* [gentoo-commits] proj/R_overlay:gsoc13/next commit in: /, doc/man/, config/
@ 2013-07-10 15:10 André Erdmann
2013-07-10 16:16 ` [gentoo-commits] proj/R_overlay:master " André Erdmann
0 siblings, 1 reply; 2+ messages in thread
From: André Erdmann @ 2013-07-10 15:10 UTC (permalink / raw
To: gentoo-commits
commit: 75458f730c96c6892df40da34a2966a349319007
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Wed Jul 10 13:57:32 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Wed Jul 10 13:57:32 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=75458f73
remove deprecated documentation files
config/*.reference and doc/man/* are out-of-date and redundant since
the provided documentation is available in doc/rst/.
---
README | 1 -
config/R-overlay.conf.reference | 342 ----------------------------------
config/repo.list.reference | 105 -----------
config/simple-deprules.conf.reference | 167 -----------------
doc/man/roverlay-deprules.5 | 185 ------------------
doc/man/roverlay-repo.5 | 173 -----------------
doc/man/roverlay.1 | 118 ------------
doc/man/show | 2 -
8 files changed, 1093 deletions(-)
diff --git a/README b/README
index 4ccb403..75cf00e 100644
--- a/README
+++ b/README
@@ -17,7 +17,6 @@ misc/ -- miscellaneous files, e.g. a sed expression that makes roverlay.py
doc/ -- documentation root directory
doc/rst -- roverlay documentation (in reStructuredText)
doc/html -- html version of the latest 'stable' rst documentation
-doc/man -- roverlay man pages
doc/pydoc -- code self-documentation in html, can be created with 'make pydoc'
diff --git a/config/R-overlay.conf.reference b/config/R-overlay.conf.reference
deleted file mode 100644
index 067e1a7..0000000
--- a/config/R-overlay.conf.reference
+++ /dev/null
@@ -1,342 +0,0 @@
-# R-overlay.conf
-# This file explains how to write a R overlay main config,
-# it can also be used as config file.
-#
-# -- Table of contents --
-#
-# 1 -- config value types and file syntax
-# 2 -- config quickstart (basic overview of options to set)
-# 3 -- config entries
-# a -- misc
-# b -- overlay
-# c -- other config files
-# d -- logging
-# e -- other (debugging, testing, ...)
-#
-# -- end of ToC --
-
-# = config value types and file syntax =
-
-# This file is parsed using shlex (shell-like syntax)
-# * '#' is the comment char
-# * variables ("${X}") are not supported
-# * whitespace is ignored (in most cases)
-# => whitespace in file paths is generally not supported,
-# but may work with some restrictions
-# * quotes are optional, but allow to span long values over multiple lines,
-# e.g. <<
-# SIMPLE_RULES_FILE="<path to first rule file>
-# <another one>
-# "
-# >>
-#
-#
-# some options have value type restrictions,
-#
-# special value types used in this config ("* allowed values: <type>"):
-#
-# log level -- choose from {DEBUG, INFO, WARN, WARNING, ERROR, CRITICAL}
-# bool -- string that represents a boolean value,
-# true := {y,yes,on,1,true,enabled}
-# false := {n,no,off,0,false,disabled}
-# other values are not allowed
-#
-#
-# implicit value types:
-#
-# list -- option has multiple values separated by whitespace,
-# use quotes to specify more than one value
-#
-# file, dir -- value will be expanded ( ~ => ${HOME}, x => ${PWD}/x etc.),
-# value has to be a file (or dir) if it exists
-#
-# <empty> -- often leads to errors (in case of value type restrictions),
-# just comment out config entries
-#
-#
-#
-# "*** NOT IN USE ***" means that an option is read and integrated into
-# the config tree, but never used (normal entry in config/entrymap).
-# => value will be validated
-#
-# "*** <option> is not available> ***" means that an option is read, but
-# ignored ("None" entry in config/entrymap).
-# => value won't be validated
-
-
-# = config quick start =
-# This is a listing of options to consider
-#
-# options that are required:
-# 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?
-# FIELD_DEFINITION (or use --field-definition <file>)
-#
-# options that are optional but essential for a usable result:
-# OVERLAY_ECLASS,
-# SIMPLE_RULES_FILE (or use --deprule-file <file>)
-#
-# some options for logging:
-# LOG_CONSOLE,
-# LOG_FILE,
-# LOG_LEVEL,
-# LOG_LEVEL_FILE,
-# LOG_LEVEL_CONSOLE
-#
-# some options for debugging and testing:
-# LOG_FILE_UNRESOLVABLE,
-# DESCRIPTION_DIR
-#
-
-
-# = config starts here =
-
-# == misc options ==
-
-# DISTFILES_ROOT
-# the root directory of repo distdirs
-# Repos will create their distdirs in this directory unless
-# they specify another location.
-# * alias: DISTDIR, DISTFILES
-# * defaults to <unset> (but required!)
-#DISTFILES_ROOT = "distfiles-root"
-
-
-# == overlay options ==
-
-# OVERLAY_NAME
-# name of the overlay
-# * defaults to <unset> (but required!)
-#OVERLAY_NAME = "ROverlay"
-
-# OVERLAY_DIR
-# overlay root directory
-# This is the directory where the overlay content, e.g. ebuilds and
-# profiles/repo_name will be written into.
-# * defaults to <unset> (but required!)
-#OVERLAY_DIR = "overlay-root"
-
-# OVERLAY_ECLASS
-# eclass files to import into the overlay and us in ebuilds
-# Note that overlay creation fails if importing any of the
-# specified eclass files fails.
-# * accepted values: a list of files that end with '.eclass' or
-# don't have an extension
-# * defaults to <unset> (empty list) - this is NOT useful
-# * alias: ECLASS
-#OVERLAY_ECLASS = "eclass/R-packages.eclass"
-
-# OVERLAY_CATEGORY
-# overlay category of the created ebuilds
-# * accepted values: no restrictions made, but don't insert a '/'!
-# * defaults to sci-R
-#OVERLAY_CATEGORY = 'dev-R'
-
-# OVERLAY_KEEP_NTH_LATEST
-# keep the n-th latest ebuilds per R package, removing all others
-# * accepted values: integer, has no effect if < 1
-# * defaults to <unset>, which disables this option (keep all ebuilds)
-#OVERLAY_KEEP_NTH_LATEST = 3
-
-# EBUILD_HEADER
-# ebuild header file that will be included in all created ebuilds
-# *** NOT IN USE ***
-#EBUILD_HEADER = "ebuild_header.txt"
-
-# OVERLAY_MANIFEST_IMPLEMENTATION
-# Manifest implementation to be used
-# Currently, there's only one implementation available, manifest
-# writing using the ebuild(1) executable.
-# * accepted values:
-# -> 'default' -- use the default implementation
-# -> 'none' -- do not use any implementation,
-# this leads to runtime errors
-# whenever write_manifest() is called
-# -> 'external:ebuild' -- generate Manifest files using ebuild(1)
-#
-# * defaults to 'default'
-# * alias: MANIFEST_IMPLEMENTATION
-
-# == other config files ==
-
-# some config options are split from this file for various reasons:
-# * no need to be modifed by users (in most cases)
-# -> FIELD_DEFINITION
-# * special syntax that is not compatible with this file
-# -> SIMPLE_RULES_FILE
-# * special syntax that eases adding/reading entries (-> all)
-# * config is independent from this file
-# -> e.g. per-repo script runs using the same main config ("-R <file>" option)
-
-
-# FIELD_DEFINITION
-# path to the config file that controls DESCRIPTION file reading
-# * defaults to <unset> (but required!)
-# * alias: FIELD_DEFINITION_FILE
-#FIELD_DEFINITION = "description_fields.conf"
-
-# REPO_CONFIG
-# path to the repo config file
-# Please see the example file for file format.
-# * defaults to <unset> (but required!)
-# * alias: REPO_CONFIG_FILE, REPO_CONFIG_FILES
-#REPO_CONFIG = "repo.list"
-
-# SIMPLE_RULES_FILE
-# list of (simple) dependency rule files or dirs
-# Please see the rule example file for file format.
-# Directories will be non-recursively scanned for files.
-# Files can also be compressed, either bzip2 (.bz2 file ext) or gzip (.gz)
-# * defaults to <unset>, which effectively disables dependency resolution
-# since no other dependency resolution methods are available.
-# This gives poor results!
-# * alias: SIMPLE_RULES_FILES
-#SIMPLE_RULES_FILE = "simple-deprules.d/R"
-
-# == logging ==
-
-# LOG_ENABLED
-# enable/disable logging (globally)
-# * accepted values: bool
-# * defaults to enabled => use per-log target settings, e.g. LOG_CONSOLE
-#LOG_ENABLED = "no"
-
-# LOG_LEVEL
-# the default log level
-# Choices are DEBUG, INFO, WARN, WARNING, ERROR, CRITICAL.
-# * defaults to <unset>, which causes console/file logging
-# to use their own defaults
-#LOG_LEVEL = DEBUG
-
-# LOG_DATE_FORMAT
-# date format used in logging
-# * defaults to '%F %H:%M:%S'.
-#LOG_DATE_FORMAT = '%a, %H:%M'
-
-# *** LOG_FORMAT is not available ***
-
-
-# === console logging ===
-
-# LOG_CONSOLE
-# enable/disable logging to console
-# * accepted values: bool
-# * defaults to enabled
-# * alias: LOG_CONSOLE_ENABLED
-#LOG_CONSOLE = "no"
-
-# LOG_FORMAT_CONSOLE
-# log format used in console logging
-# * defaults to '%(levelname)-8s %(name)-14s: %(message)s'
-# * alias: LOG_CONSOLE_FORMAT
-#LOG_FORMAT_CONSOLE = '[%(name)s] %(message)s'
-
-# LOG_LEVEL_CONSOLE
-# log level for console logging, see LOG_LEVEL
-# * accepted values: a log level
-# * defaults to INFO
-# * alias: LOG_CONSOLE_LEVEL
-#LOG_LEVEL_CONSOLE = "DEBUG"
-
-# *** LOG_CONSOLE_STREAM is not available ***
-
-
-# === file logging ===
-
-# LOG_FILE
-# log file to write
-# File logging will be disabled if left blank / commented out.
-# * defaults to <unset>
-#LOG_FILE = ""
-
-# LOG_LEVEL_FILE
-# log level used in file logging
-# * accepted values: a log level, see LOG_LEVEL
-# * defaults to: WARNING
-# * alias: LOG_FILE_LEVEL
-#LOG_LEVEL_FILE = "ERROR"
-
-# LOG_FORMAT_FILE
-# log format used in file logging
-# * defaults to '%(asctime)s %(levelname)-8s %(name)-10s: %(message)s'
-# * alias: LOG_FILE_FORMAT
-#LOG_FORMAT_FILE = '%(asctime)s $(levelname)s [%(name)s]: %(message)s'
-
-# LOG_FILE_ROTATE
-# enable/disable log file rotation
-# The log file will be rotated on every script run.
-# * accepted values: bool
-# * defaults to disabled
-#LOG_FILE_ROTATE = "yes"
-
-# LOG_FILE_ROTATE_COUNT
-# number of rotated log files to keep
-# Only used when log file rotation is enabled.
-# * accepted values: int (make sure it's >= 0)
-# * defaults to 3
-#LOG_FILE_ROTATE_COUNT = 10
-
-# LOG_FILE_BUFFERED
-# buffer log entries in memory before writing them to the log file
-# This should reduce I/O blocking when using low log levels with threads.
-# * accepted values: bool
-# * defaults to enabled
-#LOG_FILE_BUFFERED = "no"
-
-# LOG_FILE_BUFFER_COUNT
-# max number of log entries to buffer
-# Only used when log entry buffering is enabled.
-# * accepted values: integer (make sure that the value is >= 1)
-# * defaults to 250
-# * alias: LOG_FILE_BUFFER_CAPACITY
-#LOG_FILE_BUFFER_COUNT = 50
-
-# LOG_FILE_ENABLED
-# enable/disable logging to file
-# * accepted values: bool
-# * defaults to enabled (which grants LOG_FILE control over this setting)
-#LOG_FILE_ENABLED = "no"
-
-
-# == options for debugging, (manual) dependency rule creation, testing, ... ==
-
-# LOG_FILE_UNRESOLVABLE
-# file where unresolved dependency strings will be written to
-# Useful if you want to create new rules,
-# run -> read unresolvable file -> create rules -> rerun.
-# Comment out to disable.
-# * defaults to <unset>
-#LOG_FILE_UNRESOLVABLE = "log/dep_unresolvable.log"
-
-# LOG_FILE_RESOLVED
-# file where resolved dep strings will be written to
-# *** NOT IN USE ***
-#LOG_FILE_RESOLVED = ""
-
-# DESCRIPTION_DIR
-# directory where description files will be written into
-# If enabled: write all read description files to
-# <descfiles dir>/<R package name>_<R package version>.desc
-# Comment out to disable.
-# * defaults to <unset>
-# * alias: DESCRIPTION_DESCFILES_DIR
-#DESCRIPTION_DIR = "desc-files"
-
-# EBUILD_PROG
-# name of/path to the ebuild executable
-# * accepted values: no restrictions made,
-# but overlay writing will fail if the value is invalid,
-# which is a huge time loss since ebuilds have been created before writing.
-# * defaults to "ebuild"
-#EBUILD_PROG = "/usr/local/bin/ebuild"
-
-# RSYNC_BWLIMIT
-# set a max. average rsync bandwidth usage (in kilobytes/second)
-# This is a per-"rsync command" setting using rsync's "--bwlimit" option
-# Note: you can set per-repo bwlimit's in the repo config file
-# TODO-note: ^ make sure that this option doesn't interfere
-# * accepted values: int (>0 expected)
-# * defaults to <unset>
-#RSYNC_BWLIMIT = 10000
diff --git a/config/repo.list.reference b/config/repo.list.reference
deleted file mode 100644
index 378c03e..0000000
--- a/config/repo.list.reference
+++ /dev/null
@@ -1,105 +0,0 @@
-# repo.list
-# This file explains how to write repo config files.
-
-# !! out of date, see man/roverlay-repo.5
-
-# This file is parsed used ConfigParser syntax (known from .ini files).
-
-# A repo entry describes
-# * where to find R packages that will be used for overlay creation,
-# and optionally where and how to get the R packages (using repo types)
-# * how ebuilds can download the R packages (=> SRC_URI)
-
-# Each repository is introduced with [<section name>] and has to declare
-# some options.
-#
-# general options are:
-#
-# * required:
-#
-# src_uri -- this is used to determine the SRC_URI in ebuilds
-# (SRC_URI=<src_uri>/<package file name>)
-# FIXME note: check that subdirs are handled correctly
-#
-# * optional:
-#
-# name -- name of the repository
-# optional, defaults to <section name>
-# type -- the type of this repo, see below
-# optional, defaults to rsync
-# directory -- the local package directory,
-# optional, defaults to <DISTFILES ROOT (from config)>/<name>
-#
-# (base_uri -- don't use, to be removed)
-#
-#
-# There are two types of repos, "rsync" and "local" ones:
-#
-# * Local repo;
-# A Local repo represents a directory with R packages in it.
-# It will never be modified (i.e. synced) and has no special options.
-#
-# * Rsync repo:
-# An Rsync repo uses a local directory to sync with a remote.
-# Its directory will be modified whenever syncing (using the rsync program).
-# Behaves like a local repo if syncing is disabled.
-#
-# default rsync options (always passed to rsync):
-# --links, --safe-links, --times, --compress, --dirs, --prune-empty-dirs,
-# --force, --delete, --human-readable, --stats, --chmod=ugo=r,u+w,Dugo+x
-#
-# This type has special options:
-#
-# rsync_uri -- required, rsync uri
-# recursive -- optional, passes '--recursive' to rsync
-# if this option is set to 'yes'
-# extra_rsync_opts -- optional options to pass to rsync, this
-# can be used to exclude/include files,
-# show progress while syncing etc.
-# Note: options cannot contain whitespace! (#FIXME note: this could be allowed if useful)
-#
-#
-
-
-# == Repo entry examples ==
-
-# a local directory with packages in /var/www/R_packages
-#
-#[local_packages]
-#type = local
-#src_uri = http://localhost/R_packages
-#directory = /var/www/R_packages
-
-
-# a local directory with packages manually downloaded from CRAN
-# * directory will be automatically set to <DISTROOT>/CRAN/selected
-#
-#[CRAN/selected]
-#type = local
-#src_uri = http://cran.r-project.org/src/contrib
-
-# CRAN rsync repo
-# * type will be set to rsync
-# * directory will be set to <DISTROOT>/CRAN/all
-# * rsync progress will be shown during transfer
-# * not recursive, the package archive and R release won't be fetched
-# * this needs about 2.5G disk space
-#
-#[CRAN/all]
-#src_uri = http://cran.r-project.org/src/contrib
-#rsync_uri = cran.r-project.org::CRAN/src/contrib
-#extra_rsync_opts = --progress
-
-# CRAN rsync repo (selective transfer)
-# * type is explicitly set to rsync
-# * only packages starting with "r" or "R" will be fetched
-# * directory will be set to <DISTROOT>/CRAN/only_letter_R
-# * rsync progress will be shown during transfer
-# * not recursive
-# * this needs about 300M disk space
-#
-#[CRAN/only_letter_R]
-#type = rsync
-#src_uri = http://cran.r-project.org/src/contrib
-#rsync_uri = cran.r-project.org::CRAN/src/contrib
-#extra_rsync_opts = --include=r* --include=R* --exclude=* --progress
diff --git a/config/simple-deprules.conf.reference b/config/simple-deprules.conf.reference
deleted file mode 100644
index 3c15bac..0000000
--- a/config/simple-deprules.conf.reference
+++ /dev/null
@@ -1,167 +0,0 @@
-#! NOPARSE
-#
-# simple dependency rules file
-#
-# This file has been replaced by the dep rule files in simple-deprules.d/,
-# but explains the syntax.
-#
-# === Syntax ===
-#
-# You can specify single and multiline rules here,
-# the basic syntax is "<portage identifier> <matches> <keyword(s)>".
-#
-#
-# There are two types of dependency string matching:
-# standard : a dep string has to match exactly
-# "R(>=2.15)" != "R" => UNRESOLVABLE
-#
-# fuzzy : the resolver will try to find a match using string
-# interpolation/metrics
-# "R(>=2.15)" ~ "R" => ">=dev-lang/R-2.15"
-# "R(!=2.15)" ~ "R" => "(!dev-lang/R-2.15 dev-lang/R)"
-# "R(>=2.15)" % "R" => <ignored> (% is fuzzy ignore)
-#
-#
-# a single line entry looks like
-## (1) <portage package> :: <dependency string> (standard simple dep)
-## (2) ~<portage package> :: <dependency string> (fuzzy simple dep)
-## (3) <dependency string> (standard selfdep)
-## (4) ~<dependency string> (fuzzy selfdep)
-## (5) ! :: <dependency string> (standard ignored dep)
-## (6) % :: <dependency string> (fuzzy ignored dep)
-#
-# Dependency strings are case-insensitive.
-#
-# (3) and (4) are shortcuts for [~]<overlay category>/<dep> :: <dep>,
-# e.g. "fftw" matches "fftw" and resolves to "sci-R/fftw".
-# This is useful 'cause you don't have to use a hardcoded overlay category
-# here.
-# (5) and (6) are ways to define deps that should be ignored
-# (=resolved to nothing). They're identical to (1)/(2), but use ! / % as
-# portage package.
-#
-#
-# a multiline entry looks like
-## [~]<portage package> {
-## <dependency string 1>
-## <dependency string 2>
-## ...
-## <dependency string n>
-## }
-#
-# selfdeps cannot be declared in a multiline rule
-#
-# The precedence order of the rules in this file is
-## single line ignore > single line > multi line ignore > multi line
-#### this has to be fixed in the dep rule reader
-#
-# Note:
-# * you cannot write comments in a multiline rule, writing
-## dev-lang/R {
-## # the following dep should resolve to R
-## R(>= 2.15.0)
-## }
-# means that both strings '# the following dep should resolve to R' and
-# 'R(>= 2.15.0)' resolve to 'dev-lang/R'!
-#
-# * compound portage dependency statements (man 5 ebuild) are supported,
-# but only in standard simple deps, e.g.
-## || ( <dev-lang/R-2.14.0 >dev-lang/R-2.14.0 ) :: R (!= 2.14.0)
-#
-#
-
-# === Examples ===
-
-# == single line entries ==
-
-# = standard simple dep =
-# this rule matches 'R (>= 2.15.0)' and resolves it as 'dev-lang/R-2.15.0'
-dev-lang/R-2.15.0 :: R (>= 2.15.0)
-
-# = fuzzy simple dep =
-
-# this rule matches
-## (a) R <version modifier?> <version>
-## (b) R (<version modifier?> <version>)
-## (c) R [<version modifier?> <version>]
-## (d) R {<version modifier?> <version>}
-## (e) R
-# variant (a) is whitespace sensitive (>= 1 whitespace char between R and
-# the version modifier/version), the others ignore all whitespace chars.
-# variant (e) is the standard simple rule behaviour.
-#
-# the dep string is then resolved as <version modifier?>dev-lang/R-<version>
-#
-# version modifier is optional and can be one out of {>=, <=, >, <, !=, =, ! },
-# where ! / != are being resolved a 'specific version is forbidden'.
-# '>=' is assumed as version modifier if it is left out and a specific version
-# is required.
-#
-# examples matches:
-# (a) r 2.13 -> >=dev-lang/R-2.13
-# (b) R(>= 2.14) -> >=dev-lang/R-2.14
-# (c) R [<2.10] -> <dev-lang/R-2.10
-# (d) r{ !2.12 } -> ( !=dev-lang/R-2.12 dev-lang/R )
-# (e) R -> dev-lang/R
-#
-~dev-lang/R :: R
-
-# = standard selfdep =
-# resolves "tuneR","tuner",.. as "sci-R/tuneR"
-tuneR
-
-# = fuzzy selfdep =
-# * see fuzzy simple dep
-# example match: resolves "zoo 1.10" as ">=sci-R/zoo-1.10"
-~zoo
-
-# = standard ignored dep =
-# ignores "R"
-! :: R
-
-# = fuzzy ignored dep =
-# ignores everything that fuzzy-matches R (see fuzzy simple dep)
-% :: R
-
-# == multi line entries ==
-
-# = simple multiline rule =
-# matches "R (>= 2.15)", "R" and resolves them as dev-lang/R
-dev-lang/R {
- R (>= 2.15)
- R
-}
-
-# = fuzzy multiline rule =
-~dev-lang/R {
- R
- the R programming language
-}
-
-# = ignored dep multiline rule =
-# equals ! :: see README
-! {
- see README
-}
-
-# = fuzzy ignored dep multiline rule =
-# equals % :: R
-% {
- R
-}
-
-# === Extra ===
-
-# There's a special keyword that tells the rule reader to stop parsing,
-# see line #1. It has to be exactly '#! NOPARSE' or '#! BREAK', with no
-# additional content at the end of the line.
-#! NOPARSE
-#! BREAK
-
-# There's also a keyword to set the dependency type (sys, pkg or all),
-# the syntax is '#deptype <type>'.
-#deptype sys
-#deptype pkg
-#deptype all
-
-
diff --git a/doc/man/roverlay-deprules.5 b/doc/man/roverlay-deprules.5
deleted file mode 100644
index e801ee8..0000000
--- a/doc/man/roverlay-deprules.5
+++ /dev/null
@@ -1,185 +0,0 @@
-.\" NO LONGER USED - see doc/rst for deprule configuration
-.\" groff -Tascii -man
-.TH "ROVERLAY-DEPRULES" "5" "July 10 2012" "Linux/Gentoo?" "R Overlay"
-.SH "NAME"
-deprules \- R overlay dependency rule configuration
-.SH "SYNOPSIS"
-\fBsimple-deprules.conf\fR
-.SH "DESCRIPTION"
-A simple dependency rule file defines one or more rules
-that are used for dependency resolution in \fBroverlay(1)\fR.
-.PP
-A rule defines which \fIdep_string\fR read from an R package resolves
-to a specific \fIdependency\fR.
-\fIdependency\fR can be a \fBDEPEND atom\fR or \fBDynamic DEPEND\fR,
-see \fBebuild(5)\fR.
-\'The R programming language\',
-for example, should resolve to \'dev\-lang/R\'.
-Other dependencies such as packages from @system,
-should be ignored since they\'re always provided.
-This is also possible.
-
-.IP "\(bu simple rules"
-These rules are very simple and match a \fIdep_string\fR exactly.
-.IP "\(bu fuzzy rules"
-These rules try to find a match for \fIdep_string\fR using string interpolation, metrics and/or regex matches.
-.SS "RULE VARIANTS"
-.IP "\(bu normal"
-\fIdep_string\fR will be resolved as \fIdependency\fR.
-.IP "\(bu ignore"
-\fIdep_string\fR will be ignored if it matches an ignore rule.
-
-.SS "RULE STUBS"
-There\'s a special (shorter) syntax for dependencies
-that are resolved within the created overlay.
-For example, if your \fIOVERLAY_CATEGORY\fR is \'sci\-R\',
-\'zoo\' should be resolved as \'sci\-R/zoo\'.
-This rule can be written as a single word, \'zoo\'.
-The advantage is that you don\'t have to write the
-overlay category into the rule file.
-These stubs are called \fBselfdeps\fR.
-
-
-.SS "BASIC SYNTAX"
-.IP "\(bu rule that matches one \fIdep_string\fR"
-[\fIkeyword\fR and/or \fIdependency\fR] :: \fIdep_string\fR
-.br
-.IP "\(bu rule that matches multiple \fIdep_string\fRs"
-This replaces " :: \fIdep_string\fR" by a multiline variant
-.br
-[\fIkeyword\fR and/or \fIdependency\fR] \&{
-.br
-\& \fIdep_string\fR
-.br
-\& [\fIdep_string\fR]
-.br
-\& [\fIdep_string\fR]
-.br
-\& \&.\&.\&.
-.br
-\&}
-.br
-.IP "\fBselfdep\fR rule"
-[\fIkeyword\fR]\fIshort_dependency\fR
-.br
-where \fIshort_dependency\fR is a package name (\fBDEPEND atom\fR without version, category).
-This is the only way to specify selfdeps.
-
-.SS "ADDITIONAL SYNTAX"
-Comments start with \'#\', with a few exceptions:
-.TP
-dependency type
-There's a keyword to set the dependency type of all rules following this statement,
-\'#deptype <type>\' where type is \'sys\', \'pkg\' or \'all\'.
-.TP
-stop reading
-There are two special keywords that both cause reading a rule file to stop, \'#! BREAKPARSE\' and \'#! NOPARSE\'.
-The line must exactly be one of these keywords (no additional content at the end of the line).
-
-
-
-.SH "SIMPLE RULES"
-A simple rule resolves exact string matches (case-insensitive).
-.SS "SYNTAX"
-.IP "\(bu normal"
-\fIdependency\fR :: \fIdep_string\fR
-.IP "\(bu ignore"
-! :: \fIdep_string\fR
-.IP "\(bu selfdep, normal"
-\fIshort_dependency\fR
-.IP "\(bu selfdep, ignored"
-!\fIshort_dependency\fR
-
-.SH "FUZZY RULES"
-A fuzzy rule tries to resolve, i.e. "resolve \fIdep_string\fR as \fIdependency\fR if it \fIsomehow\fR matches a \fIfuzzy_string\fR".
-The \fIsomehow\fR is up to the implementation, it currently includes:
-.SS "EXACT MATCH"
-This is equal to the \fBSIMPLE RULES\fR
-.SS "VERSION\-RELATIVE MATCH"
-Uses regexes to identify \fIdep_string\fRs
-that only differ in the requested version (and/or version syntax).
-"R (\&>\&= 2.15)" and "R[2.10]", for instance, should be resolved as "dev\-lang/R".
-A single fuzzy\-rule "~dev\-lang/R :: R" does this and resolves them as
-"\&>=dev\-lang/R\-2.15" and "\&>=dev\-lang/R\-2.10", respectively.
-Note that this is just an example, \fBroverlay(1)\fR will filter out dependencies on
-dev\-lang/R when the version is \&<= the lowest version available in portage.
-.br
-In detail, this method matches if
-.br
-\& \fIdep_string\fR ~= \fIfuzzy_string\fR \&<\fIversion_statement\fR\&>
-.br
-where \fIversion_statement\fR ::= [\&<\fIversion_modifier\fR\&>] \&<\fIversion\fR\&>
-.br
-and \fIversion_modifier\fR is one out of \&{\&<, \&>, \&=, \&!, \&<\&=, \&>\&=, \&=\&=, \&!\&=\&}.
-.br
-
-Examples: \&'\&>=2.10\&', \&'\&!=0.9\&', \&'1.0\&', \&'\&<5\&'.
-
-Version statements can optionally be enclosed with braces (\&'()\&', \&'[]\&', \&'{}\&').
-Whitespace is ignored unless \fIversion_statment\fR is not enclosed,
-in which case some whitespace (more than zero chars) must exist between
-\fIfuzzy_string\fR and \fIversion_statment\fR.
-
-.SS SYNTAX
-Fuzzy rules use ~ and % as keyword.
-.IP "\(bu normal"
-\&~\fIdependency\fR :: \fIfuzzy_string\fR
-.IP "\(bu ignore"
-\&%\fIdependency\fR :: \fIfuzzy_string\fR
-.IP "\(bu selfdep"
-\&~\fIshort_dependency\fR
-.IP "\(bu selfdep, ignored"
-\&%\fIshort_dependency\fR
-
-.SH "EXAMPLES"
-Example 1:
-.RS 1
-A rule that matches many dependencies on dev\-lang/R,
-for example "r 2.12", "R(\&>= 2.14)", "R [\&<2.10]", "r{ !2.12 }", and "R".
-.RS 2
-
-\&~dev\-lang/R :: R
-.RE
-.RE
-.PP
-Example 2:
-.RS 1
-A rule that fuzzy-matches a zoo package selfdep.
-.RS 2
-
-\&~zoo
-.RE
-.RE
-.PP
-Example 3:
-.RS 1
-A standard self dep, resolves "tuneR", "tuner", ... as "sci\-R/tuneR"
-(\fIOVERLAY_CATEGORY\fR/tuneR).
-.RS 2
-
-\&tuneR
-.RE
-.RE
-.PP
-Example 4:
-.RS 1
-A simple multiline rule that ignores some text.
-This is a good way to deal with free-style text found in
-some R package DESCRIPTION files.
-.RS 2
-
-! :: {
-.RS 2
-see README
-.br
-read INSTALL
-.br
-[which can be downloaded from http://...]
-.br
-.RE
-}
-.RE
-.RE
-
-.SH "SEE ALSO"
-.BR "roverlay(1)"
diff --git a/doc/man/roverlay-repo.5 b/doc/man/roverlay-repo.5
deleted file mode 100644
index a517109..0000000
--- a/doc/man/roverlay-repo.5
+++ /dev/null
@@ -1,173 +0,0 @@
-.\" NO LONGER USED - see doc/rst for repo configuration
-.\" groff -Tascii -man
-.TH "ROVERLAY-REPO" "5" "July 10 2012" "Linux/Gentoo?" "R Overlay"
-.SH "NAME"
-roverlay-repo \- R overlay repo config file
-.SH "SYNOPSIS"
-.BR "repo.list"
-.SH "DESCRIPTION"
-A repo config file is used to define repositories, both local and remote, and
-uses ConfigParser syntax (known from .ini files).
-.SS "REPO ENTRIES"
-A repo entry describes where to find R packages that will be used for overlay creation,
-and optionally where and how to get the R packages (using \fBREPO TYPES\fR).
-It also defines how ebuilds can download the R packages (used as \fISRC_URI\fR variable in ebuilds).
-.SS "REPO TYPES"
-There are 4 types of repos, "local", "rsync", "websync_repo" and "websync_pkglist":
-.IP "\(bu local repositories (\&'local\&')"
-A \fBlocal repo\fR represents a directory with R packages in it.
-It will never be modified (i.e. synced) and has no special options.
-.IP "\(bu rsync repositories (\&'rsync\&')"
-An \fBrsync repo\fR uses a local directory to sync with a remote.
-Its directory will be modified whenever syncing (using the rsync program).
-It behaves like a local repo if syncing is disabled.
-.br
-These rsync options are always passed to rsync:
-.br
-\fB
-\-\-links, \-\-safe-links,
-\-\-times,
-\-\-dirs, \-\-prune-empty-dirs,
-\-\-human-readable, \-\-stats,
-\-\-chmod=ugo=r,u+w,Dugo+
-\fR
-.IP "\(bu websync repositories (\&'websync_repo\&')"
-A \fBwebsync repo\fR fetches an R package list (deb-control file, typically named PACKAGES)
-from a remote and downloads all packages afterwards (via http). It supports file-size and basic digest
-verification for downloaded packages.
-Nosync mode support for this type of repo is limited, it will report all packages from its
-directory as synced.
-.IP "\(bu package list websync (\&'websync_pkglist\&')"
-This is not a real repo type, it merely reads package uris from a file
-(one \&'http://...\&' entry per line) and downloads them (via http).
-Package uri entries must end with \&'.tar.gz\&', else ebuild creation is not possible.
-Nosync mode support is limited, all packages that exist locally will be reported as synced.
-.PP
-.SH "VARIABLES"
-Each repository is introduced with [\fIsection_name\fR] and has to declare some options.
-.SS "common options"
-.TP
-.BR "src_uri" " = \fIuri\fR"
-This is used to determine the \fISRC_URI\fR variable used in ebuilds.
-\fIuri\fR usually starts with 'http://' which can be left out,
-"localhost/R-packages" is the same uri as "http://localhost/R-packages".
-Always required unless \fItype\fR is websync_pkglist in which case this option has no effect.
-.TP
-.BR "name" " = \fIrepo_name\fR"
-Specify a name for the repository.
-Optional, defaults to \fIsection_name\fR
-which should be fine in most cases. The repo name should not contain whitespace.
-.TP
-.BR "type" " = \fItype\fR"
-Set the repo type. Optional, defaults to rsync (see \fBREPO_TYPES\fR).
-.TP
-.BR "directory" " = \fIdirectory\fR"
-Set the local package directory.
-Optional, defaults to \fIDISTFILES_ROOT\fR/\fIname\fR
-(see \fIDISTFILES_ROOT\fR in \fBR\-overlay.conf\fR).
-
-.SS "special options for local repos"
-None.
-
-.SS "special options for rsync repos"
-.TP
-.BR "rsync_uri" " = \fIrsync_uri\fR"
-Set the uri used for downloading the R packages into \fIdirectory\fR.
-Always required.
-.TP
-.BR "recursive" " = yes"
-If set to 'yes': pass '\-\-recursive' to rsync.
-This is optional and not enabled by default 'cause downloading sub directories is not always desirable.
-In case of CRAN, this would download the whole R package archive and all R releases.
-.TP
-.BR "extra_rsync_opts" " = \fIopts\fR"
-A whitespace-separated list of extra options that will be passed to rsync.
-Useful to in-/exclude files/dirs, show progress while running rsync etc.
-Options must not contain whitespace/quote chars.
-Note that the options won't be verified - this is \fBtotally unsafe!\fR
-.SS "special options for websync repos"
-.TP
-.BR "pkglist_file" " = \fIfilename\fR"
-Name of the package list file that will be downloaded.
-Optional, defaults to \&'PACKAGES\&', which should be fine in
-most cases. Note that reading compressed package lists (e.g. \&'PACKAGES.gz\&')
-is not supported. Has no effect if \fBpkglist_uri\fR is set.
-.TP
-.BR "pkglist_uri" " = \fIuri\fR"
-Fetch \fIuri\fR and use it as package list.
-Optional, defaults to \fIsrc_uri\fR/\fIpkglist_file\fR.
-.TP
-.BR "digest_type" " = \fIdigest_type\fR"
-Verify downloaded packages using \fIdigest_type\fR.
-Available choices are \&'md5\&' and \&'none\&'. The remote has to support this,
-i.e. list digests in the \fIpkglist_file\fR.
-.SS "special options for package list websync"
-.TP
-.BR "pkglist_file" " = \fIfile\fR"
-Path to the file that lists all package uris.
-.SH "EXAMPLES"
-Example 1:
-.RS 1
-A local directory with packages in /var/www/R-packages
-that are available on your network via "http://package_host/R-packages".
-.RS 2
-
-[local_packages]
-.br
-type = local
-.br
-src_uri = http://package_host/R-packages
-.br
-directory = /var/www/R-packages
-.RE
-.RE
-.PP
-Example 2:
-.RS 1
-A local directory with packages manually downloaded from CRAN.
-The directory will be automatically set to \fIDISTFILES_ROOT\fR/CRAN/selected.
-.RS 2
-
-[CRAN/selected]
-.br
-type = local
-.br
-src_uri = http://cran.r-project.org/src/contrib
-.RE
-.RE
-.PP
-Example 3:
-.RS 1
-An rsync repo for CRAN's current packages (CRAN without archive).
-The local DISTFILES_ROOT dir will be set to \fIDISTFILES_ROOT\fR/CRAN/all.
-This needs about 2.5G disk space (as of July 2012).
-.RS 2
-
-[CRAN/all]
-.br
-src_uri = http://cran.r-project.org/src/contrib
-.br
-rsync_uri = cran.r-project.org::CRAN/src/contrib
-.RE
-.RE
-.PP
-Example 4:
-.RS 1
-A repo that selectively syncs packages from CRAN that start with 'r' or 'R'
-to \fIDISTFILES_ROOT\fR/CRAN/only_letter_R. This can be realized using \fIextra_rsync_opts\fR.
-Also showing progress during transfer.
-This needs about 300M disk space.
-.RS 2
-
-[CRAN/only_letter_R]
-.br
-src_uri = http://cran.r-project.org/src/contrib
-.br
-rsync_uri = cran.r-project.org::CRAN/src/contrib
-.br
-extra_rsync_opts = \-\-include=r* \-\-include=R* \-\-exclude=* \-\-progress
-.RE
-.RE
-
-.SH "SEE ALSO"
-.BR "roverlay(1)"
diff --git a/doc/man/roverlay.1 b/doc/man/roverlay.1
deleted file mode 100644
index 2fda183..0000000
--- a/doc/man/roverlay.1
+++ /dev/null
@@ -1,118 +0,0 @@
-.\" groff -Tascii -man
-.TH "ROVERLAY" "1" "Auguest 20 2012" "roverlay" "R Overlay"
-
-.SH "NAME"
-roverlay \- create and maintain an overlay of R packages
-
-.SH "SYNOPSIS"
-.TP
-.BR "roverlay " "[\fIoptions\fR] [\fIcommand\fR]..."
-.TP
-.BR "roverlay " "\fB\-h\fR | \fB\-\-help\fR"
-.TP
-.BR "roverlay " "\fB\-\-help-config\fR"
-.TP
-.BR "roverlay " "\fB\-\-print-config\fR"
-.TP
-.BR "roverlay " "\fB\-V\fR | \fB\-\-version\fR"
-.SH "DESCRIPTION"
-roverlay is a program that generates a portage overlay for R packages.
-It runs without any user interaction and uses config files to control the
-overlay creation.
-.SH "COMMANDS"
-.TP
-.BR sync
-Sync all repos. Has no effect if no remote repository configured..
-.TP
-.BR create
-Create the overlay - read R packages and try to create ebuilds for them.
-Implies \fBsync\fR unless \fB\-\-nosync\fR is given.
-This is the default command.
-.SH "OPTIONS"
-.TP
-.BR "\-\-help " "(\fB\-h\fR)"
-Print a help message and exit
-.TP
-.BR "\-\-version " "(\fB\-V\fR)"
-Print the program's version and exit
-.TP
-.BR "\-\-help\-config"
-Print all known config options and exit
-.TP
-.BR "\-\-print\-config"
-Print the config tree after reading the config file and exit
-.SS "configuration files"
-.TP
-.BR "\-\-config " "\fIfilename\fR"
-Read the main configuration from \fIfilename\fR instead of ${PWD}/R-overlay.conf
-.TP
-.BR "\-\-deprule\-file " "\fIfilename\fR (\fB\-D\fR)"
-Read dependency rules from \fIfilename\fR instead of reading the
-files listed in the main config (\fISIMPLE_RULES_FILE\fR).
-Can be specified more than once.
-.TP
-.BR "\-\-field\-definition " "\fIfilename\fR (\fB\-F\fR)"
-Read the field definition from \fIfilename\fR instead
-of the \fIFIELD_DEFINITION\fR file specified in the main config.
-.TP
-.BR "\-\-repo\-config " "\fIfilename\fR (\fB\-R\fR)"
-Read the repo config from \fIfilename\fR instead
-of the files listed in the main config (\fIREPO_CONFIG\fR).
-Can be specified more than once.
-.SS "R packages"
-.TP
-.BR "\-\-distdir" "\fR, " "\-\-from " "\fIdirectory\fR"
-Create ebuilds for packages in \fIdirectory\fR.
-Implies \fBcreate\fR and \fB\-\-nosync\fR.
-Disables all other repos.
-.TP
-.BR "\-\-distroot " "\fIdirectory\fR"
-Set the distroot to \fIdirectory\fR.
-This is used as root for all per-repo package dirs that don't define another location.
-.TP
-.BR "\-\-force\-distroot"
-Use the distroot even for repos that define their own location.
-.TP
-.BR "\-\-nosync" "\fR, " "\-\-no\-sync"
-Disable repo syncing (offline mode). Blocks the \fBsync\fR command.
-.SS "overlay"
-.TP
-.BR "\-\-show" "\fR, " "\-\-show\-overlay"
-Print ebuilds/metadata after creation to stderr.
-.TP
-.BR "\-\-write" "\fR, " "\-\-write\-overlay"
-Write the whole overlay after creation.
-This includes ebuilds, metadata, Manifest files and the profiles/ dir.
-Enabled by default, making this option redundant.
-.TP
-.BR "\-\-no\-write" "\fR, " "\-\-no\-write\-overlay"
-Don't write the overlay.
-.TP
-.BR "\-\-stats" "\fR, " "\-\-no\-stats"
-Print some stats after overlay creation/writing.
-.TP
-.BR "\-\-no\-manifest"
-Skip Manifest file creation to save time. Note that the resulting overlay
-cannot be used with portage/emerge.
-.TP
-.BR "\-\-no\-incremental"
-Ignore an existing overlay and create ebuilds even if they already exist
-.TP
-.BR "\-\-immediate\-ebuild\-writes"
-Write ebuilds as soon as they're created (trade memory for speed)
-.TP
-.BR "\-\-overlay " "\fIdirectory\fR (\fB\-O\fR)"
-Set the overlay directory to \fIdirectory\fR. Else
-\fIOVERLAY_DIR\fR from the main config will be used.
-.TP
-.BR "\-\-overlay\-name " "\fIname\fR (\fB\-N\fR)"
-Set the overlay name to \fIname\fR.
-Else \fIOVERLAY_NAME\fR from the main config will be used.
-.SH "EXAMPLES"
-.TP
-roverlay \-c \fIconfig\fR
-Run overlay creation with sync, all options (overlay name/dir,...) are read from \fIconfig\fR
-.TP
-roverlay \-\-from \fIpkgdir\fR \-O \fIoverlay\fR \-N R_Overlay \-\-field-definition \fIfield_definition\fR \-D \fIdeprules\fR
-Run overlay creation for packages from \fIpkgdir\fR and write the overlay named R_Overlay to \fIoverlay\fR.
-Use the given \fIfield_definition\fR and \fIdeprules\fR files.
diff --git a/doc/man/show b/doc/man/show
deleted file mode 100755
index 6c0fa0e..0000000
--- a/doc/man/show
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-groff -Tascii -man "${1:?}" | ${PAGER:-less}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/R_overlay:master commit in: /, doc/man/, config/
2013-07-10 15:10 [gentoo-commits] proj/R_overlay:gsoc13/next commit in: /, doc/man/, config/ André Erdmann
@ 2013-07-10 16:16 ` André Erdmann
0 siblings, 0 replies; 2+ messages in thread
From: André Erdmann @ 2013-07-10 16:16 UTC (permalink / raw
To: gentoo-commits
commit: 75458f730c96c6892df40da34a2966a349319007
Author: André Erdmann <dywi <AT> mailerd <DOT> de>
AuthorDate: Wed Jul 10 13:57:32 2013 +0000
Commit: André Erdmann <dywi <AT> mailerd <DOT> de>
CommitDate: Wed Jul 10 13:57:32 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=75458f73
remove deprecated documentation files
config/*.reference and doc/man/* are out-of-date and redundant since
the provided documentation is available in doc/rst/.
---
README | 1 -
config/R-overlay.conf.reference | 342 ----------------------------------
config/repo.list.reference | 105 -----------
config/simple-deprules.conf.reference | 167 -----------------
doc/man/roverlay-deprules.5 | 185 ------------------
doc/man/roverlay-repo.5 | 173 -----------------
doc/man/roverlay.1 | 118 ------------
doc/man/show | 2 -
8 files changed, 1093 deletions(-)
diff --git a/README b/README
index 4ccb403..75cf00e 100644
--- a/README
+++ b/README
@@ -17,7 +17,6 @@ misc/ -- miscellaneous files, e.g. a sed expression that makes roverlay.py
doc/ -- documentation root directory
doc/rst -- roverlay documentation (in reStructuredText)
doc/html -- html version of the latest 'stable' rst documentation
-doc/man -- roverlay man pages
doc/pydoc -- code self-documentation in html, can be created with 'make pydoc'
diff --git a/config/R-overlay.conf.reference b/config/R-overlay.conf.reference
deleted file mode 100644
index 067e1a7..0000000
--- a/config/R-overlay.conf.reference
+++ /dev/null
@@ -1,342 +0,0 @@
-# R-overlay.conf
-# This file explains how to write a R overlay main config,
-# it can also be used as config file.
-#
-# -- Table of contents --
-#
-# 1 -- config value types and file syntax
-# 2 -- config quickstart (basic overview of options to set)
-# 3 -- config entries
-# a -- misc
-# b -- overlay
-# c -- other config files
-# d -- logging
-# e -- other (debugging, testing, ...)
-#
-# -- end of ToC --
-
-# = config value types and file syntax =
-
-# This file is parsed using shlex (shell-like syntax)
-# * '#' is the comment char
-# * variables ("${X}") are not supported
-# * whitespace is ignored (in most cases)
-# => whitespace in file paths is generally not supported,
-# but may work with some restrictions
-# * quotes are optional, but allow to span long values over multiple lines,
-# e.g. <<
-# SIMPLE_RULES_FILE="<path to first rule file>
-# <another one>
-# "
-# >>
-#
-#
-# some options have value type restrictions,
-#
-# special value types used in this config ("* allowed values: <type>"):
-#
-# log level -- choose from {DEBUG, INFO, WARN, WARNING, ERROR, CRITICAL}
-# bool -- string that represents a boolean value,
-# true := {y,yes,on,1,true,enabled}
-# false := {n,no,off,0,false,disabled}
-# other values are not allowed
-#
-#
-# implicit value types:
-#
-# list -- option has multiple values separated by whitespace,
-# use quotes to specify more than one value
-#
-# file, dir -- value will be expanded ( ~ => ${HOME}, x => ${PWD}/x etc.),
-# value has to be a file (or dir) if it exists
-#
-# <empty> -- often leads to errors (in case of value type restrictions),
-# just comment out config entries
-#
-#
-#
-# "*** NOT IN USE ***" means that an option is read and integrated into
-# the config tree, but never used (normal entry in config/entrymap).
-# => value will be validated
-#
-# "*** <option> is not available> ***" means that an option is read, but
-# ignored ("None" entry in config/entrymap).
-# => value won't be validated
-
-
-# = config quick start =
-# This is a listing of options to consider
-#
-# options that are required:
-# 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?
-# FIELD_DEFINITION (or use --field-definition <file>)
-#
-# options that are optional but essential for a usable result:
-# OVERLAY_ECLASS,
-# SIMPLE_RULES_FILE (or use --deprule-file <file>)
-#
-# some options for logging:
-# LOG_CONSOLE,
-# LOG_FILE,
-# LOG_LEVEL,
-# LOG_LEVEL_FILE,
-# LOG_LEVEL_CONSOLE
-#
-# some options for debugging and testing:
-# LOG_FILE_UNRESOLVABLE,
-# DESCRIPTION_DIR
-#
-
-
-# = config starts here =
-
-# == misc options ==
-
-# DISTFILES_ROOT
-# the root directory of repo distdirs
-# Repos will create their distdirs in this directory unless
-# they specify another location.
-# * alias: DISTDIR, DISTFILES
-# * defaults to <unset> (but required!)
-#DISTFILES_ROOT = "distfiles-root"
-
-
-# == overlay options ==
-
-# OVERLAY_NAME
-# name of the overlay
-# * defaults to <unset> (but required!)
-#OVERLAY_NAME = "ROverlay"
-
-# OVERLAY_DIR
-# overlay root directory
-# This is the directory where the overlay content, e.g. ebuilds and
-# profiles/repo_name will be written into.
-# * defaults to <unset> (but required!)
-#OVERLAY_DIR = "overlay-root"
-
-# OVERLAY_ECLASS
-# eclass files to import into the overlay and us in ebuilds
-# Note that overlay creation fails if importing any of the
-# specified eclass files fails.
-# * accepted values: a list of files that end with '.eclass' or
-# don't have an extension
-# * defaults to <unset> (empty list) - this is NOT useful
-# * alias: ECLASS
-#OVERLAY_ECLASS = "eclass/R-packages.eclass"
-
-# OVERLAY_CATEGORY
-# overlay category of the created ebuilds
-# * accepted values: no restrictions made, but don't insert a '/'!
-# * defaults to sci-R
-#OVERLAY_CATEGORY = 'dev-R'
-
-# OVERLAY_KEEP_NTH_LATEST
-# keep the n-th latest ebuilds per R package, removing all others
-# * accepted values: integer, has no effect if < 1
-# * defaults to <unset>, which disables this option (keep all ebuilds)
-#OVERLAY_KEEP_NTH_LATEST = 3
-
-# EBUILD_HEADER
-# ebuild header file that will be included in all created ebuilds
-# *** NOT IN USE ***
-#EBUILD_HEADER = "ebuild_header.txt"
-
-# OVERLAY_MANIFEST_IMPLEMENTATION
-# Manifest implementation to be used
-# Currently, there's only one implementation available, manifest
-# writing using the ebuild(1) executable.
-# * accepted values:
-# -> 'default' -- use the default implementation
-# -> 'none' -- do not use any implementation,
-# this leads to runtime errors
-# whenever write_manifest() is called
-# -> 'external:ebuild' -- generate Manifest files using ebuild(1)
-#
-# * defaults to 'default'
-# * alias: MANIFEST_IMPLEMENTATION
-
-# == other config files ==
-
-# some config options are split from this file for various reasons:
-# * no need to be modifed by users (in most cases)
-# -> FIELD_DEFINITION
-# * special syntax that is not compatible with this file
-# -> SIMPLE_RULES_FILE
-# * special syntax that eases adding/reading entries (-> all)
-# * config is independent from this file
-# -> e.g. per-repo script runs using the same main config ("-R <file>" option)
-
-
-# FIELD_DEFINITION
-# path to the config file that controls DESCRIPTION file reading
-# * defaults to <unset> (but required!)
-# * alias: FIELD_DEFINITION_FILE
-#FIELD_DEFINITION = "description_fields.conf"
-
-# REPO_CONFIG
-# path to the repo config file
-# Please see the example file for file format.
-# * defaults to <unset> (but required!)
-# * alias: REPO_CONFIG_FILE, REPO_CONFIG_FILES
-#REPO_CONFIG = "repo.list"
-
-# SIMPLE_RULES_FILE
-# list of (simple) dependency rule files or dirs
-# Please see the rule example file for file format.
-# Directories will be non-recursively scanned for files.
-# Files can also be compressed, either bzip2 (.bz2 file ext) or gzip (.gz)
-# * defaults to <unset>, which effectively disables dependency resolution
-# since no other dependency resolution methods are available.
-# This gives poor results!
-# * alias: SIMPLE_RULES_FILES
-#SIMPLE_RULES_FILE = "simple-deprules.d/R"
-
-# == logging ==
-
-# LOG_ENABLED
-# enable/disable logging (globally)
-# * accepted values: bool
-# * defaults to enabled => use per-log target settings, e.g. LOG_CONSOLE
-#LOG_ENABLED = "no"
-
-# LOG_LEVEL
-# the default log level
-# Choices are DEBUG, INFO, WARN, WARNING, ERROR, CRITICAL.
-# * defaults to <unset>, which causes console/file logging
-# to use their own defaults
-#LOG_LEVEL = DEBUG
-
-# LOG_DATE_FORMAT
-# date format used in logging
-# * defaults to '%F %H:%M:%S'.
-#LOG_DATE_FORMAT = '%a, %H:%M'
-
-# *** LOG_FORMAT is not available ***
-
-
-# === console logging ===
-
-# LOG_CONSOLE
-# enable/disable logging to console
-# * accepted values: bool
-# * defaults to enabled
-# * alias: LOG_CONSOLE_ENABLED
-#LOG_CONSOLE = "no"
-
-# LOG_FORMAT_CONSOLE
-# log format used in console logging
-# * defaults to '%(levelname)-8s %(name)-14s: %(message)s'
-# * alias: LOG_CONSOLE_FORMAT
-#LOG_FORMAT_CONSOLE = '[%(name)s] %(message)s'
-
-# LOG_LEVEL_CONSOLE
-# log level for console logging, see LOG_LEVEL
-# * accepted values: a log level
-# * defaults to INFO
-# * alias: LOG_CONSOLE_LEVEL
-#LOG_LEVEL_CONSOLE = "DEBUG"
-
-# *** LOG_CONSOLE_STREAM is not available ***
-
-
-# === file logging ===
-
-# LOG_FILE
-# log file to write
-# File logging will be disabled if left blank / commented out.
-# * defaults to <unset>
-#LOG_FILE = ""
-
-# LOG_LEVEL_FILE
-# log level used in file logging
-# * accepted values: a log level, see LOG_LEVEL
-# * defaults to: WARNING
-# * alias: LOG_FILE_LEVEL
-#LOG_LEVEL_FILE = "ERROR"
-
-# LOG_FORMAT_FILE
-# log format used in file logging
-# * defaults to '%(asctime)s %(levelname)-8s %(name)-10s: %(message)s'
-# * alias: LOG_FILE_FORMAT
-#LOG_FORMAT_FILE = '%(asctime)s $(levelname)s [%(name)s]: %(message)s'
-
-# LOG_FILE_ROTATE
-# enable/disable log file rotation
-# The log file will be rotated on every script run.
-# * accepted values: bool
-# * defaults to disabled
-#LOG_FILE_ROTATE = "yes"
-
-# LOG_FILE_ROTATE_COUNT
-# number of rotated log files to keep
-# Only used when log file rotation is enabled.
-# * accepted values: int (make sure it's >= 0)
-# * defaults to 3
-#LOG_FILE_ROTATE_COUNT = 10
-
-# LOG_FILE_BUFFERED
-# buffer log entries in memory before writing them to the log file
-# This should reduce I/O blocking when using low log levels with threads.
-# * accepted values: bool
-# * defaults to enabled
-#LOG_FILE_BUFFERED = "no"
-
-# LOG_FILE_BUFFER_COUNT
-# max number of log entries to buffer
-# Only used when log entry buffering is enabled.
-# * accepted values: integer (make sure that the value is >= 1)
-# * defaults to 250
-# * alias: LOG_FILE_BUFFER_CAPACITY
-#LOG_FILE_BUFFER_COUNT = 50
-
-# LOG_FILE_ENABLED
-# enable/disable logging to file
-# * accepted values: bool
-# * defaults to enabled (which grants LOG_FILE control over this setting)
-#LOG_FILE_ENABLED = "no"
-
-
-# == options for debugging, (manual) dependency rule creation, testing, ... ==
-
-# LOG_FILE_UNRESOLVABLE
-# file where unresolved dependency strings will be written to
-# Useful if you want to create new rules,
-# run -> read unresolvable file -> create rules -> rerun.
-# Comment out to disable.
-# * defaults to <unset>
-#LOG_FILE_UNRESOLVABLE = "log/dep_unresolvable.log"
-
-# LOG_FILE_RESOLVED
-# file where resolved dep strings will be written to
-# *** NOT IN USE ***
-#LOG_FILE_RESOLVED = ""
-
-# DESCRIPTION_DIR
-# directory where description files will be written into
-# If enabled: write all read description files to
-# <descfiles dir>/<R package name>_<R package version>.desc
-# Comment out to disable.
-# * defaults to <unset>
-# * alias: DESCRIPTION_DESCFILES_DIR
-#DESCRIPTION_DIR = "desc-files"
-
-# EBUILD_PROG
-# name of/path to the ebuild executable
-# * accepted values: no restrictions made,
-# but overlay writing will fail if the value is invalid,
-# which is a huge time loss since ebuilds have been created before writing.
-# * defaults to "ebuild"
-#EBUILD_PROG = "/usr/local/bin/ebuild"
-
-# RSYNC_BWLIMIT
-# set a max. average rsync bandwidth usage (in kilobytes/second)
-# This is a per-"rsync command" setting using rsync's "--bwlimit" option
-# Note: you can set per-repo bwlimit's in the repo config file
-# TODO-note: ^ make sure that this option doesn't interfere
-# * accepted values: int (>0 expected)
-# * defaults to <unset>
-#RSYNC_BWLIMIT = 10000
diff --git a/config/repo.list.reference b/config/repo.list.reference
deleted file mode 100644
index 378c03e..0000000
--- a/config/repo.list.reference
+++ /dev/null
@@ -1,105 +0,0 @@
-# repo.list
-# This file explains how to write repo config files.
-
-# !! out of date, see man/roverlay-repo.5
-
-# This file is parsed used ConfigParser syntax (known from .ini files).
-
-# A repo entry describes
-# * where to find R packages that will be used for overlay creation,
-# and optionally where and how to get the R packages (using repo types)
-# * how ebuilds can download the R packages (=> SRC_URI)
-
-# Each repository is introduced with [<section name>] and has to declare
-# some options.
-#
-# general options are:
-#
-# * required:
-#
-# src_uri -- this is used to determine the SRC_URI in ebuilds
-# (SRC_URI=<src_uri>/<package file name>)
-# FIXME note: check that subdirs are handled correctly
-#
-# * optional:
-#
-# name -- name of the repository
-# optional, defaults to <section name>
-# type -- the type of this repo, see below
-# optional, defaults to rsync
-# directory -- the local package directory,
-# optional, defaults to <DISTFILES ROOT (from config)>/<name>
-#
-# (base_uri -- don't use, to be removed)
-#
-#
-# There are two types of repos, "rsync" and "local" ones:
-#
-# * Local repo;
-# A Local repo represents a directory with R packages in it.
-# It will never be modified (i.e. synced) and has no special options.
-#
-# * Rsync repo:
-# An Rsync repo uses a local directory to sync with a remote.
-# Its directory will be modified whenever syncing (using the rsync program).
-# Behaves like a local repo if syncing is disabled.
-#
-# default rsync options (always passed to rsync):
-# --links, --safe-links, --times, --compress, --dirs, --prune-empty-dirs,
-# --force, --delete, --human-readable, --stats, --chmod=ugo=r,u+w,Dugo+x
-#
-# This type has special options:
-#
-# rsync_uri -- required, rsync uri
-# recursive -- optional, passes '--recursive' to rsync
-# if this option is set to 'yes'
-# extra_rsync_opts -- optional options to pass to rsync, this
-# can be used to exclude/include files,
-# show progress while syncing etc.
-# Note: options cannot contain whitespace! (#FIXME note: this could be allowed if useful)
-#
-#
-
-
-# == Repo entry examples ==
-
-# a local directory with packages in /var/www/R_packages
-#
-#[local_packages]
-#type = local
-#src_uri = http://localhost/R_packages
-#directory = /var/www/R_packages
-
-
-# a local directory with packages manually downloaded from CRAN
-# * directory will be automatically set to <DISTROOT>/CRAN/selected
-#
-#[CRAN/selected]
-#type = local
-#src_uri = http://cran.r-project.org/src/contrib
-
-# CRAN rsync repo
-# * type will be set to rsync
-# * directory will be set to <DISTROOT>/CRAN/all
-# * rsync progress will be shown during transfer
-# * not recursive, the package archive and R release won't be fetched
-# * this needs about 2.5G disk space
-#
-#[CRAN/all]
-#src_uri = http://cran.r-project.org/src/contrib
-#rsync_uri = cran.r-project.org::CRAN/src/contrib
-#extra_rsync_opts = --progress
-
-# CRAN rsync repo (selective transfer)
-# * type is explicitly set to rsync
-# * only packages starting with "r" or "R" will be fetched
-# * directory will be set to <DISTROOT>/CRAN/only_letter_R
-# * rsync progress will be shown during transfer
-# * not recursive
-# * this needs about 300M disk space
-#
-#[CRAN/only_letter_R]
-#type = rsync
-#src_uri = http://cran.r-project.org/src/contrib
-#rsync_uri = cran.r-project.org::CRAN/src/contrib
-#extra_rsync_opts = --include=r* --include=R* --exclude=* --progress
diff --git a/config/simple-deprules.conf.reference b/config/simple-deprules.conf.reference
deleted file mode 100644
index 3c15bac..0000000
--- a/config/simple-deprules.conf.reference
+++ /dev/null
@@ -1,167 +0,0 @@
-#! NOPARSE
-#
-# simple dependency rules file
-#
-# This file has been replaced by the dep rule files in simple-deprules.d/,
-# but explains the syntax.
-#
-# === Syntax ===
-#
-# You can specify single and multiline rules here,
-# the basic syntax is "<portage identifier> <matches> <keyword(s)>".
-#
-#
-# There are two types of dependency string matching:
-# standard : a dep string has to match exactly
-# "R(>=2.15)" != "R" => UNRESOLVABLE
-#
-# fuzzy : the resolver will try to find a match using string
-# interpolation/metrics
-# "R(>=2.15)" ~ "R" => ">=dev-lang/R-2.15"
-# "R(!=2.15)" ~ "R" => "(!dev-lang/R-2.15 dev-lang/R)"
-# "R(>=2.15)" % "R" => <ignored> (% is fuzzy ignore)
-#
-#
-# a single line entry looks like
-## (1) <portage package> :: <dependency string> (standard simple dep)
-## (2) ~<portage package> :: <dependency string> (fuzzy simple dep)
-## (3) <dependency string> (standard selfdep)
-## (4) ~<dependency string> (fuzzy selfdep)
-## (5) ! :: <dependency string> (standard ignored dep)
-## (6) % :: <dependency string> (fuzzy ignored dep)
-#
-# Dependency strings are case-insensitive.
-#
-# (3) and (4) are shortcuts for [~]<overlay category>/<dep> :: <dep>,
-# e.g. "fftw" matches "fftw" and resolves to "sci-R/fftw".
-# This is useful 'cause you don't have to use a hardcoded overlay category
-# here.
-# (5) and (6) are ways to define deps that should be ignored
-# (=resolved to nothing). They're identical to (1)/(2), but use ! / % as
-# portage package.
-#
-#
-# a multiline entry looks like
-## [~]<portage package> {
-## <dependency string 1>
-## <dependency string 2>
-## ...
-## <dependency string n>
-## }
-#
-# selfdeps cannot be declared in a multiline rule
-#
-# The precedence order of the rules in this file is
-## single line ignore > single line > multi line ignore > multi line
-#### this has to be fixed in the dep rule reader
-#
-# Note:
-# * you cannot write comments in a multiline rule, writing
-## dev-lang/R {
-## # the following dep should resolve to R
-## R(>= 2.15.0)
-## }
-# means that both strings '# the following dep should resolve to R' and
-# 'R(>= 2.15.0)' resolve to 'dev-lang/R'!
-#
-# * compound portage dependency statements (man 5 ebuild) are supported,
-# but only in standard simple deps, e.g.
-## || ( <dev-lang/R-2.14.0 >dev-lang/R-2.14.0 ) :: R (!= 2.14.0)
-#
-#
-
-# === Examples ===
-
-# == single line entries ==
-
-# = standard simple dep =
-# this rule matches 'R (>= 2.15.0)' and resolves it as 'dev-lang/R-2.15.0'
-dev-lang/R-2.15.0 :: R (>= 2.15.0)
-
-# = fuzzy simple dep =
-
-# this rule matches
-## (a) R <version modifier?> <version>
-## (b) R (<version modifier?> <version>)
-## (c) R [<version modifier?> <version>]
-## (d) R {<version modifier?> <version>}
-## (e) R
-# variant (a) is whitespace sensitive (>= 1 whitespace char between R and
-# the version modifier/version), the others ignore all whitespace chars.
-# variant (e) is the standard simple rule behaviour.
-#
-# the dep string is then resolved as <version modifier?>dev-lang/R-<version>
-#
-# version modifier is optional and can be one out of {>=, <=, >, <, !=, =, ! },
-# where ! / != are being resolved a 'specific version is forbidden'.
-# '>=' is assumed as version modifier if it is left out and a specific version
-# is required.
-#
-# examples matches:
-# (a) r 2.13 -> >=dev-lang/R-2.13
-# (b) R(>= 2.14) -> >=dev-lang/R-2.14
-# (c) R [<2.10] -> <dev-lang/R-2.10
-# (d) r{ !2.12 } -> ( !=dev-lang/R-2.12 dev-lang/R )
-# (e) R -> dev-lang/R
-#
-~dev-lang/R :: R
-
-# = standard selfdep =
-# resolves "tuneR","tuner",.. as "sci-R/tuneR"
-tuneR
-
-# = fuzzy selfdep =
-# * see fuzzy simple dep
-# example match: resolves "zoo 1.10" as ">=sci-R/zoo-1.10"
-~zoo
-
-# = standard ignored dep =
-# ignores "R"
-! :: R
-
-# = fuzzy ignored dep =
-# ignores everything that fuzzy-matches R (see fuzzy simple dep)
-% :: R
-
-# == multi line entries ==
-
-# = simple multiline rule =
-# matches "R (>= 2.15)", "R" and resolves them as dev-lang/R
-dev-lang/R {
- R (>= 2.15)
- R
-}
-
-# = fuzzy multiline rule =
-~dev-lang/R {
- R
- the R programming language
-}
-
-# = ignored dep multiline rule =
-# equals ! :: see README
-! {
- see README
-}
-
-# = fuzzy ignored dep multiline rule =
-# equals % :: R
-% {
- R
-}
-
-# === Extra ===
-
-# There's a special keyword that tells the rule reader to stop parsing,
-# see line #1. It has to be exactly '#! NOPARSE' or '#! BREAK', with no
-# additional content at the end of the line.
-#! NOPARSE
-#! BREAK
-
-# There's also a keyword to set the dependency type (sys, pkg or all),
-# the syntax is '#deptype <type>'.
-#deptype sys
-#deptype pkg
-#deptype all
-
-
diff --git a/doc/man/roverlay-deprules.5 b/doc/man/roverlay-deprules.5
deleted file mode 100644
index e801ee8..0000000
--- a/doc/man/roverlay-deprules.5
+++ /dev/null
@@ -1,185 +0,0 @@
-.\" NO LONGER USED - see doc/rst for deprule configuration
-.\" groff -Tascii -man
-.TH "ROVERLAY-DEPRULES" "5" "July 10 2012" "Linux/Gentoo?" "R Overlay"
-.SH "NAME"
-deprules \- R overlay dependency rule configuration
-.SH "SYNOPSIS"
-\fBsimple-deprules.conf\fR
-.SH "DESCRIPTION"
-A simple dependency rule file defines one or more rules
-that are used for dependency resolution in \fBroverlay(1)\fR.
-.PP
-A rule defines which \fIdep_string\fR read from an R package resolves
-to a specific \fIdependency\fR.
-\fIdependency\fR can be a \fBDEPEND atom\fR or \fBDynamic DEPEND\fR,
-see \fBebuild(5)\fR.
-\'The R programming language\',
-for example, should resolve to \'dev\-lang/R\'.
-Other dependencies such as packages from @system,
-should be ignored since they\'re always provided.
-This is also possible.
-
-.IP "\(bu simple rules"
-These rules are very simple and match a \fIdep_string\fR exactly.
-.IP "\(bu fuzzy rules"
-These rules try to find a match for \fIdep_string\fR using string interpolation, metrics and/or regex matches.
-.SS "RULE VARIANTS"
-.IP "\(bu normal"
-\fIdep_string\fR will be resolved as \fIdependency\fR.
-.IP "\(bu ignore"
-\fIdep_string\fR will be ignored if it matches an ignore rule.
-
-.SS "RULE STUBS"
-There\'s a special (shorter) syntax for dependencies
-that are resolved within the created overlay.
-For example, if your \fIOVERLAY_CATEGORY\fR is \'sci\-R\',
-\'zoo\' should be resolved as \'sci\-R/zoo\'.
-This rule can be written as a single word, \'zoo\'.
-The advantage is that you don\'t have to write the
-overlay category into the rule file.
-These stubs are called \fBselfdeps\fR.
-
-
-.SS "BASIC SYNTAX"
-.IP "\(bu rule that matches one \fIdep_string\fR"
-[\fIkeyword\fR and/or \fIdependency\fR] :: \fIdep_string\fR
-.br
-.IP "\(bu rule that matches multiple \fIdep_string\fRs"
-This replaces " :: \fIdep_string\fR" by a multiline variant
-.br
-[\fIkeyword\fR and/or \fIdependency\fR] \&{
-.br
-\& \fIdep_string\fR
-.br
-\& [\fIdep_string\fR]
-.br
-\& [\fIdep_string\fR]
-.br
-\& \&.\&.\&.
-.br
-\&}
-.br
-.IP "\fBselfdep\fR rule"
-[\fIkeyword\fR]\fIshort_dependency\fR
-.br
-where \fIshort_dependency\fR is a package name (\fBDEPEND atom\fR without version, category).
-This is the only way to specify selfdeps.
-
-.SS "ADDITIONAL SYNTAX"
-Comments start with \'#\', with a few exceptions:
-.TP
-dependency type
-There's a keyword to set the dependency type of all rules following this statement,
-\'#deptype <type>\' where type is \'sys\', \'pkg\' or \'all\'.
-.TP
-stop reading
-There are two special keywords that both cause reading a rule file to stop, \'#! BREAKPARSE\' and \'#! NOPARSE\'.
-The line must exactly be one of these keywords (no additional content at the end of the line).
-
-
-
-.SH "SIMPLE RULES"
-A simple rule resolves exact string matches (case-insensitive).
-.SS "SYNTAX"
-.IP "\(bu normal"
-\fIdependency\fR :: \fIdep_string\fR
-.IP "\(bu ignore"
-! :: \fIdep_string\fR
-.IP "\(bu selfdep, normal"
-\fIshort_dependency\fR
-.IP "\(bu selfdep, ignored"
-!\fIshort_dependency\fR
-
-.SH "FUZZY RULES"
-A fuzzy rule tries to resolve, i.e. "resolve \fIdep_string\fR as \fIdependency\fR if it \fIsomehow\fR matches a \fIfuzzy_string\fR".
-The \fIsomehow\fR is up to the implementation, it currently includes:
-.SS "EXACT MATCH"
-This is equal to the \fBSIMPLE RULES\fR
-.SS "VERSION\-RELATIVE MATCH"
-Uses regexes to identify \fIdep_string\fRs
-that only differ in the requested version (and/or version syntax).
-"R (\&>\&= 2.15)" and "R[2.10]", for instance, should be resolved as "dev\-lang/R".
-A single fuzzy\-rule "~dev\-lang/R :: R" does this and resolves them as
-"\&>=dev\-lang/R\-2.15" and "\&>=dev\-lang/R\-2.10", respectively.
-Note that this is just an example, \fBroverlay(1)\fR will filter out dependencies on
-dev\-lang/R when the version is \&<= the lowest version available in portage.
-.br
-In detail, this method matches if
-.br
-\& \fIdep_string\fR ~= \fIfuzzy_string\fR \&<\fIversion_statement\fR\&>
-.br
-where \fIversion_statement\fR ::= [\&<\fIversion_modifier\fR\&>] \&<\fIversion\fR\&>
-.br
-and \fIversion_modifier\fR is one out of \&{\&<, \&>, \&=, \&!, \&<\&=, \&>\&=, \&=\&=, \&!\&=\&}.
-.br
-
-Examples: \&'\&>=2.10\&', \&'\&!=0.9\&', \&'1.0\&', \&'\&<5\&'.
-
-Version statements can optionally be enclosed with braces (\&'()\&', \&'[]\&', \&'{}\&').
-Whitespace is ignored unless \fIversion_statment\fR is not enclosed,
-in which case some whitespace (more than zero chars) must exist between
-\fIfuzzy_string\fR and \fIversion_statment\fR.
-
-.SS SYNTAX
-Fuzzy rules use ~ and % as keyword.
-.IP "\(bu normal"
-\&~\fIdependency\fR :: \fIfuzzy_string\fR
-.IP "\(bu ignore"
-\&%\fIdependency\fR :: \fIfuzzy_string\fR
-.IP "\(bu selfdep"
-\&~\fIshort_dependency\fR
-.IP "\(bu selfdep, ignored"
-\&%\fIshort_dependency\fR
-
-.SH "EXAMPLES"
-Example 1:
-.RS 1
-A rule that matches many dependencies on dev\-lang/R,
-for example "r 2.12", "R(\&>= 2.14)", "R [\&<2.10]", "r{ !2.12 }", and "R".
-.RS 2
-
-\&~dev\-lang/R :: R
-.RE
-.RE
-.PP
-Example 2:
-.RS 1
-A rule that fuzzy-matches a zoo package selfdep.
-.RS 2
-
-\&~zoo
-.RE
-.RE
-.PP
-Example 3:
-.RS 1
-A standard self dep, resolves "tuneR", "tuner", ... as "sci\-R/tuneR"
-(\fIOVERLAY_CATEGORY\fR/tuneR).
-.RS 2
-
-\&tuneR
-.RE
-.RE
-.PP
-Example 4:
-.RS 1
-A simple multiline rule that ignores some text.
-This is a good way to deal with free-style text found in
-some R package DESCRIPTION files.
-.RS 2
-
-! :: {
-.RS 2
-see README
-.br
-read INSTALL
-.br
-[which can be downloaded from http://...]
-.br
-.RE
-}
-.RE
-.RE
-
-.SH "SEE ALSO"
-.BR "roverlay(1)"
diff --git a/doc/man/roverlay-repo.5 b/doc/man/roverlay-repo.5
deleted file mode 100644
index a517109..0000000
--- a/doc/man/roverlay-repo.5
+++ /dev/null
@@ -1,173 +0,0 @@
-.\" NO LONGER USED - see doc/rst for repo configuration
-.\" groff -Tascii -man
-.TH "ROVERLAY-REPO" "5" "July 10 2012" "Linux/Gentoo?" "R Overlay"
-.SH "NAME"
-roverlay-repo \- R overlay repo config file
-.SH "SYNOPSIS"
-.BR "repo.list"
-.SH "DESCRIPTION"
-A repo config file is used to define repositories, both local and remote, and
-uses ConfigParser syntax (known from .ini files).
-.SS "REPO ENTRIES"
-A repo entry describes where to find R packages that will be used for overlay creation,
-and optionally where and how to get the R packages (using \fBREPO TYPES\fR).
-It also defines how ebuilds can download the R packages (used as \fISRC_URI\fR variable in ebuilds).
-.SS "REPO TYPES"
-There are 4 types of repos, "local", "rsync", "websync_repo" and "websync_pkglist":
-.IP "\(bu local repositories (\&'local\&')"
-A \fBlocal repo\fR represents a directory with R packages in it.
-It will never be modified (i.e. synced) and has no special options.
-.IP "\(bu rsync repositories (\&'rsync\&')"
-An \fBrsync repo\fR uses a local directory to sync with a remote.
-Its directory will be modified whenever syncing (using the rsync program).
-It behaves like a local repo if syncing is disabled.
-.br
-These rsync options are always passed to rsync:
-.br
-\fB
-\-\-links, \-\-safe-links,
-\-\-times,
-\-\-dirs, \-\-prune-empty-dirs,
-\-\-human-readable, \-\-stats,
-\-\-chmod=ugo=r,u+w,Dugo+
-\fR
-.IP "\(bu websync repositories (\&'websync_repo\&')"
-A \fBwebsync repo\fR fetches an R package list (deb-control file, typically named PACKAGES)
-from a remote and downloads all packages afterwards (via http). It supports file-size and basic digest
-verification for downloaded packages.
-Nosync mode support for this type of repo is limited, it will report all packages from its
-directory as synced.
-.IP "\(bu package list websync (\&'websync_pkglist\&')"
-This is not a real repo type, it merely reads package uris from a file
-(one \&'http://...\&' entry per line) and downloads them (via http).
-Package uri entries must end with \&'.tar.gz\&', else ebuild creation is not possible.
-Nosync mode support is limited, all packages that exist locally will be reported as synced.
-.PP
-.SH "VARIABLES"
-Each repository is introduced with [\fIsection_name\fR] and has to declare some options.
-.SS "common options"
-.TP
-.BR "src_uri" " = \fIuri\fR"
-This is used to determine the \fISRC_URI\fR variable used in ebuilds.
-\fIuri\fR usually starts with 'http://' which can be left out,
-"localhost/R-packages" is the same uri as "http://localhost/R-packages".
-Always required unless \fItype\fR is websync_pkglist in which case this option has no effect.
-.TP
-.BR "name" " = \fIrepo_name\fR"
-Specify a name for the repository.
-Optional, defaults to \fIsection_name\fR
-which should be fine in most cases. The repo name should not contain whitespace.
-.TP
-.BR "type" " = \fItype\fR"
-Set the repo type. Optional, defaults to rsync (see \fBREPO_TYPES\fR).
-.TP
-.BR "directory" " = \fIdirectory\fR"
-Set the local package directory.
-Optional, defaults to \fIDISTFILES_ROOT\fR/\fIname\fR
-(see \fIDISTFILES_ROOT\fR in \fBR\-overlay.conf\fR).
-
-.SS "special options for local repos"
-None.
-
-.SS "special options for rsync repos"
-.TP
-.BR "rsync_uri" " = \fIrsync_uri\fR"
-Set the uri used for downloading the R packages into \fIdirectory\fR.
-Always required.
-.TP
-.BR "recursive" " = yes"
-If set to 'yes': pass '\-\-recursive' to rsync.
-This is optional and not enabled by default 'cause downloading sub directories is not always desirable.
-In case of CRAN, this would download the whole R package archive and all R releases.
-.TP
-.BR "extra_rsync_opts" " = \fIopts\fR"
-A whitespace-separated list of extra options that will be passed to rsync.
-Useful to in-/exclude files/dirs, show progress while running rsync etc.
-Options must not contain whitespace/quote chars.
-Note that the options won't be verified - this is \fBtotally unsafe!\fR
-.SS "special options for websync repos"
-.TP
-.BR "pkglist_file" " = \fIfilename\fR"
-Name of the package list file that will be downloaded.
-Optional, defaults to \&'PACKAGES\&', which should be fine in
-most cases. Note that reading compressed package lists (e.g. \&'PACKAGES.gz\&')
-is not supported. Has no effect if \fBpkglist_uri\fR is set.
-.TP
-.BR "pkglist_uri" " = \fIuri\fR"
-Fetch \fIuri\fR and use it as package list.
-Optional, defaults to \fIsrc_uri\fR/\fIpkglist_file\fR.
-.TP
-.BR "digest_type" " = \fIdigest_type\fR"
-Verify downloaded packages using \fIdigest_type\fR.
-Available choices are \&'md5\&' and \&'none\&'. The remote has to support this,
-i.e. list digests in the \fIpkglist_file\fR.
-.SS "special options for package list websync"
-.TP
-.BR "pkglist_file" " = \fIfile\fR"
-Path to the file that lists all package uris.
-.SH "EXAMPLES"
-Example 1:
-.RS 1
-A local directory with packages in /var/www/R-packages
-that are available on your network via "http://package_host/R-packages".
-.RS 2
-
-[local_packages]
-.br
-type = local
-.br
-src_uri = http://package_host/R-packages
-.br
-directory = /var/www/R-packages
-.RE
-.RE
-.PP
-Example 2:
-.RS 1
-A local directory with packages manually downloaded from CRAN.
-The directory will be automatically set to \fIDISTFILES_ROOT\fR/CRAN/selected.
-.RS 2
-
-[CRAN/selected]
-.br
-type = local
-.br
-src_uri = http://cran.r-project.org/src/contrib
-.RE
-.RE
-.PP
-Example 3:
-.RS 1
-An rsync repo for CRAN's current packages (CRAN without archive).
-The local DISTFILES_ROOT dir will be set to \fIDISTFILES_ROOT\fR/CRAN/all.
-This needs about 2.5G disk space (as of July 2012).
-.RS 2
-
-[CRAN/all]
-.br
-src_uri = http://cran.r-project.org/src/contrib
-.br
-rsync_uri = cran.r-project.org::CRAN/src/contrib
-.RE
-.RE
-.PP
-Example 4:
-.RS 1
-A repo that selectively syncs packages from CRAN that start with 'r' or 'R'
-to \fIDISTFILES_ROOT\fR/CRAN/only_letter_R. This can be realized using \fIextra_rsync_opts\fR.
-Also showing progress during transfer.
-This needs about 300M disk space.
-.RS 2
-
-[CRAN/only_letter_R]
-.br
-src_uri = http://cran.r-project.org/src/contrib
-.br
-rsync_uri = cran.r-project.org::CRAN/src/contrib
-.br
-extra_rsync_opts = \-\-include=r* \-\-include=R* \-\-exclude=* \-\-progress
-.RE
-.RE
-
-.SH "SEE ALSO"
-.BR "roverlay(1)"
diff --git a/doc/man/roverlay.1 b/doc/man/roverlay.1
deleted file mode 100644
index 2fda183..0000000
--- a/doc/man/roverlay.1
+++ /dev/null
@@ -1,118 +0,0 @@
-.\" groff -Tascii -man
-.TH "ROVERLAY" "1" "Auguest 20 2012" "roverlay" "R Overlay"
-
-.SH "NAME"
-roverlay \- create and maintain an overlay of R packages
-
-.SH "SYNOPSIS"
-.TP
-.BR "roverlay " "[\fIoptions\fR] [\fIcommand\fR]..."
-.TP
-.BR "roverlay " "\fB\-h\fR | \fB\-\-help\fR"
-.TP
-.BR "roverlay " "\fB\-\-help-config\fR"
-.TP
-.BR "roverlay " "\fB\-\-print-config\fR"
-.TP
-.BR "roverlay " "\fB\-V\fR | \fB\-\-version\fR"
-.SH "DESCRIPTION"
-roverlay is a program that generates a portage overlay for R packages.
-It runs without any user interaction and uses config files to control the
-overlay creation.
-.SH "COMMANDS"
-.TP
-.BR sync
-Sync all repos. Has no effect if no remote repository configured..
-.TP
-.BR create
-Create the overlay - read R packages and try to create ebuilds for them.
-Implies \fBsync\fR unless \fB\-\-nosync\fR is given.
-This is the default command.
-.SH "OPTIONS"
-.TP
-.BR "\-\-help " "(\fB\-h\fR)"
-Print a help message and exit
-.TP
-.BR "\-\-version " "(\fB\-V\fR)"
-Print the program's version and exit
-.TP
-.BR "\-\-help\-config"
-Print all known config options and exit
-.TP
-.BR "\-\-print\-config"
-Print the config tree after reading the config file and exit
-.SS "configuration files"
-.TP
-.BR "\-\-config " "\fIfilename\fR"
-Read the main configuration from \fIfilename\fR instead of ${PWD}/R-overlay.conf
-.TP
-.BR "\-\-deprule\-file " "\fIfilename\fR (\fB\-D\fR)"
-Read dependency rules from \fIfilename\fR instead of reading the
-files listed in the main config (\fISIMPLE_RULES_FILE\fR).
-Can be specified more than once.
-.TP
-.BR "\-\-field\-definition " "\fIfilename\fR (\fB\-F\fR)"
-Read the field definition from \fIfilename\fR instead
-of the \fIFIELD_DEFINITION\fR file specified in the main config.
-.TP
-.BR "\-\-repo\-config " "\fIfilename\fR (\fB\-R\fR)"
-Read the repo config from \fIfilename\fR instead
-of the files listed in the main config (\fIREPO_CONFIG\fR).
-Can be specified more than once.
-.SS "R packages"
-.TP
-.BR "\-\-distdir" "\fR, " "\-\-from " "\fIdirectory\fR"
-Create ebuilds for packages in \fIdirectory\fR.
-Implies \fBcreate\fR and \fB\-\-nosync\fR.
-Disables all other repos.
-.TP
-.BR "\-\-distroot " "\fIdirectory\fR"
-Set the distroot to \fIdirectory\fR.
-This is used as root for all per-repo package dirs that don't define another location.
-.TP
-.BR "\-\-force\-distroot"
-Use the distroot even for repos that define their own location.
-.TP
-.BR "\-\-nosync" "\fR, " "\-\-no\-sync"
-Disable repo syncing (offline mode). Blocks the \fBsync\fR command.
-.SS "overlay"
-.TP
-.BR "\-\-show" "\fR, " "\-\-show\-overlay"
-Print ebuilds/metadata after creation to stderr.
-.TP
-.BR "\-\-write" "\fR, " "\-\-write\-overlay"
-Write the whole overlay after creation.
-This includes ebuilds, metadata, Manifest files and the profiles/ dir.
-Enabled by default, making this option redundant.
-.TP
-.BR "\-\-no\-write" "\fR, " "\-\-no\-write\-overlay"
-Don't write the overlay.
-.TP
-.BR "\-\-stats" "\fR, " "\-\-no\-stats"
-Print some stats after overlay creation/writing.
-.TP
-.BR "\-\-no\-manifest"
-Skip Manifest file creation to save time. Note that the resulting overlay
-cannot be used with portage/emerge.
-.TP
-.BR "\-\-no\-incremental"
-Ignore an existing overlay and create ebuilds even if they already exist
-.TP
-.BR "\-\-immediate\-ebuild\-writes"
-Write ebuilds as soon as they're created (trade memory for speed)
-.TP
-.BR "\-\-overlay " "\fIdirectory\fR (\fB\-O\fR)"
-Set the overlay directory to \fIdirectory\fR. Else
-\fIOVERLAY_DIR\fR from the main config will be used.
-.TP
-.BR "\-\-overlay\-name " "\fIname\fR (\fB\-N\fR)"
-Set the overlay name to \fIname\fR.
-Else \fIOVERLAY_NAME\fR from the main config will be used.
-.SH "EXAMPLES"
-.TP
-roverlay \-c \fIconfig\fR
-Run overlay creation with sync, all options (overlay name/dir,...) are read from \fIconfig\fR
-.TP
-roverlay \-\-from \fIpkgdir\fR \-O \fIoverlay\fR \-N R_Overlay \-\-field-definition \fIfield_definition\fR \-D \fIdeprules\fR
-Run overlay creation for packages from \fIpkgdir\fR and write the overlay named R_Overlay to \fIoverlay\fR.
-Use the given \fIfield_definition\fR and \fIdeprules\fR files.
diff --git a/doc/man/show b/doc/man/show
deleted file mode 100755
index 6c0fa0e..0000000
--- a/doc/man/show
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-groff -Tascii -man "${1:?}" | ${PAGER:-less}
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