---------------+-------------+------------------------------------+
-# | nocase-string | ,= =,       | case-insensitive string match      |
-# +---------------+-------------+------------------------------------+
-# | exact-regex   | ~= =~       | exact regex match (^<expression>$) |
-# +---------------+-------------+------------------------------------+
-# | regex         | ~~ ~        | partial regex match                |
-# +---------------+-------------+------------------------------------+
-#
-#
-# +==============+==================+================================+
-# | keyword      | default operator | description                    |
-# +==============+==================+================================+
-# | repo         | nocase-string    | alias to repo_name             |
-# +--------------+------------------+--------------------------------+
-# | repo_name    | nocase-string    | name of the repo, e.g. 'CRAN'  |
-# +--------------+------------------+--------------------------------+
-# | package      | implicit         | package name + version         |
-# +--------------+------------------+--------------------------------+
-# | package_name | implicit         | the package name (package file |
-# |              |                  | name without version and file  |
-# |              |                  | extension)                     |
-# +--------------+------------------+--------------------------------+
-# | name         | implicit         | alias to package_name          |
-# +--------------+------------------+--------------------------------+
-#
-# implicit operator: exact-regex if any wildcard char ('?','*') in string
-#                     else exact-string (wildcards will be replaced when
-#                     using the implicit op.)
-#
-#
-# -------------
-# Action blocks
-# -------------
-#
-# action keywords
-# +================+============+==========================+
-# | keyword        | has value? | description              |
-# +================+============+==========================+
-# | ignore         | no         | ignore package           |
-# +----------------+------------+--------------------------+
-# | do-not-process | no         | ignore package           |
-# +----------------+------------+--------------------------+
-# | keywords       | yes        | set per-package KEYWORDS |
-# +----------------+------------+--------------------------+
-#
-# TODO;
-#
-#
-# ========
-# Examples
-# ========
-#
-# ignore all packages starting with R <<<
+# move packages from CRAN and its archive to the sci-CRAN category
+# and prefix their source files with "cran_"
 #
 # MATCH:
-#    package_name R*
+#   or
+#   * repo CRAN
+#   * repo CRAN-Archive
 # ACTION:
-#    ignore
+#    set category sci-CRAN
+#    rename destfile s/^/cran_/
 # END;
 #
-# >>>
 #
-# set KEYWORDS to "-x86 amd64" for all packages from CRAN that have "x86_64"
-# or "amd64" in their name
+# move packages from the bioc repos (BIOC/*) to the sci-BIOC category
 #
 # MATCH:
-#    repo == CRAN
-#    or
-#    * package ~ x86_64
-#    * package ~ amd64
+#    repo ~ ^BIOC
 # ACTION:
-#    keywords "-x86 amd64"
+#    set category sci-BIOC
 # END;
 #

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

[André Erdmann]

commit:     27d34b0f65180c8e8af400515f9443ae5ffeb076
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Fri Aug  9 12:06:29 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Fri Aug  9 12:06:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=27d34b0f

config/R-overlay.conf.install (generated file)

---
 config/R-overlay.conf.install | 25 ++++++++++++++++++++++---
 1 file changed, 22 insertions(+), 3 deletions(-)

diff --git a/config/R-overlay.conf.install b/config/R-overlay.conf.install
index 5285bc7..e30382a 100644
--- a/config/R-overlay.conf.install
+++ b/config/R-overlay.conf.install
@@ -27,8 +27,8 @@ PORTDIR="/usr/portage"
 
 # --- Logging Configuration (optional) ---
 
-# global log level, choices are ERROR, CRITICAL, WARNING, INFO, DEBUG,
-#  WARN.
+# global log level, choices are DEBUG, INFO, WARN, WARNING, ERROR,
+#  CRITICAL.
 #LOG_LEVEL="WARNING"
 
 #LOG_LEVEL_CONSOLE="INFO"
@@ -60,12 +60,23 @@ SIMPLE_RULES_FILE="/etc/roverlay/simple-deprules.d"
 # list of package rule files/dirs
 PACKAGE_RULES="/etc/roverlay/package-rules.d"
 
+# stats database file
+#  Defaults to "" (disable persistent stats).
+STATS_DB="~/roverlay/cache/stats.rrd"
+
+# database update interval (only used for creating new database files)
+# expected time span between overlay creation runs, in seconds
+#  Defaults to "7200" (2 hours).
+#STATS_INTERVAL="14400"
+
 # script that is run on certain events, e.g. overlay_success
 EVENT_HOOK="/usr/share/roverlay/hooks/mux.sh"
 
 # mask for running hooks
+# Note:
+#  setting -user is highly recommended when running roverlay as root
 #  Defaults to "*" (allow all).
-#EVENT_HOOK_RESTRICT="-* overlay_success"
+EVENT_HOOK_RESTRICT="-* db_written overlay_success user"
 
 # dictionary file for translating license strings
 LICENSE_MAP="/etc/roverlay/license.map"
@@ -99,6 +110,14 @@ DISTDIR_STRATEGY="hardlink symlink"
 #  Defaults to "<CACHEDIR>/distmap.db".
 #DISTMAP_FILE=""
 
+# try to read licenses from PORTDIR/licenses
+#  Defaults to "yes".
+#USE_PORTAGE_LICENSES="no"
+
+# create a licenses file after reading portage licenses
+#  Defaults to "yes".
+#CREATE_LICENSES_FILE="no"
+
 # forbid/allow syncing with remotes
 #  Defaults to "no".
 #NOSYNC="yes"

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

[André Erdmann]

commit:     a17317efef4cf7de370ca72deba0816817d101ca
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Fri Aug 23 13:29:19 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Fri Aug 23 13:32:03 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=a17317ef

config/package_rules: set per-repo categories

---
 config/package_rules | 60 ++++++++++++++++++++++------------------------------
 1 file changed, 25 insertions(+), 35 deletions(-)

diff --git a/config/package_rules b/config/package_rules
index ee56bf2..16644e7 100644
--- a/config/package_rules
+++ b/config/package_rules
@@ -4,38 +4,28 @@
 #  Refer to "Package Rules" in the usage guide (doc/rst/usage.rst or
 #  doc/html/usage.html).
 #
-#
-# set KEYWORDS to "-x86 amd64" for all packages from CRAN that have "x86_64"
-# or "amd64" in their name
-#
-# MATCH:
-#    repo == CRAN
-#    or
-#    * package ~ x86_64
-#    * package ~ amd64
-# ACTION:
-#    keywords "-x86 amd64"
-# END;
-#
-#
-# move packages from CRAN and its archive to the sci-CRAN category
-# and prefix their source files with "cran_"
-#
-# MATCH:
-#   or
-#   * repo CRAN
-#   * repo CRAN-Archive
-# ACTION:
-#    set category sci-CRAN
-#    rename destfile s/^/cran_/
-# END;
-#
-#
-# move packages from the bioc repos (BIOC/*) to the sci-BIOC category
-#
-# MATCH:
-#    repo ~ ^BIOC
-# ACTION:
-#    set category sci-BIOC
-# END;
-#
+
+# per-repo categories
+#
+#  The following rule puts packages from CRAN and its archive into sci-CRAN,
+#  packages from BIOC-2.10/bioc, BIOC-2.10/experiment into sci-BIOC,
+#  omegahat into sci-omegahat etc., while leaving packages from a few
+#  repos (R-Forge and rstan) in the default category.
+#
+MATCH:
+   or
+   * repo R-Forge
+   * repo rstan
+ACTION:
+   # use default category
+   pass
+ELSE:
+   rename category s=^(?P<repo>[^-/]+)([-/].*)?$=sci-\g<repo>=
+END;
+
+## uncomment to move all source files into a separate directory
+#MATCH:
+#   any
+#ACTION:
+#   set destfile R_packages/{package_filename}
+#END;

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

[André Erdmann]

commit:     d4b91461b78d9f56dfdaee3460212fa407b088a0
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Fri Aug 23 13:27:34 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Fri Aug 23 13:27:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=d4b91461

config/repo.list: add rstan

rstan is suggested by a few packages (namely BayesR and ggmcmc).

---
 config/repo.list | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/config/repo.list b/config/repo.list
index 4d8f25d..837ea1b 100644
--- a/config/repo.list
+++ b/config/repo.list
@@ -41,6 +41,11 @@ src_uri = http://www.omegahat.org/R/src/contrib
 # !! RKML has wrong md5 sum in PACKAGES
 digest  = md5
 
+[rstan]
+type    = websync_repo
+src_uri = http://wiki.stan.googlecode.com/git/R/src/contrib
+digest  = none
+
 #[http-packages]
 #type    = websync_pkglist
 #pkglist = config/pkglist_http

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

[André Erdmann]

commit:     0ac5b5496eea464d564e608738971a33692f1b72
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Thu Sep  5 14:40:28 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Thu Sep  5 14:40:28 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=0ac5b549

config/license.map: new entries

---
 config/license.map | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 58 insertions(+), 2 deletions(-)

diff --git a/config/license.map b/config/license.map
index bcaf168..db4c855 100644
--- a/config/license.map
+++ b/config/license.map
@@ -39,7 +39,13 @@ Boost-1.0 {
 }
 
 BSD {
+   bsd_3_clause
+   bsd3clauselicense
+}
+
+BSD-2 {
    freebsd
+   bsd_2_clause
 }
 
 CC0-1.0 {
@@ -49,10 +55,19 @@ CC0-1.0 {
 CC-BY-SA-3.0 {
    ccby-sa3.0us
 }
+
 CC-BY-SA-2.0 {
    ccbysa2.0
 }
 
+CC-BY-NC-SA-3.0 {
+   ccbyncsa3.0
+}
+
+CC-BY-NC-ND-3.0 {
+   ccbyncnd3.0us
+}
+
 || ( CC-BY-SA-3.0 CC-BY-NC-SA-3.0 ) {
    ccbysa3.0us|ccbyncsa3.0
 }
@@ -66,6 +81,10 @@ CPL-0.5 {
    commonpubliclicense1.0
 }
 
+CPL-1.0 {
+   cpl1.0
+}
+
 EPL-1.0 {
    epl
 }
@@ -92,20 +111,38 @@ GPL-2+ {
    gpl2ornewer
    gpl2ornewercopying.
    gpl2ornewer.thetermsofthislicenseareinafilecalledcopyingwhichisprovidedwithr.
+   gnugeneralpubliclicense>2
 }
 
 || ( GPL-2 Artistic-2 ) {
    gpl2|artistic2.0
 }
 
+|| ( BSD-2 GPL-2 ) {
+   freebsd|gpl2
+}
+
+|| ( BSD GPL-2 ) {
+   bsd|gpl2
+}
+
+|| ( GPL-2+ BSD-2 ) {
+   gpl>2|freebsd
+   bsd_2_clause|gpl>2
+}
+
 || ( GPL-2+ BSD ) {
    gpl>2|bsd
-   gpl>2|freebsd
+}
+
+GPL-1 {
+   gpl<2
 }
 
 GPL-3 {
    gpl3
    gpl3.0
+   gplv3
 }
 
 GPL-3+ {
@@ -114,7 +151,7 @@ GPL-3+ {
 }
 
 # gpl licenses without version:
-GPL-3+ {
+GPL-2+ {
    gnugeneralpubliclicense
    gnugeneralpubliclicensegpl
    gnugpl
@@ -122,6 +159,11 @@ GPL-3+ {
    gpl.
 }
 
+# FIXME: non-versioned license statement
+|| ( BSD GPL-2+ Apache-2.0 ) {
+   bsd|gpl|apachelicense
+}
+
 || ( GPL-3+ BSD ) {
    gpl|bsd
 }
@@ -134,6 +176,10 @@ GPL-3+ {
    gpl2|gpl3
 }
 
+|| ( GPL-2+ LGPL-3+ ) {
+   gpl>2|lgpl>3
+}
+
 LGPL-2 {
    lgpl2
 }
@@ -164,6 +210,14 @@ LGPL-3+ {
    lgpl
 }
 
+|| ( LGPL-2 LGPL-2.1 ) {
+   lgpl>2.0,<3
+}
+
+|| ( AGPL-3 GPL-1+ LGPL-2+ ) {
+   gnusomething
+}
+
 MIT {
    mitlicense
 }
@@ -182,7 +236,9 @@ MPL-1.1 {
 
 MPL-2.0 {
    mozillapubliclicense
+   mozillapubliclicense2.0
    mpl2.0
+   mpl>2.0
 }
 
 public-domain {

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

[André Erdmann]

commit:     96b745e406b1030b4f3e7c84deaec4a938235e88
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Sep 23 14:13:30 2013 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Sep 23 14:13:30 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=96b745e4

config/hookrc: more detailed comment

... about GIT_DEFAULT_REMOTE

---
 config/hookrc | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/config/hookrc b/config/hookrc
index 59e3c75..a68eeca 100644
--- a/config/hookrc
+++ b/config/hookrc
@@ -2,13 +2,13 @@
 #
 #  Defaults to "roverlay".
 #
-#GIT_REPO_USER_NAME=""
+GIT_REPO_USER_NAME="Andre Erdmann"
 
 # GIT_REPO_USER_EMAIL
 #
 #  Defaults to "roverlay@undef.org".
 #
-#GIT_REPO_USER_EMAIL=""
+GIT_REPO_USER_EMAIL="dywi@mailerd.de"
 
 # GIT_COMMIT_MESSAGE
 #
@@ -24,12 +24,13 @@
 
 # GIT_DEFAULT_REMOTE
 #
-#  URL to the remote that is used as "origin" when initializing
-#  a new git repo.
+#  URL to the remote that is used as "origin" when (re-)initializing
+#  a git repo that has no remote configured.
 #
 #  Defaults to <not set>.
 #
 #GIT_DEFAULT_REMOTE=""
+GIT_DEFAULT_REMOTE="git://server.exists/repo.too"
 
 # GIT_REMOTES
 #  zero or more "<remote> [<refspec>...]" lines specifying what to push

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

[André Erdmann]

commit:     1a8cbb4d2e34e5f379ed5b61d7e9d1962b22b0fe
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Sat Feb 15 19:45:46 2014 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Sat Feb 15 19:45:46 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=1a8cbb4d

config/repo.list, rstan: fix src_uri

This repo has been moved.

---
 config/repo.list | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/repo.list b/config/repo.list
index 837ea1b..ca68cee 100644
--- a/config/repo.list
+++ b/config/repo.list
@@ -43,7 +43,7 @@ digest  = md5
 
 [rstan]
 type    = websync_repo
-src_uri = http://wiki.stan.googlecode.com/git/R/src/contrib
+src_uri = http://wiki.rstan-repo.googlecode.com/git/src/contrib/
 digest  = none
 
 #[http-packages]

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

[Benda XU]

commit:     a4620f63593f9a7b32043aada57004db3f257804
Author:     Benda Xu <heroxbd <AT> gmail <DOT> com>
AuthorDate: Sun Feb 16 00:18:12 2014 +0000
Commit:     Benda XU <heroxbd <AT> gentoo <DOT> org>
CommitDate: Sun Feb 16 00:20:31 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=a4620f63

config/repo.list: url and rsync args update:

1. bioconductor is at 2.13 release now
2. pass --delete to rsync commandline to save disk space

---
 config/repo.list | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/config/repo.list b/config/repo.list
index ca68cee..f53d5bc 100644
--- a/config/repo.list
+++ b/config/repo.list
@@ -2,38 +2,38 @@
 type             = rsync
 rsync_uri        = cran.r-project.org::CRAN/src/contrib
 src_uri          = http://cran.r-project.org/src/contrib
-extra_rsync_opts = --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
+extra_rsync_opts = --delete --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
 
 #[CRAN-Archive]
 #type             = rsync
 #rsync_uri        = cran.r-project.org::CRAN/src/contrib/Archive
 #src_uri          = http://cran.r-project.org/src/contrib/Archive
-#extra_rsync_opts = --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
+#extra_rsync_opts = --delete --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
 #recursive = yes
 
-[BIOC-2.10/bioc]
+[BIOC-2.13/bioc]
 type             = rsync
-rsync_uri        = bioconductor.org::2.10/bioc/src/contrib
-src_uri          = http://bioconductor.org/packages/2.10/bioc/src/contrib/
-extra_rsync_opts = --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
+rsync_uri        = master.bioconductor.org::2.13/bioc/src/contrib
+src_uri          = http://master.bioconductor.org/packages/2.13/bioc/src/contrib/
+extra_rsync_opts = --delete --exclude=/PACKAGES --exclude=/PACKAGES.gz --progress
 
-[BIOC-2.10/annotation]
+[BIOC-2.13/annotation]
 type             = rsync
-rsync_uri        = bioconductor.org::2.10/data/annotation/src/contrib
-src_uri          = http://bioconductor.org/packages/2.10/data/annotation/src/contrib
-extra_rsync_opts = --progress --exclude=/PACKAGES --exclude=/PACKAGES.gz
+rsync_uri        = master.bioconductor.org::2.13/data/annotation/src/contrib
+src_uri          = http://master.bioconductor.org/packages/2.13/data/annotation/src/contrib
+extra_rsync_opts = --progress --delete --exclude=/PACKAGES --exclude=/PACKAGES.gz
 
-[BIOC-2.10/experiment]
+[BIOC-2.13/experiment]
 type             = rsync
-rsync_uri        = bioconductor.org::2.10/data/experiment/src/contrib
-src_uri          = http://bioconductor.org/packages/2.10/data/experiment/src/contrib
-extra_rsync_opts = --progress --exclude=/PACKAGES --exclude=/PACKAGES.gz
+rsync_uri        = master.bioconductor.org::2.13/data/experiment/src/contrib
+src_uri          = http://master.bioconductor.org/packages/2.13/data/experiment/src/contrib
+extra_rsync_opts = --progress --delete --exclude=/PACKAGES --exclude=/PACKAGES.gz
 
 [R-Forge]
 type             = rsync
 rsync_uri        = download.r-forge.r-project.org::R-Forge/src/contrib
 src_uri          = http://download.r-forge.r-project.org/src/contrib
-extra_rsync_opts = --progress --exclude=/PACKAGES --exclude=/PACKAGES.gz
+extra_rsync_opts = --progress --delete --exclude=/PACKAGES --exclude=/PACKAGES.gz
 
 [omegahat]
 type    = websync_repo

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

[André Erdmann]

commit:     25b1ad1fb8921eba4f1b811ee27430ede6af4f56
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Feb 17 17:31:23 2014 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Feb 17 17:31:23 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=25b1ad1f

config/hookrc: remove debug/test entries

---
 config/hookrc | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/config/hookrc b/config/hookrc
index a68eeca..8eb686c 100644
--- a/config/hookrc
+++ b/config/hookrc
@@ -2,13 +2,13 @@
 #
 #  Defaults to "roverlay".
 #
-GIT_REPO_USER_NAME="Andre Erdmann"
+#GIT_REPO_USER_NAME=""
 
 # GIT_REPO_USER_EMAIL
 #
 #  Defaults to "roverlay@undef.org".
 #
-GIT_REPO_USER_EMAIL="dywi@mailerd.de"
+#GIT_REPO_USER_EMAIL=""
 
 # GIT_COMMIT_MESSAGE
 #
@@ -30,7 +30,6 @@ GIT_REPO_USER_EMAIL="dywi@mailerd.de"
 #  Defaults to <not set>.
 #
 #GIT_DEFAULT_REMOTE=""
-GIT_DEFAULT_REMOTE="git://server.exists/repo.too"
 
 # GIT_REMOTES
 #  zero or more "<remote> [<refspec>...]" lines specifying what to push

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

[André Erdmann]

commit:     f4531ed9e7d9086f4bb391d93274d276f313aea2
Author:     André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Mon Jul 14 00:00:14 2014 +0000
Commit:     André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Mon Jul 14 00:00:17 2014 +0000
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
 }