Package 'kwb.package'

Title: Install / Unstall KWB Packages and Show Package Dependencies
Description: This package contains some helper functions for (un-)installing KWB packages and for showing package dependencies. The function of main interest may be updateKwbPackages() that checks for the latest package version on KWB's server and installs the packages from there if required.
Authors: Hauke Sonnenberg [aut, cre] , Michael Rustler [ctb] , FAKIN [fnd], OPTIWELLS-2 [fnd], Kompetenzzentrum Wasser Berlin gGmbH [cph]
Maintainer: Hauke Sonnenberg <[email protected]>
License: MIT + file LICENSE
Version: 0.4.0
Built: 2024-11-01 04:39:43 UTC
Source: https://github.com/KWB-R/kwb.package

Help Index

Add Labels to the Nodes Drawn on a Circle Line

Description

Add Labels to the Nodes Drawn on a Circle Line

Usage

addNodeLabels(nodes, cex = 1, distance.factor = 1)

Arguments

nodes

data frame as returned by toNodes
cex

character expansion factor as given to text
distance.factor

expansion factor applied to the x and y coordinates of the nodes to get the coordinates of the labels

Angle in Unit Circle to Point Coordinate

Description

Convert angles in a unit circle to point coordinates (x, y)

Usage

anglesToPoints(angles.grad)

Arguments

angles.grad

vector of angles in degree

Value

matrix with columns x and y containing the coordinates of points corresponding to the given angles in a unit circle

Examples

plot(anglesToPoints(equidistantAngles(n = 10)), type = "b")

Archived CRAN versions

Description

Archived CRAN versions

Usage

archivedCranVersions(package, ref_date = NULL)

Arguments

package

package name
ref_date

default: NULL

Examples

packages <- c("ggplot2", "swmmr", "kwb.hantush")
archivedCranVersions(packages)
archivedCranVersions(packages, ref_date= "2012-12-01")

Compare Package Versions Between Libraries

Description

Compare Package Versions Between Libraries

Usage

compareInstalledVersions(lib1, lib2)

Arguments

lib1

path to first R library
lib2

path to second R library

Value

data frame with columns name (package name), version.1, version.2 (version string of package in lib1 and lib2, respectively), differs (logical indicating whether the version is different in the two libraries)

Copy Base R Packages from the System Library to the Target Library

Description

Copy Base R Packages from the System Library to the Target Library

Usage

copyBasePackages(
  target_lib,
  set_number = 2L,
  system_lib = utils::tail(.libPaths(), 1L),
  packages = systemPackages(set_number)
)

Arguments

target_lib

path to the target library
set_number

number defining the base packages to be copied, see systemPackages
system_lib

path to the system library from which to copy packages
packages

vector of names of packages to be copied

Get versions of CRAN packages

Description

Get versions of CRAN packages

Usage

cranVersions(name, dbg = TRUE)

Arguments

name

package name
dbg

logical indicating whether or not to show debug messages. Default: TRUE

Default Package Directory

Description

Default Package Directory

Usage

defaultPackageDir()

Detach all Non-System Packages

Description

Detach all Non-System Packages

Usage

detachAllNonSystemPackages()

Detach Packages Recursively

Description

Detach a package and all the depending packages

Usage

detachRecursively(package, pattern = ".*", dbg = FALSE)

Arguments

package

name of package to be detached
pattern

pattern matching the names of depending packages that are actually to be detached, e.g. use pattern = "^kwb\." to only detach kwb packages. Default: ".*" (matching all package names)
dbg

if TRUE, debug messages are shown

Download an R Package from GitHub

Description

Download an R Package from GitHub

Usage

downloadGitHubPackage(repo, destdir = "~/../Downloads")

Arguments

repo

path to repository, relative to https://github,com, e.g. "kwb-r/kwb.utils"
destdir

path to download folder, default: "~/../Downloads"

Value

path to downloaded file in the destdir folder with attribute "origin" pointing to the original file in tempdir().

Download Package Archive from Microsoft R Archive Network

Description

Download Package Archive from Microsoft R Archive Network

Usage

downloadPackagesFromSnapshot(
  packages,
  snapshot_date,
  destdir = NULL,
  type = c("source", "win.binary")[1L]
)

Arguments

packages

names of packages (vector of character)
snapshot_date

date of snapshot of CRAN package versions, as a string in yyyy-mm-dd format
destdir

path to download folder
type

one of c("source", "win.binary")

Value

paths to the downloaded files (vector of character)

Draw Lines between Nodes

Description

Draw Lines between Nodes

Usage

drawDependencies(nodes, dependencies, nodeColours, ...)

Arguments

nodes

data frame as returned by toNodes
dependencies

list of package dependencies as returned by packageDependencies
nodeColours

colours given to the lines starting at the same start node
...

arguments passed to arrows

Equidistantly Distributed Angles in Degrees Between 0 and 360

Description

Equidistantly Distributed Angles in Degrees Between 0 and 360

Usage

equidistantAngles(n, from = 0)

Arguments

n

number of angles to be returned
from

start angle in degrees. Default: 0

Examples

x <- equidistantAngles(90)

plot(x, sin(gradToRad(x)), xlab = "angle in degree", ylab = "sin(angle)")

Example Links and Nodes

Description

Example Links and Nodes

Usage

exampleLinksAndNodes()

Get Information on Package Authors

Description

Get Information on Package Authors

Usage

getAuthors(package)

Arguments

package

name of (installed) package

Get Matrix with Information on All CRAN Packages

Description

Get Matrix with Information on All CRAN Packages

Usage

getCranPackageDatabase()

Get Package Dependency Data from Package Database

Description

Get Package Dependency Data from Package Database

Usage

getDependencyData(
  db,
  fields = c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")
)

Arguments

db

package data base as e.g. returned by getCranPackageDatabase
fields

types of dependencies to be considered. Default: c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")

Get Package Files to Install

Description

Get paths/names of package files available in a directory

Usage

getPackageFilesToInstall(
  package.dir = defaultPackageDir(),
  packageNames = NULL,
  filepattern = "",
  full.names = TRUE,
  dbg = FALSE,
  warn = TRUE
)

Arguments

package.dir

full path to directory containing the package files
packageNames

optional vector of character containing the names of the packages to be installed. If NULL (default), all available packages in package.dir are installed,
filepattern

pattern matching names of files to be considered. Default: "^kwb\..*\.zip$"
full.names

if TRUE (default) the full paths to the package files are returned, else only the file names
dbg

if TRUE (default) debug messages are shown
warn

if TRUE (default) warnings are given if no corresponding package files are found

Value

character vector containing the full paths to or just the names of the available package files

Which Licences are Specified for the Packages?

Description

Which Licences are Specified for the Packages?

Usage

getPackageLicences(packages, db = utils::installed.packages())

Arguments

packages

names of (installed) packages
db

optional. Package database, similar to what is returned by installed.packages. Default: installed.packages()

Value

data frame

Helper: Get R major minor version string

Description

Helper: Get R major minor version string

Usage

getRVersionMajorMinor()

Value

returns R version major.minor string (e.g. 4.0), used by standard R libraries for grouping all R packages into one folder

Examples

getRVersionMajorMinor()

Get KWB Servername

Description

Get KWB Servername

Usage

getServername()

Get Versions of Packages on GitHub

Description

Get Versions of Packages on GitHub

Usage

githubVersions(name, github_user = "KWB-R")

Arguments

name

package name
github_user

name of github account, default: "KWB-R"

Value

data frame with one row per available version

Examples

githubVersions("kwb.utils")

Angle in Degree to Angle in rad

Description

Angle in Degree to Angle in rad

Usage

gradToRad(grad)

Arguments

grad

vector of angles in degrees

Examples

gradToRad(c(0, 90, 180, 270, 360)) / pi

Do Packages have a GPL Licence?

Description

Do Packages have a GPL Licence?

Usage

hasGplLicence(packages)

Arguments

packages

package name(s) as a vector of character

Value

vector of logical

Create the folder structure for a local CRAN-like repository

Description

Create the folder structure for a local CRAN-like repository

Usage

initLocalCRAN(local_cran)

Arguments

local_cran

full path to the folder representing the local CRAN

What Versions of Package Dependencies are Installed?

Description

What Versions of Package Dependencies are Installed?

Usage

installedDependencies(package, recursive = TRUE)

Arguments

package

name of the package of which to check the dependencies
recursive

whether to look recursively for dependencies or only for the direct dependencies of package. Passed to packageDependencies, defaults to TRUE

Examples

installedDependencies(package = "kwb.package")
installedDependencies(package = "kwb.package", recursive = FALSE)

Installed KWB-Packages

Description

Installed KWB-Packages

Usage

installedKwbPackages()

Value

vector of names of installed kwb-packages

Install GitHub Packages

Description

Install GitHub Packages

Usage

installGithubPackages(
  lib,
  repos,
  dependencies = TRUE,
  upgrade = "never",
  auth_token = Sys.getenv("GITHUB_PAT")
)

Arguments

lib

path to R library where packages should be installed
repos

vector of relative paths to GitHub repositories containing R packages (e.g. "kwb-r/kwb.utils")
dependencies

passed to remotes::install_github(). TRUE is shorthand for "Depends", "Imports", "LinkingTo" and "Suggests" NA is shorthand for "Depends", "Imports" and "LinkingTo" and is the default. FALSE is shorthand for no dependencies (i.e. just check this package, not its dependencies), (default: TRUE)
upgrade

passed to install_github, (default: "never")
auth_token

GitHub Personal Access token, required with scope "private" if access to non-public R packages is required (default: Sys.getenv("GITHUB_PAT"))

Value

installs multiple GitHub R packages into one R library

Examples

## Not run: 
remotes::install_github("kwb-r/pkgmeta") 
pkgs <- pkgmeta::get_github_packages()
paths_list <- list(
  r_version = kwb.packages::getRVersionMajorMinor(),
  lib_linux = "/usr/lib/R/site-library",
  lib_win = "<win_root_dir>/kwbran/<r_version>"
)

paths <- kwb.utils::resolve(paths_list, win_root_dir = tempdir())

pkgs <- pkgmeta::get_github_packages()

installGithubPackages(lib = paths$lib_win, pkgs$full_name)
installGithubPackages(lib = paths$lib_linux, pkgs$full_name)

## End(Not run)

Install the remotes Package to the Given Library

Description

Install the remotes Package to the Given Library

Usage

installRemotes(lib)

Arguments

lib

path to the library to which to install the remotes package

Package Dependencies

Description

This is just a wrapper around package_dependencies with some defaults defined.

Usage

packageDependencies(
  packages = NULL,
  db = utils::installed.packages(),
  which = c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")[1:3],
  recursive = TRUE,
  reverse = FALSE,
  verbose = FALSE
)

Arguments

packages

a character vector of package names.
db

character matrix as from available.packages() (with the default NULL the results of this call) or data frame variants thereof. Alternatively, a package database like the one available from https://cran.r-project.org/web/packages/packages.rds.

which

a character vector listing the types of dependencies, a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances"). Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector.

recursive

a logical indicating whether (reverse) dependencies of (reverse) dependencies (and so on) should be included, or a character vector like which indicating the type of (reverse) dependencies to be added recursively.
reverse

logical: if FALSE (default), regular dependencies are calculated, otherwise reverse dependencies.
verbose

logical indicating if output should monitor the package search cycles.

Package Dependencies by Type

Description

Package Dependencies by Type

Usage

packageDependenciesByType(
  packages = NULL,
  db = utils::installed.packages(),
  which = c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")[1:3],
  recursive = TRUE,
  reverse = FALSE,
  verbose = FALSE
)

Arguments

packages

a character vector of package names.
db

character matrix as from available.packages() (with the default NULL the results of this call) or data frame variants thereof. Alternatively, a package database like the one available from https://cran.r-project.org/web/packages/packages.rds.

which

a character vector listing the types of dependencies, a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances"). Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector.

recursive

a logical indicating whether (reverse) dependencies of (reverse) dependencies (and so on) should be included, or a character vector like which indicating the type of (reverse) dependencies to be added recursively.
reverse

logical: if FALSE (default), regular dependencies are calculated, otherwise reverse dependencies.
verbose

logical indicating if output should monitor the package search cycles.

Package String

Description

Package String

Usage

packageString(package)

Arguments

package

Package name

Value

package, preceded by package:

Plot all Package Dependencies

Description

Plot all Package Dependencies

Usage

plotAllDependencies(dependencies, r = 1.5, for.each = TRUE, ...)

Arguments

dependencies

list of package dependencies as returned by packageDependencies
r

radius of the unit circle in which to arrange the package names. Passed to plotNodes
for.each

if TRUE (default) not only an overview plot showing all dependencies but also one plot per package of which dependency information are contained in dependencies is created.
...

arguments passed to plotDependencies

Examples

kwb.packages <- installedKwbPackages()
  
# Plot all (direct and indirect) dependencies of installed kwb packages
plotAllDependencies(packageDependencies(kwb.packages))
  
# Plot only direct dependencies
plotAllDependencies(packageDependencies(kwb.packages, recursive = FALSE))

Plot Dependencies Between Nodes on a Circle Line

Description

Plot Dependencies Between Nodes on a Circle Line

Usage

plotDependencies(
  nodes,
  dependencies,
  main = "",
  r = 1.5,
  nodeColours = grDevices::rainbow(nrow(nodes)),
  ...
)

Arguments

nodes

data frame as returned by toNodes
dependencies

list of package dependencies as returned by packageDependencies
main

plot title
r

radius of the circle
nodeColours

colours to be given to the nodes
...

passed to drawDependencies

Plot Nodes

Description

Plot Nodes

Usage

plotNodes(nodes, r = 1, col = "red", ...)

Arguments

nodes

data frame as returned by toNodes
r

Radius of a circle that fits into the plot range: xlim is set to c(-r, r)
col

colour used to plot the nodes (default: "red")
...

arguments passed to plot

Plot Package Versions

Description

Plot Package Versions

Usage

plotPackageVersions(
  versions,
  r_range = c(1, 10),
  rmax = 1.1 * r_range[2L],
  dphi = NULL,
  ticklen = 1
)

Arguments

versions

versions
r_range

r_range (default: c(1, 10))
rmax

rmax (default: 1.1 * r_range[2L])
dphi

dphi (default: NULL)
ticklen

ticklen (default: 1)

Plot Sankey Network

Description

Plot Sankey Network

Usage

plotSankeyNetwork(functionName, where = 1, ...)

Arguments

functionName

name of function from which to start the network
where

passed to foodweb
...

additional arguments passed to foodweb

Provide a Source Package in the Local Cran

Description

Provide a Source Package in the Local Cran

Usage

provideInLocalCRAN(
  package,
  rebuild = TRUE,
  local_cran = defaultLocalCRAN(drive_letter = TRUE)
)

Arguments

package

name of the package to be looked up in either of these locations: <home>/Documents/R-Development/RPackages, <home>/Desktop/R_Development/RPackages
rebuild

logical. If TRUE the package is rebuild before all .tar.gz-files from the parent folder of the package folder are copied to the local CRAN folder structure
local_cran

full path to the folder representing the local CRAN

readGithubPackageDescription ————————————————

Description

Read DESCRIPTION File for R Package on GitHub

Usage

readGithubPackageDescription(
  repo,
  sha,
  auth_token = remotes_github_pat(),
  destdir = tempdir()
)

Arguments

repo

GitHub repository, e.g. "kwb-r/kwb.utils"
sha

SHA (hash) of the commit
auth_token

GitHub token
destdir

path to destination directory, i.e. directory to which the DESCRIPTION file is copied. Default: tempdir()

Set Options for Using Packrat

Description

Add the path to the local repository to the option "repos" and set the option "pkgType" to "source".

Usage

setOptionsForPackrat()

Value

The old options are returned invisibly.

Sorted Package Dependencies

Description

Names of depending packages in the order of their dependency

Usage

sortedDependencies(package, dbg = FALSE)

Arguments

package

name of package(s) of which dependencies are to be found
dbg

if TRUE, debug messages are shown and the user is asked to press Enter each time the body of the main loop is passed!

Value

vector of package names. The first element is the package itself, followed by the names of depending packages. You should be able to detach the packages in this order without any "package ... is required by ..." error

Is a Package Installed?

Description

Is a Package Installed?

Usage

stopIfNotInstalled(package)

Arguments

package

package name (character vector of length one)

Names of Base R Packages

Description

Names of Base R Packages

Usage

systemPackages(set_number = 1L)

Arguments

set_number

integer number specifying a set of packages: 1 or 2.

Value

vector of character representing package names

Convert Links to List of Links and Nodes

Description

Convert Links to List of Links and Nodes

Usage

toLinksAndNodes(links)

Arguments

links

list with elements source and target

Value

list with elements links (input list links with new elements value, source, target) and nodes (data frame with column name)

Examples

kwb.package:::toLinksAndNodes(list(
  source = c("s1", "s1"), target = c("t1", "t2")
))

Nodes in a Unit Circle

Description

Node names to node coordinates in a unit circle

Usage

toNodes(nodeNames)

Arguments

nodeNames

character vector of nodes to be arranged in a unit circle

Value

data frame with columns x and y giving the coordinates of the nodes arranged in a circle. The row names represent the node names.

Examples

nodes <- toNodes(LETTERS)

plot(nodes)
text(nodes, labels = row.names(nodes), adj = c(0, 0))

Update or Install KWB-Packages

Description

Update installed KWB-packages or install KWB-packages for the first time

Usage

updateKwbPackages(
  packageNames = sort(installedKwbPackages()),
  skip = character(),
  package.dir = defaultPackageDir()
)

Arguments

packageNames

vector of packages to be installed. Default: names of all installed KWB-packages
skip

vector of packages not to be installed, even if they are listed in packageNames
package.dir

full path to the folder containing the binary package files