R/Rpackage.R
In sboehringer/package: Create packages from R-code directly
Defines functions
SetupPackage
LibraryPackage
SourcePackage
createPackage
checkPackage
probeDefinition
packageDefFromPath
createPackageWithConfig
installVignettes
build_vignettes_to_md
installVignette
popcharif
installTests
gitActions
packageDescription
packageInterpolateVars
packageInterpolationDict
Documented in
createPackage
#
# Rpackage.R
#Thu Oct 17 16:52:03 CEST 2019
packageDefinition = list(
name = 'package',
files = c('Rmeta.R', 'Rdata.R', 'Rsystem.R', 'Rfunctions.R', 'RpropertyList.R'),
instFiles = list(Rscripts = 'Dev/pkg-minimal.R'),
testing = list(
doInstall = TRUE,
tests = c('RtestsPackages/package/package.R')
),
description = list(
title = 'Create packages from R-code directly',
# version to be documented in news section
#version = '0.1-0',
author = 'Stefan B\uf6hringer <r-packages@s-boehringer.org>',
description = 'This package simplifies package generation by automating the use of `devtools` and `roxygen`. It also makes the development workflow more efficient by allowing ad-hoc development of packages. Use `?"package-package"` for a tutorial or visit the project wiki (belonging to the source repository).',
depends = c('roxygen2', 'devtools', 'methods'),
suggests = c('testme', 'jsonlite', 'yaml', 'knitr'),
enhances = c(),
systemrequirements = c(),
news = "0.11-4 noGit option for checkPackage\n0.11-3 Bug fix Windows support\n0.11-2 Bug fix\n0.11-1 Removed shell constructs in system calls\n0.11-0 Windows support\n0.10-0 Support for enhances, SystemRequirements in NAMESPACE\n0.9-0 Finished vignette. Clean test. RC1\n0.8-1 Bug fix automatic dependency addition.\n0.8-0 Vignette building finished. Project vignette in progress.\n0.7-0 Vignette building. Started vignette for package `package`\n0.6-0 Clean CRAN check\n0.5-1 Resolved documentation\n0.5-0 Error free CRAN check. Warnings left.\n0.4-4 bugfix NAMESPACE generation\n0.4-3 `createPackage` fully documented.\n0.4-2 More documentation\n0.4-1 Bug fix NEWS file\n0.4-0 Self-contained example\n0.3-1 bug fix for missing files\n0.3-0 Beta, self-contained\n0.2-0 Alpha version\n0.1-0 Initial release",
license = 'LGPL-2',
vignettes = "vignettes/vignette-package.Rmd"
),
git = list(
readme = '## Installation\n```{r}\nlibrary(devtools);\ninstall_github("sboehringer/package")\n```\n',
push = F,
pushOnNewVersion = T,
remote = 'https://github.com/sboehringer/package.git'
)
);
# Imports
#' @import methods
#' @import roxygen2
#' @import devtools
#' @importFrom "stats" "as.formula" "median" "model.matrix" "na.omit" "runif" "setNames" "optimize" "sd"
#' @importFrom "utils" "read.table" "recover" "write.table"
globalVariables(c('valueMapperStandard', 'read_yaml', 'read_json'))
#__PACKAGE_DOC__
# This package allows you to create a full-fledged R-package from a single R-file reducing the added work-load for maintaining a package to a minimum. Depending on the project, collections of files can be used and configuration can be seperated into a stand-alone configuration file, providing full flexibility. It can also handle git interaction. This package is created with itself and you can look at the single R-file `Rpackage.R` for a self-referring example.
# The package contains a self-contained package example defined in the single R-file \code{pkg-minimal.R} which can be inspected and installed as in the example below.
# @examples
# \dontrun{
# file.show(system.file('Rscripts/pkg-minimal.R', package = 'package'))
# createPackage(system.file('Rscripts/pkg-minimal.R', package = 'package'))
# }
# @seealso {createPackage()} for starting the main workflow
#__PACKAGE_DOC_END__
packageDocPrefix = "# This is package `%{name}s`\n#\n# %{title}s\n#\n# @details\n# %{description}s\n";
#packageDocPrefix = "# This is package `%{name}s`\n#\n# @details\n# %{description}s\n#\n";
packageReadmeTemplate = "# R-package `%{PACKAGE_NAME}s`, version %{VERSION}s\n%{README}s\n# Description\n%{DESCRIPTION_MD}s";
packageDescTemplate = "Package: %{PACKAGE_NAME}s\nType: %{TYPE}s\nTitle: %{TITLE}s\nVersion: %{VERSION}s\nDate: %{DATE}s\nAuthor: %{AUTHOR}s\nMaintainer: %{MAINTAINER}s\nDescription: %{DESCRIPTION}s\nLicense: %{LICENSE}s\nEncoding: %{ENCODING}s\nDepends: %{DEPENDS}s\nCollate: %{COLLATE}s\nSuggests: %{SUGGESTS}s\nEnhances: %{ENHANCES}s\nSystemRequirements: %{SYSTEMREQUIREMENTS}s\n%{ADDITIONS}s";
packageInterpolationDict = function(o, debug = F) {
additions = '';
if (length(o$description$vignettes) > 0) {
o$description$suggests = unique(c(o$description$suggests, c('knitr', 'rmarkdown')));
additions = paste0(additions, "VignetteBuilder: knitr\n");
}
d = o$description;
vars = list(
PACKAGE_NAME = o$name,
TYPE = firstDef(d$type, 'Package'),
TITLE = d$title,
VERSION = o$version, # determined in probeDefinition
DATE = firstDef(d$date, format(Sys.time(), "%Y-%m-%d")),
AUTHOR = firstDef(d$author, 'anonymous'),
MAINTAINER = firstDef(d$maintainer, d$author, 'anonymous'),
DESCRIPTION = firstDef(d$description, ''),
LICENSE = firstDef(d$license, 'LGPL-2'),
ENCODING = firstDef(d$encoding, 'UTF-8'),
COLLATE = circumfix(join(sapply(o$files, function(f)splitPath(f)$file), "\n "), pre = "\n "),
DEPENDS = circumfix(join(d$depends, ",\n "), pre = "\n "),
SUGGESTS = circumfix(join(d$suggests, ",\n "), pre = "\n "),
ENHANCES = circumfix(join(d$enhances, ",\n "), pre = "\n "),
SYSTEMREQUIREMENTS = circumfix(join(d$systemrequirements, ",\n "), pre = "\n "),
README = firstDef(o$git$readme, ''),
ADDITIONS = additions
);
# <!> code w/ {}'s
vars$DESCRIPTION_MD = gsub("\\\\code[{](.*?)[}]", "`\\1`", vars$DESCRIPTION, perl = T);
if (debug) print(vars);
return(vars);
}
packageInterpolateVars = function(o, templ, debug = F) {
if (debug) cat(templ);
vars = packageInterpolationDict(o, debug);
return(with(vars, Sprintf(templ)));
}
packageDescription = function(o, debug = F) {
templ = firstDef(o$descriptionTemplate, packageDescTemplate);
if (debug) cat(templ);
return(packageInterpolateVars(o, templ, debug));
}
gitOptionsDefault = list(doPull = F, doPush = F);
gitActions = function(o, packagesDir, debug, gitOptions = gitOptionsDefault) {
gitOptions = merge.lists(gitOptionsDefault, gitOptions);
i = packageInterpolationDict(o, debug);
pdir = Sprintf('%{packagesDir}s/%{name}s', o);
if (gitOptions$doPull) System('git pull', 2, wd = pdir);
readme = packageInterpolateVars(o, firstDef(o$git$readmeTemplate, packageReadmeTemplate));
writeFile(Sprintf('%{pdir}s/README.md'), readme);
# initialize git
if (!file.exists(with(o, Sprintf('%{packagesDir}s/%{name}s/.git')))) {
System('git init', 2, wd = pdir);
}
System('git add --all', 2, wd = pdir);
System(with(i, Sprintf('git commit -a -m "Commit for onward development of version %{VERSION}s"')), 2, wd = pdir);
tags = System('git tag', 2, wd = pdir, return.output = T)$output;
# tag new version
newVersion = F;
if (length(Regexpr(Sprintf('\\Q%{VERSION}s\\E', i), tags)[[1]]) == 0) {
System(with(i, Sprintf('git tag %{VERSION}s')), wd = pdir);
newVersion = T;
}
# remote
if (notE(o$git$remote)) {
remotes = System('git remote -v', 2, wd = pdir, return.output = T)$output;
if (remotes == '' && o$git$remote != '')
System(Sprintf('git remote add origin %{remote}s', o$git), 2, wd = pdir);
if (o$git$pushOnNewVersion && newVersion || gitOptions$doPush) {
System('git push -u origin master', 2, wd = pdir);
System(Sprintf('git push origin %{VERSION}s', i), 2, wd = pdir);
}
}
}
installTests = function(o, packageDir, loadTestMe = FALSE, asCran = FALSE) {
#if (loadTestMe) requireNamespace('testme'); # <i> trick shiny not to install testme
if (is.null(rget('installPackageTests', NULL))) {
Log('Package testme not available, skipping tests creation', 1);
return(NULL);
}
#testme::installPackageTests(packageDir, o$testing$tests, createReference = TRUE, asCran);
installPackageTests(packageDir, o$testing$tests, createReference = TRUE, asCran);
}
# <N> values are interpolated by Sprintf, '%' -> '%%'
vignetteDefaultKeys = list(
title = 'How to use %{packageName}s',
date = '"`r Sys.Date()`"',
vignette = ">\n %%\\VignetteIndexEntry{%{file}s}\n %%\\%{Vignette}sEngine{knitr::rmarkdown}\n %%\\%{Vignette}sEncoding{UTF-8}",
output = "rmarkdown::html_vignette"
#output = "\n html_document:\n keep_md: TRUE"
#output = "\n rmarkdown::html_vignette:\n keep_md: TRUE"
);
popcharif = function(s, char = "\n") {
N = nchar(s);
if (N == 0) return(s);
if (substr(s, N, N) == char) return(substr(s, 1, N -1));
return(s);
}
installVignette = function(name, path, o, packageDir, noGit = F) {
name = splitPath(name)$base; # normalize, allow path as name
v = readFile(path);
cat(v);
m0 = unlist(Regexpr("(?six)^---\\n+
((?:
(?:\\S*)[\\t ]*:[\\t ]*
(?:[^\\n]+\\n (?:[ \\t]+[^\\n]+\\n)* ) \\n*
)+)---\\n(.*)", v, captures = T, concatMatches = F));
dictR0 = Regexpr("(?six)
(?<key>[a-z]\\S*)[\\t ]*:[\\t ]*
(?<value> [^\\n]+\\n (?:[ \\t]+[^\\n]+\\n)* ) \\n*
", m0[1], captures = T, concatMatches = F, global = T);
dictR1 = list.transpose(dictR0[[1]]);
dictR2 = listKeyValue(list.kp(dictR1, 'key'), sapply(list.kp(dictR1, 'value'), popcharif));
dict = merge.lists(vignetteDefaultKeys, list(
author = o$description$author,
packageName = o$name,
file = Sprintf('%{name}s.Rmd')
), dictR2);
meta = Sprintf(join(nelapply(dict, function(n, e)Sprintf('%{n}s: %{e}s')), "\n"),
c(dict, list(Vignette = 'Vignette'))); #<!> hack to avoid warning
vignette = m0[2];
Rmd = Sprintf('---\n%{meta}s\n---\n%{vignette}s');
writeFile(Sprintf('%{packageDir}s/vignettes/%{name}s.Rmd'), Rmd, mkpath = T);
if (!noGit) {
ignore = Sprintf('%{packageDir}s/vignettes/.gitignore');
if (!file.exists(ignore)) writeFile(ignore, "vignettes/*.html\nvignettes/*.R\n");
}
}
build_vignettes_to_md = function(o, packageDir) {
nelapply(o$description$vignettes, function(name, p){
name = splitPath(name)$base;
knitr::knit(
Sprintf('%{packageDir}s/vignettes/%{name}s.Rmd'),
Sprintf('%{packageDir}s/doc/%{name}s.md')
);
});
}
installVignettes = function(o, packageDir, keep_md = TRUE) {
vignettes = o$description$vignettes;
if (!is.list(vignettes)) o$description$vignettes = listKeyValue(vignettes, vignettes);
nelapply(o$description$vignettes, installVignette, o = o, packageDir = packageDir);
# keep_md = T does not seem to work, even in conjunction with a markdown parameter -> workaround
build_vignettes(packageDir, keep_md = FALSE);
if (keep_md) build_vignettes_to_md(o, packageDir);
}
#doInstall = FALSE, debug = F, gitOptions = list(), noGit = F, lib = NULL, tarDir = packagesDir)
createPackageWithConfig = function(o, packagesDir = '~/src/Rpackages',
doInstall = FALSE, debug = F, gitOptions = list(), noGit = F, lib = NULL, tarDir = tempdir(),
asCran = FALSE) {
if (debug) print(o);
i = packageInterpolationDict(o, debug);
pdir = Sprintf('%{packagesDir}s/%{name}s', o);
packageDir = Sprintf('%{packagesDir}s/%{name}s', o);
# <p> folders
Dir.create(Sprintf('%{pdir}s'));
Dir.create(Sprintf('%{pdir}s/R'));
# <p> copy R files
#src = Sprintf('%{dir}s/%{files}s', dir = o$dir, files = o$files, sprintf_cartesian = T);
#src = Sprintf('%{dir}s/%{files}s', o, sprintf_cartesian = T);
src = sapply(o$files, function(f)if (splitPath(f)$isAbsolute) f else Sprintf('%{dir}s/%{f}s', o));
dest = Sprintf('%{packageDir}s/R/');
LogS(2, 'Copying files: %{f}s -> %{dest}s', f = join(src, ', '));
File.copy(src, dest, symbolicLinkIfLocal = F, overwrite = T);
# <p> copy files for inst sub-folder
nelapply(o$instFiles, function(n, files) {
dest = Sprintf('%{packageDir}s/inst/%{n}s');
Dir.create(dest, recursive = T);
LogS(2, 'Copying files: %{f}s -> %{dest}s', f = join(src, ', '));
File.copy(files, dest, symbolicLinkIfLocal = F, overwrite = T);
});
# <p> extract package documentation
doc = sapply(src, function(f)
Regexpr('(?s)(?<=#__PACKAGE_DOC__\\n).*?(?=#__PACKAGE_DOC_END__\\n)', readFile(f))
);
# conflicts
Ndoc = length(which(sapply(doc, nchar) > 0));
if (Ndoc > 1) stop('More than one package documentation files/sections found');
if (Ndoc == 1) {
if (any(sapply(src, function(f)splitPath(f)$file) == Sprintf('%{name}s.R', o)))
stop(Sprintf('%{name}s.R should contain package documentation which is also given elsewhere. %{name}s.R will be overwritten so that it cannot be used as an input file.', o));
# substitute in fields from configuration [description]
#doc0 = paste0(packageDocPrefix, join(doc, ''), "\n\"_PACKAGE\"\n");
doc0 = paste0(packageDocPrefix, unlist(doc), "\n\"_PACKAGE\"\n");
doc1 = Sprintf(doc0, o$description, name = o$name);
doc2 = gsub("(^#)|((?<=\n)#)", "#'", doc1, perl = T);
#print(doc2);
writeFile(Sprintf('%{pdir}s/R/%{name}s.R', o), doc2);
o$files = c(Sprintf('%{name}s.R', o), o$files); # documentation file to list of files
}
# <p> update NEWS file
writeFile(with(o, Sprintf('%{pdir}s/NEWS')), firstDef(o$description$news, '0.1-0 Initial release'));
writeFile(with(o, Sprintf('%{pdir}s/DESCRIPTION')), packageDescription(o));
# <p> testing
if (notE(o$testing) && o$testing$doInstall && !nif(o$testing$prevent))
installTests(o, packageDir, asCran = asCran);
# <p> roxigen2
#Library(c('roxygen2', 'devtools'));
#document(packageDir, roclets = c('namespace', 'rd'));
#document(packageDir, roclets = c('rd'));
#roxygenize(packageDir, roclets = c('rd'), clean = TRUE);
roxygenize(packageDir, clean = TRUE);
# <p> vignettes
if (notE(o$description$vignettes)) installVignettes(o, packageDir);
# <p> git
if (!noGit && notE(o$git)) gitActions(o, packagesDir, debug, gitOptions);
# <p> install
if (doInstall) Install_local(Sprintf('%{packageDir}s'), upgrade = 'never', lib = lib, tarDir = tarDir);
return(o);
}
packageDefFromPath = function(path) {
myEnv = new.env();
# <N> instead of Source: avoid RCurl dependency
SourceLocal(path, local = myEnv);
def = get('packageDefinition', envir = myEnv);
# add definition file as first file <!> (no forward declarations)
# <!> 30.9.2021 changed to last position to allow referencing
def$files = unique(c(def$files, splitPath(path)$file));
return(def);
}
probeDefinition = function(desc, dir = NULL) {
path = Sprintf('%{pre}s%{file}s', pre = circumfix(dir, '/'), file = desc[1]);
sp = splitPath(path);
o = switch(sp$ext,
# <!> assume unique is stable
R = packageDefFromPath(desc[1]),
plist = propertyFromStringExt(readFile(path)),
json = ({ requireNamespace('jsonlite'); read_json(path) }),
yaml = ({ requireNamespace('yaml'); read_yaml(path) })
);
o$dir = firstDef(dir, sp$dir);
o$version = firstDef(o$description$version, Regexpr('\\S+', o$description$news)[[1]], '0.1-0');
return(o);
}
packageTarOSOptions = list(Linux = '--overwrite', Windows = c());
checkPackage = function(packageDesc, packagesDir, asCran = TRUE, copyCranTarball = TRUE, clean = TRUE, noGit = FALSE)
with (packageDesc, {
checkDir = packageDir = Sprintf("%{packagesDir}s/%{name}s");
packagesDirPrev = packagesDir;
if (!noGit && file.exists(Sprintf("%{packageDir}s/.git"))) {
packagesDir = tempdir();
checkDir = Sprintf('%{packagesDir}s/%{name}s');
# <i> move if exists
if (file.exists(checkDir) && clean) {
file.rename(checkDir, Sprintf('%{checkDir}s-%{i}d', i = as.integer(runif(1)*1e6)))
}
dir.create(checkDir, FALSE);
#SystemS('cd %{packageDir}q ; git archive --format tar HEAD | ( cd %{checkDir}q ; tar xf - --exclude inst/doc --overwrite )', 2);
#SystemS('cd %{packageDir}q ; git archive --format tar HEAD | ( cd %{checkDir}q ; tar xf - --overwrite )', 2);
#SystemS('cd %{packageDir}q ; git archive --format tar HEAD | ( cd %{checkDir}q ; tar xf - --overwrite )', 2);
# cmdGit = JoinCmds(Sprintf(c('cd %{packageDir}q', 'git archive --format tar HEAD')));
# cmdTar = JoinCmds(Sprintf(c('cd %{checkDir}q', 'tar xf - --overwrite')));
# SystemS('%{cmdGit}s | ( %{cmdTar}s )', 2);
fArchive = tempfile();
SystemS('git archive --format tar HEAD -o %{fArchive}q', 2, wd = packageDir);
#SystemS('tar xf %{fArchive}q --overwrite', 2, wd = checkDir);
untar(fArchive, exdir = checkDir, extras = packageTarOSOptions[[ Sys.info()['sysname'] ]]);
}
cran = if (asCran) '--as-cran' else '';
# SystemS(JoinCmds(c(
# 'cd %{packagesDir}q',
# 'R CMD build %{name}q',
# 'R CMD check %{cran}s %{name}q_%{version}s.tar.gz'
# )), 2);
SystemS('R CMD build %{name}q', 2, wd = packagesDir);
SystemS('R CMD check %{cran}s %{name}q_%{version}s.tar.gz', 2, wd = packagesDir);
if (asCran && copyCranTarball) {
from = Sprintf('%{packagesDir}s/%{name}q_%{version}s.tar.gz');
to = Sprintf('%{packagesDirPrev}s/%{name}q_%{version}s-cran.tar.gz');
File.copy(from, to, overwrite = T, symbolicLinkIfLocal = F, logLevel = 2);
}
})
#' Create package from vector of source files and single configuration
#'
#' This function creates a package dir, runs documentation generation using roxygen and optionally installs the package. It can also update via git and manage version numbers. In a minimal configuration, a single file is sufficient to create a fully documented R package.
#'
#' @alias createPackageWithConfig
#' @param packageDesc path to the configuration file (R, extended plist format, json, yaml).
#' If an R-file is provided, it is sourced in a seperate environment and needs to define the variable
#' `packageDefinition`. This variable has to be a list which is further specified in the details below.
#' If a propertyList/JSON/YAML-file is provided, they have to parse into a list corresponding to
#' `packageDefinition`. Functions \code{propertyFromStringExt}, \code{read_json}, and \code{read_yaml} are
#' used for parsing, coming from packages \code{package}, \code{jsonlite}, and \code{yaml}.
#' @param packagesDir folder in which the folder structure of the package is written
#' @param doInstall flag to indicate whether the package should also be installed
#' @param doCheck whether to run R CMD check --as-cran on the package
#' @param dir directory to search for package definition
#' @param gitOptions list with options for git interaction
#' @param noGit boolean to suppress git calls, overwrites other options
#' @param lib Path to package library as forwarded to \code{install.packages}
#' @param asCran boolean to indicate whether check should be including --as-cran
#'
#' @details This function creates a valid R package folder with DESCRIPTION, LICENSE and NEWS files.
#' All R-files listed are copied to this directory and documentation is created by
#' running the \code{devtools::document} function on this folder.
#' The package is specified through a list coming from an R script or configuration file.
#' The following elements control package generation. In this list \code{key1-key2} indicates a
#' sublist-element, i.e. it stand for \code{packageDefinition[[key1]][[key2]]}.
#'
#' \itemize{
#' \item{name: }{The name of the pacakge}
#' \item{files: }{R-files to be put into the package. If an R-file is used for the configuration,
#' it will automatically be include. This allows package definition through a single R-file.}
#' \item{instFiles: }{Other files to be installed. This is a list, the names of which specify
#' sub-folders in the \code{inst} sub-directory of the package. Values are character vectors
#' specifying files to be put there.}
#' \item{description: }{A sub-list with elements specifying the \code{DESCRIPTION} file of the package.}
#' \item{description-title: }{The title of the help page 'package-myPackage' (myPackage is the name
#' of the package) and the title fiedl in DESCRIPTION.}
#' \item{description-author: }{The \code{Author} field in DESCRIPTION.
#' \item{description-description: } The \code{Description} field in DESCRIPTION. The text is re-used
#' for the package documentation as displayed by ?'package-myPackage' and is prepended to the
#' seperate package documentation. It is also inserted as a Description section of a Markdown file
#' if git is used. This string should therefore not make use of roxygen/markdown markup.}
#' \item{description-depends: }{A character vector with package dependencies.}
#' \item{description-suggests: }{A character vector with package suggestions.}
#' \item{description-news: }{A character vector with a single element containing the \code{NEWS}
#' file of the package. It is assumed that a line starting with a non white space character
#' indicates a new version. The version identifier is taken to be all characters until the
#' first white space. Once a new version is detected, git actions might be triggered (see below).}
#' \item{git: }{A sub-list specifying git behavior. If you do not
#' want to use git, omit this entry from \code{packageDefinition}. If present, a git repository
#' is created and maintained in the target folder. Default \code{git} settings for the package can be
#' overwritten using the \code{gitOptions} argument.}
#' \item{git-push: }{Logical, whether to push each commit, defaults to \code{FALSE}.}
#' \item{git-pushOnNewVersion: }{Logical, whether to push each when a new release is created
#' (see item \code{description-news}. Defaults to \code{TRUE}.
#' A push is automatically performed, once a new release is created, irrespective of this setting.
#' To suppress a push in these cases, push has to set to \code{FALSE} in the. }
#' \item{git-readme: }{Character vector with single entry with the content of a readme file that is put
#' as \code{README.md} into the package main folder. The description given under
#' \code{description-description} is appended to this text.}
#' }
#' @author Stefan Böhringer, \email{r-packages@@s-boehringer.org}
#' @seealso package-package
#' @keywords create package createPackage
#' @examples
#'
#' packageDefinition = list(
#' name = 'pkg-minimal',
#' files = c(),
#' instFiles = list(),
#' description = list(
#' title = 'Minimal R-package created with `package`',
#' # version to be documented in news section
#' #version = '0.1-0',
#' author = 'Stefan Böhringer <r-packages@s-boehringer.org>',
#' description = 'This appears in the package-documentaion, the markdown of the git-repository and in the package details.',
#' depends = c(),
#' suggests = c(),
#' license = 'LGPL',
#' news = "0.1-0 Initial release"
#' ),
#' git = list(
#' readme = '## Installation\n```{r}\nlibrary(devtools);\ninstall_github("user/pkg-minimal")\n```\n',
#' push = FALSE,
#' pushOnNewVersion = FALSE
#' )
#' );
#'
#'
#' @export createPackage
createPackage = function(packageDesc, packagesDir = '~/src/Rpackages',
dir = NULL, doInstall = FALSE, doCheck = T, gitOptions = list(), noGit = F, lib = NULL, asCran = FALSE) {
packageDef = probeDefinition(packageDesc, dir);
#print(packageDef);
r = createPackageWithConfig(packageDef, packagesDir, doInstall,
gitOptions = gitOptions, noGit = noGit,
lib = lib, asCran = asCran
);
if (doCheck) checkPackage(packageDef, packagesDir, asCran, noGit = noGit);
return(r);
}
#
# <p> local development
#
SourcePackage = function(path) {
def = packageDefFromPath(path);
Source(def$files, locations = splitPath(path)$dir);
}
LibraryPackage = function(path, suggests = TRUE) {
def = packageDefFromPath(path);
Library(def$description$depends);
if (suggests) Library(def$description$suggests);
}
SetupPackage = function(path, suggests = TRUE) {
LibraryPackage(path, suggests = suggests);
SourcePackage(path);
}
sboehringer/package documentation built on Jan. 12, 2023, 6:33 a.m.
R Package Documentation
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Defines functions SetupPackage LibraryPackage SourcePackage createPackage checkPackage probeDefinition packageDefFromPath createPackageWithConfig installVignettes build_vignettes_to_md installVignette popcharif installTests gitActions packageDescription packageInterpolateVars packageInterpolationDict
Documented in createPackage
#
# Rpackage.R
#Thu Oct 17 16:52:03 CEST 2019
packageDefinition = list(
name = 'package',
files = c('Rmeta.R', 'Rdata.R', 'Rsystem.R', 'Rfunctions.R', 'RpropertyList.R'),
instFiles = list(Rscripts = 'Dev/pkg-minimal.R'),
testing = list(
doInstall = TRUE,
tests = c('RtestsPackages/package/package.R')
),
description = list(
title = 'Create packages from R-code directly',
# version to be documented in news section
#version = '0.1-0',
author = 'Stefan B\uf6hringer <r-packages@s-boehringer.org>',
description = 'This package simplifies package generation by automating the use of `devtools` and `roxygen`. It also makes the development workflow more efficient by allowing ad-hoc development of packages. Use `?"package-package"` for a tutorial or visit the project wiki (belonging to the source repository).',
depends = c('roxygen2', 'devtools', 'methods'),
suggests = c('testme', 'jsonlite', 'yaml', 'knitr'),
enhances = c(),
systemrequirements = c(),
news = "0.11-4 noGit option for checkPackage\n0.11-3 Bug fix Windows support\n0.11-2 Bug fix\n0.11-1 Removed shell constructs in system calls\n0.11-0 Windows support\n0.10-0 Support for enhances, SystemRequirements in NAMESPACE\n0.9-0 Finished vignette. Clean test. RC1\n0.8-1 Bug fix automatic dependency addition.\n0.8-0 Vignette building finished. Project vignette in progress.\n0.7-0 Vignette building. Started vignette for package `package`\n0.6-0 Clean CRAN check\n0.5-1 Resolved documentation\n0.5-0 Error free CRAN check. Warnings left.\n0.4-4 bugfix NAMESPACE generation\n0.4-3 `createPackage` fully documented.\n0.4-2 More documentation\n0.4-1 Bug fix NEWS file\n0.4-0 Self-contained example\n0.3-1 bug fix for missing files\n0.3-0 Beta, self-contained\n0.2-0 Alpha version\n0.1-0 Initial release",
license = 'LGPL-2',
vignettes = "vignettes/vignette-package.Rmd"
),
git = list(
readme = '## Installation\n```{r}\nlibrary(devtools);\ninstall_github("sboehringer/package")\n```\n',
push = F,
pushOnNewVersion = T,
remote = 'https://github.com/sboehringer/package.git'
)
);
# Imports
#' @import methods
#' @import roxygen2
#' @import devtools
#' @importFrom "stats" "as.formula" "median" "model.matrix" "na.omit" "runif" "setNames" "optimize" "sd"
#' @importFrom "utils" "read.table" "recover" "write.table"
globalVariables(c('valueMapperStandard', 'read_yaml', 'read_json'))
#__PACKAGE_DOC__
# This package allows you to create a full-fledged R-package from a single R-file reducing the added work-load for maintaining a package to a minimum. Depending on the project, collections of files can be used and configuration can be seperated into a stand-alone configuration file, providing full flexibility. It can also handle git interaction. This package is created with itself and you can look at the single R-file `Rpackage.R` for a self-referring example.
# The package contains a self-contained package example defined in the single R-file \code{pkg-minimal.R} which can be inspected and installed as in the example below.
# @examples
# \dontrun{
# file.show(system.file('Rscripts/pkg-minimal.R', package = 'package'))
# createPackage(system.file('Rscripts/pkg-minimal.R', package = 'package'))
# }
# @seealso {createPackage()} for starting the main workflow
#__PACKAGE_DOC_END__
packageDocPrefix = "# This is package `%{name}s`\n#\n# %{title}s\n#\n# @details\n# %{description}s\n";
#packageDocPrefix = "# This is package `%{name}s`\n#\n# @details\n# %{description}s\n#\n";
packageReadmeTemplate = "# R-package `%{PACKAGE_NAME}s`, version %{VERSION}s\n%{README}s\n# Description\n%{DESCRIPTION_MD}s";
packageDescTemplate = "Package: %{PACKAGE_NAME}s\nType: %{TYPE}s\nTitle: %{TITLE}s\nVersion: %{VERSION}s\nDate: %{DATE}s\nAuthor: %{AUTHOR}s\nMaintainer: %{MAINTAINER}s\nDescription: %{DESCRIPTION}s\nLicense: %{LICENSE}s\nEncoding: %{ENCODING}s\nDepends: %{DEPENDS}s\nCollate: %{COLLATE}s\nSuggests: %{SUGGESTS}s\nEnhances: %{ENHANCES}s\nSystemRequirements: %{SYSTEMREQUIREMENTS}s\n%{ADDITIONS}s";
packageInterpolationDict = function(o, debug = F) {
additions = '';
if (length(o$description$vignettes) > 0) {
o$description$suggests = unique(c(o$description$suggests, c('knitr', 'rmarkdown')));
additions = paste0(additions, "VignetteBuilder: knitr\n");
}
d = o$description;
vars = list(
PACKAGE_NAME = o$name,
TYPE = firstDef(d$type, 'Package'),
TITLE = d$title,
VERSION = o$version, # determined in probeDefinition
DATE = firstDef(d$date, format(Sys.time(), "%Y-%m-%d")),
AUTHOR = firstDef(d$author, 'anonymous'),
MAINTAINER = firstDef(d$maintainer, d$author, 'anonymous'),
DESCRIPTION = firstDef(d$description, ''),
LICENSE = firstDef(d$license, 'LGPL-2'),
ENCODING = firstDef(d$encoding, 'UTF-8'),
COLLATE = circumfix(join(sapply(o$files, function(f)splitPath(f)$file), "\n "), pre = "\n "),
DEPENDS = circumfix(join(d$depends, ",\n "), pre = "\n "),
SUGGESTS = circumfix(join(d$suggests, ",\n "), pre = "\n "),
ENHANCES = circumfix(join(d$enhances, ",\n "), pre = "\n "),
SYSTEMREQUIREMENTS = circumfix(join(d$systemrequirements, ",\n "), pre = "\n "),
README = firstDef(o$git$readme, ''),
ADDITIONS = additions
);
# <!> code w/ {}'s
vars$DESCRIPTION_MD = gsub("\\\\code[{](.*?)[}]", "`\\1`", vars$DESCRIPTION, perl = T);
if (debug) print(vars);
return(vars);
}
packageInterpolateVars = function(o, templ, debug = F) {
if (debug) cat(templ);
vars = packageInterpolationDict(o, debug);
return(with(vars, Sprintf(templ)));
}
packageDescription = function(o, debug = F) {
templ = firstDef(o$descriptionTemplate, packageDescTemplate);
if (debug) cat(templ);
return(packageInterpolateVars(o, templ, debug));
}
gitOptionsDefault = list(doPull = F, doPush = F);
gitActions = function(o, packagesDir, debug, gitOptions = gitOptionsDefault) {
gitOptions = merge.lists(gitOptionsDefault, gitOptions);
i = packageInterpolationDict(o, debug);
pdir = Sprintf('%{packagesDir}s/%{name}s', o);
if (gitOptions$doPull) System('git pull', 2, wd = pdir);
readme = packageInterpolateVars(o, firstDef(o$git$readmeTemplate, packageReadmeTemplate));
writeFile(Sprintf('%{pdir}s/README.md'), readme);
# initialize git
if (!file.exists(with(o, Sprintf('%{packagesDir}s/%{name}s/.git')))) {
System('git init', 2, wd = pdir);
}
System('git add --all', 2, wd = pdir);
System(with(i, Sprintf('git commit -a -m "Commit for onward development of version %{VERSION}s"')), 2, wd = pdir);
tags = System('git tag', 2, wd = pdir, return.output = T)$output;
# tag new version
newVersion = F;
if (length(Regexpr(Sprintf('\\Q%{VERSION}s\\E', i), tags)[[1]]) == 0) {
System(with(i, Sprintf('git tag %{VERSION}s')), wd = pdir);
newVersion = T;
}
# remote
if (notE(o$git$remote)) {
remotes = System('git remote -v', 2, wd = pdir, return.output = T)$output;
if (remotes == '' && o$git$remote != '')
System(Sprintf('git remote add origin %{remote}s', o$git), 2, wd = pdir);
if (o$git$pushOnNewVersion && newVersion || gitOptions$doPush) {
System('git push -u origin master', 2, wd = pdir);
System(Sprintf('git push origin %{VERSION}s', i), 2, wd = pdir);
}
}
}
installTests = function(o, packageDir, loadTestMe = FALSE, asCran = FALSE) {
#if (loadTestMe) requireNamespace('testme'); # <i> trick shiny not to install testme
if (is.null(rget('installPackageTests', NULL))) {
Log('Package testme not available, skipping tests creation', 1);
return(NULL);
}
#testme::installPackageTests(packageDir, o$testing$tests, createReference = TRUE, asCran);
installPackageTests(packageDir, o$testing$tests, createReference = TRUE, asCran);
}
# <N> values are interpolated by Sprintf, '%' -> '%%'
vignetteDefaultKeys = list(
title = 'How to use %{packageName}s',
date = '"`r Sys.Date()`"',
vignette = ">\n %%\\VignetteIndexEntry{%{file}s}\n %%\\%{Vignette}sEngine{knitr::rmarkdown}\n %%\\%{Vignette}sEncoding{UTF-8}",
output = "rmarkdown::html_vignette"
#output = "\n html_document:\n keep_md: TRUE"
#output = "\n rmarkdown::html_vignette:\n keep_md: TRUE"
);
popcharif = function(s, char = "\n") {
N = nchar(s);
if (N == 0) return(s);
if (substr(s, N, N) == char) return(substr(s, 1, N -1));
return(s);
}
installVignette = function(name, path, o, packageDir, noGit = F) {
name = splitPath(name)$base; # normalize, allow path as name
v = readFile(path);
cat(v);
m0 = unlist(Regexpr("(?six)^---\\n+
((?:
(?:\\S*)[\\t ]*:[\\t ]*
(?:[^\\n]+\\n (?:[ \\t]+[^\\n]+\\n)* ) \\n*
)+)---\\n(.*)", v, captures = T, concatMatches = F));
dictR0 = Regexpr("(?six)
(?<key>[a-z]\\S*)[\\t ]*:[\\t ]*
(?<value> [^\\n]+\\n (?:[ \\t]+[^\\n]+\\n)* ) \\n*
", m0[1], captures = T, concatMatches = F, global = T);
dictR1 = list.transpose(dictR0[[1]]);
dictR2 = listKeyValue(list.kp(dictR1, 'key'), sapply(list.kp(dictR1, 'value'), popcharif));
dict = merge.lists(vignetteDefaultKeys, list(
author = o$description$author,
packageName = o$name,
file = Sprintf('%{name}s.Rmd')
), dictR2);
meta = Sprintf(join(nelapply(dict, function(n, e)Sprintf('%{n}s: %{e}s')), "\n"),
c(dict, list(Vignette = 'Vignette'))); #<!> hack to avoid warning
vignette = m0[2];
Rmd = Sprintf('---\n%{meta}s\n---\n%{vignette}s');
writeFile(Sprintf('%{packageDir}s/vignettes/%{name}s.Rmd'), Rmd, mkpath = T);
if (!noGit) {
ignore = Sprintf('%{packageDir}s/vignettes/.gitignore');
if (!file.exists(ignore)) writeFile(ignore, "vignettes/*.html\nvignettes/*.R\n");
}
}
build_vignettes_to_md = function(o, packageDir) {
nelapply(o$description$vignettes, function(name, p){
name = splitPath(name)$base;
knitr::knit(
Sprintf('%{packageDir}s/vignettes/%{name}s.Rmd'),
Sprintf('%{packageDir}s/doc/%{name}s.md')
);
});
}
installVignettes = function(o, packageDir, keep_md = TRUE) {
vignettes = o$description$vignettes;
if (!is.list(vignettes)) o$description$vignettes = listKeyValue(vignettes, vignettes);
nelapply(o$description$vignettes, installVignette, o = o, packageDir = packageDir);
# keep_md = T does not seem to work, even in conjunction with a markdown parameter -> workaround
build_vignettes(packageDir, keep_md = FALSE);
if (keep_md) build_vignettes_to_md(o, packageDir);
}
#doInstall = FALSE, debug = F, gitOptions = list(), noGit = F, lib = NULL, tarDir = packagesDir)
createPackageWithConfig = function(o, packagesDir = '~/src/Rpackages',
doInstall = FALSE, debug = F, gitOptions = list(), noGit = F, lib = NULL, tarDir = tempdir(),
asCran = FALSE) {
if (debug) print(o);
i = packageInterpolationDict(o, debug);
pdir = Sprintf('%{packagesDir}s/%{name}s', o);
packageDir = Sprintf('%{packagesDir}s/%{name}s', o);
# <p> folders
Dir.create(Sprintf('%{pdir}s'));
Dir.create(Sprintf('%{pdir}s/R'));
# <p> copy R files
#src = Sprintf('%{dir}s/%{files}s', dir = o$dir, files = o$files, sprintf_cartesian = T);
#src = Sprintf('%{dir}s/%{files}s', o, sprintf_cartesian = T);
src = sapply(o$files, function(f)if (splitPath(f)$isAbsolute) f else Sprintf('%{dir}s/%{f}s', o));
dest = Sprintf('%{packageDir}s/R/');
LogS(2, 'Copying files: %{f}s -> %{dest}s', f = join(src, ', '));
File.copy(src, dest, symbolicLinkIfLocal = F, overwrite = T);
# <p> copy files for inst sub-folder
nelapply(o$instFiles, function(n, files) {
dest = Sprintf('%{packageDir}s/inst/%{n}s');
Dir.create(dest, recursive = T);
LogS(2, 'Copying files: %{f}s -> %{dest}s', f = join(src, ', '));
File.copy(files, dest, symbolicLinkIfLocal = F, overwrite = T);
});
# <p> extract package documentation
doc = sapply(src, function(f)
Regexpr('(?s)(?<=#__PACKAGE_DOC__\\n).*?(?=#__PACKAGE_DOC_END__\\n)', readFile(f))
);
# conflicts
Ndoc = length(which(sapply(doc, nchar) > 0));
if (Ndoc > 1) stop('More than one package documentation files/sections found');
if (Ndoc == 1) {
if (any(sapply(src, function(f)splitPath(f)$file) == Sprintf('%{name}s.R', o)))
stop(Sprintf('%{name}s.R should contain package documentation which is also given elsewhere. %{name}s.R will be overwritten so that it cannot be used as an input file.', o));
# substitute in fields from configuration [description]
#doc0 = paste0(packageDocPrefix, join(doc, ''), "\n\"_PACKAGE\"\n");
doc0 = paste0(packageDocPrefix, unlist(doc), "\n\"_PACKAGE\"\n");
doc1 = Sprintf(doc0, o$description, name = o$name);
doc2 = gsub("(^#)|((?<=\n)#)", "#'", doc1, perl = T);
#print(doc2);
writeFile(Sprintf('%{pdir}s/R/%{name}s.R', o), doc2);
o$files = c(Sprintf('%{name}s.R', o), o$files); # documentation file to list of files
}
# <p> update NEWS file
writeFile(with(o, Sprintf('%{pdir}s/NEWS')), firstDef(o$description$news, '0.1-0 Initial release'));
writeFile(with(o, Sprintf('%{pdir}s/DESCRIPTION')), packageDescription(o));
# <p> testing
if (notE(o$testing) && o$testing$doInstall && !nif(o$testing$prevent))
installTests(o, packageDir, asCran = asCran);
# <p> roxigen2
#Library(c('roxygen2', 'devtools'));
#document(packageDir, roclets = c('namespace', 'rd'));
#document(packageDir, roclets = c('rd'));
#roxygenize(packageDir, roclets = c('rd'), clean = TRUE);
roxygenize(packageDir, clean = TRUE);
# <p> vignettes
if (notE(o$description$vignettes)) installVignettes(o, packageDir);
# <p> git
if (!noGit && notE(o$git)) gitActions(o, packagesDir, debug, gitOptions);
# <p> install
if (doInstall) Install_local(Sprintf('%{packageDir}s'), upgrade = 'never', lib = lib, tarDir = tarDir);
return(o);
}
packageDefFromPath = function(path) {
myEnv = new.env();
# <N> instead of Source: avoid RCurl dependency
SourceLocal(path, local = myEnv);
def = get('packageDefinition', envir = myEnv);
# add definition file as first file <!> (no forward declarations)
# <!> 30.9.2021 changed to last position to allow referencing
def$files = unique(c(def$files, splitPath(path)$file));
return(def);
}
probeDefinition = function(desc, dir = NULL) {
path = Sprintf('%{pre}s%{file}s', pre = circumfix(dir, '/'), file = desc[1]);
sp = splitPath(path);
o = switch(sp$ext,
# <!> assume unique is stable
R = packageDefFromPath(desc[1]),
plist = propertyFromStringExt(readFile(path)),
json = ({ requireNamespace('jsonlite'); read_json(path) }),
yaml = ({ requireNamespace('yaml'); read_yaml(path) })
);
o$dir = firstDef(dir, sp$dir);
o$version = firstDef(o$description$version, Regexpr('\\S+', o$description$news)[[1]], '0.1-0');
return(o);
}
packageTarOSOptions = list(Linux = '--overwrite', Windows = c());
checkPackage = function(packageDesc, packagesDir, asCran = TRUE, copyCranTarball = TRUE, clean = TRUE, noGit = FALSE)
with (packageDesc, {
checkDir = packageDir = Sprintf("%{packagesDir}s/%{name}s");
packagesDirPrev = packagesDir;
if (!noGit && file.exists(Sprintf("%{packageDir}s/.git"))) {
packagesDir = tempdir();
checkDir = Sprintf('%{packagesDir}s/%{name}s');
# <i> move if exists
if (file.exists(checkDir) && clean) {
file.rename(checkDir, Sprintf('%{checkDir}s-%{i}d', i = as.integer(runif(1)*1e6)))
}
dir.create(checkDir, FALSE);
#SystemS('cd %{packageDir}q ; git archive --format tar HEAD | ( cd %{checkDir}q ; tar xf - --exclude inst/doc --overwrite )', 2);
#SystemS('cd %{packageDir}q ; git archive --format tar HEAD | ( cd %{checkDir}q ; tar xf - --overwrite )', 2);
#SystemS('cd %{packageDir}q ; git archive --format tar HEAD | ( cd %{checkDir}q ; tar xf - --overwrite )', 2);
# cmdGit = JoinCmds(Sprintf(c('cd %{packageDir}q', 'git archive --format tar HEAD')));
# cmdTar = JoinCmds(Sprintf(c('cd %{checkDir}q', 'tar xf - --overwrite')));
# SystemS('%{cmdGit}s | ( %{cmdTar}s )', 2);
fArchive = tempfile();
SystemS('git archive --format tar HEAD -o %{fArchive}q', 2, wd = packageDir);
#SystemS('tar xf %{fArchive}q --overwrite', 2, wd = checkDir);
untar(fArchive, exdir = checkDir, extras = packageTarOSOptions[[ Sys.info()['sysname'] ]]);
}
cran = if (asCran) '--as-cran' else '';
# SystemS(JoinCmds(c(
# 'cd %{packagesDir}q',
# 'R CMD build %{name}q',
# 'R CMD check %{cran}s %{name}q_%{version}s.tar.gz'
# )), 2);
SystemS('R CMD build %{name}q', 2, wd = packagesDir);
SystemS('R CMD check %{cran}s %{name}q_%{version}s.tar.gz', 2, wd = packagesDir);
if (asCran && copyCranTarball) {
from = Sprintf('%{packagesDir}s/%{name}q_%{version}s.tar.gz');
to = Sprintf('%{packagesDirPrev}s/%{name}q_%{version}s-cran.tar.gz');
File.copy(from, to, overwrite = T, symbolicLinkIfLocal = F, logLevel = 2);
}
})
#' Create package from vector of source files and single configuration
#'
#' This function creates a package dir, runs documentation generation using roxygen and optionally installs the package. It can also update via git and manage version numbers. In a minimal configuration, a single file is sufficient to create a fully documented R package.
#'
#' @alias createPackageWithConfig
#' @param packageDesc path to the configuration file (R, extended plist format, json, yaml).
#' If an R-file is provided, it is sourced in a seperate environment and needs to define the variable
#' `packageDefinition`. This variable has to be a list which is further specified in the details below.
#' If a propertyList/JSON/YAML-file is provided, they have to parse into a list corresponding to
#' `packageDefinition`. Functions \code{propertyFromStringExt}, \code{read_json}, and \code{read_yaml} are
#' used for parsing, coming from packages \code{package}, \code{jsonlite}, and \code{yaml}.
#' @param packagesDir folder in which the folder structure of the package is written
#' @param doInstall flag to indicate whether the package should also be installed
#' @param doCheck whether to run R CMD check --as-cran on the package
#' @param dir directory to search for package definition
#' @param gitOptions list with options for git interaction
#' @param noGit boolean to suppress git calls, overwrites other options
#' @param lib Path to package library as forwarded to \code{install.packages}
#' @param asCran boolean to indicate whether check should be including --as-cran
#'
#' @details This function creates a valid R package folder with DESCRIPTION, LICENSE and NEWS files.
#' All R-files listed are copied to this directory and documentation is created by
#' running the \code{devtools::document} function on this folder.
#' The package is specified through a list coming from an R script or configuration file.
#' The following elements control package generation. In this list \code{key1-key2} indicates a
#' sublist-element, i.e. it stand for \code{packageDefinition[[key1]][[key2]]}.
#'
#' \itemize{
#' \item{name: }{The name of the pacakge}
#' \item{files: }{R-files to be put into the package. If an R-file is used for the configuration,
#' it will automatically be include. This allows package definition through a single R-file.}
#' \item{instFiles: }{Other files to be installed. This is a list, the names of which specify
#' sub-folders in the \code{inst} sub-directory of the package. Values are character vectors
#' specifying files to be put there.}
#' \item{description: }{A sub-list with elements specifying the \code{DESCRIPTION} file of the package.}
#' \item{description-title: }{The title of the help page 'package-myPackage' (myPackage is the name
#' of the package) and the title fiedl in DESCRIPTION.}
#' \item{description-author: }{The \code{Author} field in DESCRIPTION.
#' \item{description-description: } The \code{Description} field in DESCRIPTION. The text is re-used
#' for the package documentation as displayed by ?'package-myPackage' and is prepended to the
#' seperate package documentation. It is also inserted as a Description section of a Markdown file
#' if git is used. This string should therefore not make use of roxygen/markdown markup.}
#' \item{description-depends: }{A character vector with package dependencies.}
#' \item{description-suggests: }{A character vector with package suggestions.}
#' \item{description-news: }{A character vector with a single element containing the \code{NEWS}
#' file of the package. It is assumed that a line starting with a non white space character
#' indicates a new version. The version identifier is taken to be all characters until the
#' first white space. Once a new version is detected, git actions might be triggered (see below).}
#' \item{git: }{A sub-list specifying git behavior. If you do not
#' want to use git, omit this entry from \code{packageDefinition}. If present, a git repository
#' is created and maintained in the target folder. Default \code{git} settings for the package can be
#' overwritten using the \code{gitOptions} argument.}
#' \item{git-push: }{Logical, whether to push each commit, defaults to \code{FALSE}.}
#' \item{git-pushOnNewVersion: }{Logical, whether to push each when a new release is created
#' (see item \code{description-news}. Defaults to \code{TRUE}.
#' A push is automatically performed, once a new release is created, irrespective of this setting.
#' To suppress a push in these cases, push has to set to \code{FALSE} in the. }
#' \item{git-readme: }{Character vector with single entry with the content of a readme file that is put
#' as \code{README.md} into the package main folder. The description given under
#' \code{description-description} is appended to this text.}
#' }
#' @author Stefan Böhringer, \email{r-packages@@s-boehringer.org}
#' @seealso package-package
#' @keywords create package createPackage
#' @examples
#'
#' packageDefinition = list(
#' name = 'pkg-minimal',
#' files = c(),
#' instFiles = list(),
#' description = list(
#' title = 'Minimal R-package created with `package`',
#' # version to be documented in news section
#' #version = '0.1-0',
#' author = 'Stefan Böhringer <r-packages@s-boehringer.org>',
#' description = 'This appears in the package-documentaion, the markdown of the git-repository and in the package details.',
#' depends = c(),
#' suggests = c(),
#' license = 'LGPL',
#' news = "0.1-0 Initial release"
#' ),
#' git = list(
#' readme = '## Installation\n```{r}\nlibrary(devtools);\ninstall_github("user/pkg-minimal")\n```\n',
#' push = FALSE,
#' pushOnNewVersion = FALSE
#' )
#' );
#'
#'
#' @export createPackage
createPackage = function(packageDesc, packagesDir = '~/src/Rpackages',
dir = NULL, doInstall = FALSE, doCheck = T, gitOptions = list(), noGit = F, lib = NULL, asCran = FALSE) {
packageDef = probeDefinition(packageDesc, dir);
#print(packageDef);
r = createPackageWithConfig(packageDef, packagesDir, doInstall,
gitOptions = gitOptions, noGit = noGit,
lib = lib, asCran = asCran
);
if (doCheck) checkPackage(packageDef, packagesDir, asCran, noGit = noGit);
return(r);
}
#
# <p> local development
#
SourcePackage = function(path) {
def = packageDefFromPath(path);
Source(def$files, locations = splitPath(path)$dir);
}
LibraryPackage = function(path, suggests = TRUE) {
def = packageDefFromPath(path);
Library(def$description$depends);
if (suggests) Library(def$description$suggests);
}
SetupPackage = function(path, suggests = TRUE) {
LibraryPackage(path, suggests = suggests);
SourcePackage(path);
}
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