Type: Package
Title: A Way to Perform Code Review or QA on Other Packages
Version: 0.1.15
Language: en-US
Description: Reviews other packages during code review by looking at their dependencies, code style, code complexity, and how internally defined functions interact with one another.
URL: https://github.com/darwin-eu-dev/PaRe
BugReports: https://github.com/darwin-eu-dev/PaRe/issues
License: Apache License (≥ 2)
Encoding: UTF-8
RoxygenNote: 7.3.1
Imports: cli (≥ 3.6.0), cyclocomp (≥ 1.1.0), desc (≥ 1.4.2), DiagrammeR (≥ 1.0.9), DiagrammeRsvg (≥ 0.1), dplyr (≥ 1.1.0), glue (≥ 1.6.2), lintr (≥ 3.0.2), magrittr (≥ 2.0.3), pak (≥ 0.2.0), rmarkdown (≥ 2.20), rsvg (≥ 2.4.0), stringr (≥ 1.5.0), igraph (≥ 1.3.5), utils, R6 (≥ 2.5.1), git2r (≥ 0.31.0), checkmate (≥ 2.1.0), parallel
Suggests: ggplot2, plotly, ggraph, DT, magick, withr, cowplot, knitr, curl, testthat (≥ 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/testthat/parallel: true
NeedsCompilation: no
Packaged: 2024-11-29 15:09:28 UTC; mvankessel
Author: Maarten van Kessel ORCID iD [aut, cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
Repository: CRAN
Date/Publication: 2024-12-02 10:10:06 UTC

PaRe: A Way to Perform Code Review or QA on Other Packages

Description

logo

Reviews other packages during code review by looking at their dependencies, code style, code complexity, and how internally defined functions interact with one another.

Author(s)

Maintainer: Maarten van Kessel m.l.vankessel@erasmusmc.nl (ORCID)

See Also

Useful links:

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

lhs

A value or the magrittr placeholder.

rhs

A function call using the magrittr semantics.

Value

The result of calling rhs(lhs).

R6 Code class

Description

Class representing a piece of code.

Methods

Public methods

Method new()

Initializer method

Usage
Code$new(name, lines)
Arguments
name

(character(1))
Name of Code object.

lines

(character(n))
Vector of lines Code object.

Returns

invisible(self)

Method print()

Overload generic print, to print Code object.

Usage
Code$print(...)
Arguments
...

further arguments passed to or from other methods. See print.

Returns

(character(n))

Method getLines()

Get method for lines.

Usage
Code$getLines()
Returns

(character(n)) Vector of lines in the Code object.

Method getNLines()

Get method for number of lines.

Usage
Code$getNLines()
Returns

(numeric(1)) Number of lines in the Code object.

Method getName()

Get method for Name.

Usage
Code$getName()
Returns

(character(1)) Name of the Code object.

Method clone()

The objects of this class are cloneable with this method.

Usage
Code$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Representations: File, Function, Repository

R6 File class

Description

Class representing a file containing code.

Super class

PaRe::Code -> File

Methods

Public methods

Inherited methods

Method new()

Initializer method

Usage
File$new(repoPath, filePath)
Arguments
repoPath

(character)
Path to repository.

filePath

(character)
Relative path to file

Returns

invisible(self)

Method getFunctions()

Get method to get a list of Function objects

Usage
File$getFunctions()
Returns

(list)
List of Function objects.

Method getFunctionTable()

Get method to retrieve the function table.

Usage
File$getFunctionTable()
Returns

(data.frame)

column data type
name character
lineStart integer
lineEnd numeric
nArgs integer
cycloComp integer

Method getType()

Gets type of file

Usage
File$getType()
Returns

(character)

Method getFilePath()

Gets relative file path

Usage
File$getFilePath()
Returns

(character)

Method getBlameTable()

Gets table of git blame

Usage
File$getBlameTable()
Returns

(tibble)

Method clone()

The objects of this class are cloneable with this method.

Usage
File$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Representations: Code, Function, Repository

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  files <- repo$getRFiles()
  files[[1]]
}

R6 Function class.

Description

Class representing a function.

Super class

PaRe::Code -> Function

Methods

Public methods

Inherited methods

Method new()

Initializer for Function object.

Usage
Function$new(name, lineStart, lineEnd, lines)
Arguments
name

(character)
Name of Function.

lineStart

(numeric)
Line number where function starts in File.

lineEnd

(numeric)
Line number where function ends in File.

lines

(c)
Vector of type character Lines of just the function in File.

Returns

invisible(self)

Method getFunction()

Get method to get defined functions in a File object.

Usage
Function$getFunction()
Returns

(data.frame)

column data type
name (character)
lineStart (integer)
lineEnd (numeric)
nArgs (integer)
cycloComp (integer)

Method clone()

The objects of this class are cloneable with this method.

Usage
Function$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Representations: Code, File, Repository

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  files <- repo$getRFiles()
  file <- files[[1]]
  funs <- file$getFunctions()
  funs[[1]]
}

R6 Repository class.

Description

Class representing the Repository

Methods

Public methods

Method new()

Initializer for Repository class

Usage
Repository$new(path)
Arguments
path

(character)
Path to R package project

Returns

invisible(self)

Method getName()

Get method for name.

Usage
Repository$getName()
Returns

(character)
Repository name

Method getPath()

Get method fro path

Usage
Repository$getPath()
Returns

(character)
Path to Repository folder

Method getFiles()

Get method to get a list of File objects.

Usage
Repository$getFiles()
Returns

(list)
List of File objects.

Method getRFiles()

Get method to get only R-files.

Usage
Repository$getRFiles()
Returns

(list)
List of File objects.

Method getDescription()

Get method to get the description of the package. See: description.

Usage
Repository$getDescription()
Returns

(description)
Description object.

Method getFunctionUse()

Get method for functionUse, will check if functionUse has already been fetched or not.

Usage
Repository$getFunctionUse()
Returns

(data.frame)
See getFunctionUse.

Method gitCheckout()

Method to run 'git checkout <branch/commit hash>'

Usage
Repository$gitCheckout(branch, ...)
Arguments
branch

(character)
Name of branch or a hash referencing a specific commit.

...

Further parameters for checkout.

Returns

invisible(self)

Method gitPull()

Method to run 'git pull'

Usage
Repository$gitPull(...)
Arguments
...

Further parameters for pull.

Returns

invisible(self)

Method gitBlame()

Method to fetch data generated by 'git blame'.

Usage
Repository$gitBlame()
Returns

(tibble)

column data type
repository character
author character
file character
date character
lines integer

Method clone()

The objects of this class are cloneable with this method.

Usage
Repository$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Other Representations: Code, File, Function

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  repo
}

addPareArticle

Description

Writes an Rmd-file to ./vignettes/articles/PaReReport.Rmd. The relative path is dictated by the specified path in the Repository object.

Usage

addPareArticle(repo)

Arguments

repo

(Repository) Repository object.

Value

NULL Writes Rmd-file to ./vignettes/articles/PaReReport.Rmd

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/darwin-eu/IncidencePrevalence.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run makeReport on the Repository object.
  addPaReArticle(repo)
}

checkDependencies

Description

Check package dependencies

Usage

checkDependencies(repo, dependencyType = c("Imports", "Depends"), nThreads = 1)

Arguments

repo

(Repository)
Repository object.

dependencyType

(character())
Types of dependencies to be included

nThreads

(numeric(1): 1) Number of threads to use to fetch permitted packages

Value

(data.frame())
Data frame with all the packages that are now permitted.

column data type
package character()
version character()

Examples


# Set cahce, usually not required.
withr::local_envvar(
  R_USER_CACHE_DIR = tempfile()
)

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Use checkDependencies on the Repository object.
  checkDependencies(repo)
  checkDependencies(repo, dependencyType = c("Imports", "Suggests"))
}

checkInstalled

Description

Checks if suggested packages are installed.

Usage

checkInstalled()

Value

logical
Logical depending if suggested packages are installed.

countPackageLines

Description

Counts the package lines of a Repository object.

Usage

countPackageLines(repo)

Arguments

repo

(Repository)
Repository object.

Value

(tibble
) Tibble containing the amount of lines per file in the Repository object.

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run countPackageLines on the Repository object.
  countPackageLines(repo = repo)
}

exportDiagram

Description

Exports the diagram from pkgDiagram to a PDF-file.

Usage

exportDiagram(diagram, fileName)

Arguments

diagram

(grViz)
Graph object from pkgDiagram.

fileName

(character)
Path to save the diagram to, as PDF.

Value

(NULL)

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run pkgDiagram on the Repository object.
  pkgDiagram(repo = repo) %>%
    # Export the diagram to a temp file.
    exportDiagram(fileName = tempfile())
}

functionUseGraph

Description

functionUseGraph

Usage

functionUseGraph(repo)

Arguments

repo

(Repository)

Value

(graph)

funsUsedInFile

Description

Support function

Usage

funsUsedInFile(files, verbose = FALSE)

Arguments

files

(list) of (File)

verbose

(logical)

Value

(list)

funsUsedInLine

Description

Support function for funsUsedInFile.

Usage

funsUsedInLine(lines, name, i, verbose = FALSE)

Arguments

lines

(c) of (character)

name

(character)

i

(numeric)

verbose

(logical: FALSE)

Value

(data.frame)

column data type
pkg character
fun character
line numeric

getApplyCall

Description

getApplyCall

Usage

getApplyCall(fun, defFuns)

Arguments

fun

(Function)
Function object.

defFuns

(data.frame)
See getDefinedFunctions

Value

(data.frame)

getApplyFromLines

Description

getApplyFromLines

Usage

getApplyFromLines(lines)

Arguments

lines

(c)
Vector of (character). See getDefinedFunctions

Value

(character)

getDefaultPermittedPackages

Description

Gets permitted packages. An internet connection is required.

Usage

getDefaultPermittedPackages(nThreads = 1)

Arguments

nThreads

(numeric(1): 1) Number of threads to use to fetch permitted packages

Value

(tibble)

column data type
package character
version character

Examples


# Set cache
withr::local_envvar(
  R_USER_CACHE_DIR = tempfile()
)

if (interactive()) {
  getDefaultPermittedPackages()
}

getDefinedFunctions

Description

Gets all the defined functions from a Repository object.

Usage

getDefinedFunctions(repo)

Arguments

repo

(Repository)
Repository object.

Value

(data.frame)

column data type
name character
lineStart integer
lineEnd numeric
nArgs integer
cycloComp integer
fileName character

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  repo <- PaRe::Repository$new(pathToRepo)

  getDefinedFunctions(repo)
}

getDlplyCall

Description

getDlplyCall

Usage

getDlplyCall(fun, defFuns)

Arguments

fun

(Function)
Function object.

defFuns

(data.frame)
See getDefinedFunctions

Value

(data.frame)

getDlplyCallFromLines

Description

getDlplyCallFromLines

Usage

getDlplyCallFromLines(lines)

Arguments

lines

(c)
Vector of (character).

Value

(character)

getDoCall

Description

getDoCall

Usage

getDoCall(fun, defFuns)

Arguments

fun

(Function)
Function object.

defFuns

(data.frame)
See getDefinedFunctions

Value

(data.frame)

getDoCallFromLines

Description

getDoCallFromLines

Usage

getDoCallFromLines(lines)

Arguments

lines

(c)
Vector of (character). See getDefinedFunctions

Value

(character)

getExportedFunctions

Description

Gets all the exported functions of a package, from NAMESPACE.

Usage

getExportedFunctions(path)

Arguments

path

(character)
Path to package

Value

(c) Vector of character exported functions.

getFunCall

Description

getFunCall

Usage

getFunCall(fun, defFuns)

Arguments

fun

(Function)
Function object.

defFuns

(data.frame)
See getDefinedFunctions.

Value

(data.frame)

subsetGraph

Description

Create a subset of the package diagram containing all in comming and out going paths from a specified function.

Usage

getFunctionDiagram(repo, functionName)

Arguments

repo

(Repository) Repository object.

functionName

(character) Name of the function to get all paths from.

Value

(htmlwidgets)
Subsetted diagram. See grViz

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run getFunctionDiagram on the Repository object.
  getFunctionDiagram(repo = repo, functionName = "glue")
}

summariseFunctionUse

Description

Summarise functions used in R package.

Usage

getFunctionUse(repo, verbose = FALSE)

Arguments

repo

(Repository)
Repository object.

verbose

(logical: FALSE)
Prints message to console which file is currently being worked on.

Value

(tibble)

column data type
file character
line numeric
pkg character
fun character

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run getFunctionUse on the Repository object.
  getFunctionUse(repo = repo, verbose = TRUE)
}

getFunsPerDefFun

Description

getFunsPerDefFun

Usage

getFunsPerDefFun(files, defFuns)

Arguments

files

(list)
List of File objects.

defFuns

(data.frame)
See getDefinedFunctions.

Value

data.frame

column data type
from character
to character

getGraphData

Description

Get the dependency interactions as a graph representation.

Usage

getGraphData(repo, packageTypes = c("Imports"), nThreads = 1)

Arguments

repo

(Repository)
Repository object.

packageTypes

(c: c("Imports")) of (character) Any of the following options may be included in a vector:

  • "imports"

  • "depends"

  • "suggests"

  • "enhances"

  • "linkingto"

nThreads

(numeric(1): 1) Number of threads to use to fetch permitted packages

Value

(as_tbl_graph)

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run getGraphData on the Repository object.
  if (interactive()) {
    getGraphData(repo = repo, packageTypes = c("Imports"))
  }
}

getMultiLineFun

Description

getMultiLineFun

Usage

getMultiLineFun(line, lines)

Arguments

line

(numeric)
Current line number.

lines

(c)
Vector of (character) lines.

Value

(character)

graphToDot

Description

graphToDot

Usage

graphToDot(graph)

Arguments

graph

(graph)

Value

htmlwidgets
See grViz.

lintRepo

Description

Get all the lintr messages of the Repository object.

Usage

lintRepo(repo)

Arguments

repo

(Repository)

Value

(data.frame)

column data type description
filename character Name of the file
line_number double Line in which the message was found
column_number double Column in which the message was found
type character Type of message
message character Style, warning, or error message
line character Line of code in which the message was found
linter character Linter used

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run lintRepo on the Repository object.
  messages <- lintRepo(repo = repo)
}

lintScore

Description

Function that scores the lintr output as a percentage per message type (style, warning, error). Lintr messages / lines assessed * 100

Usage

lintScore(repo, messages)

Arguments

repo

(Repository)
Repository object.

messages

(data.frame)
Data frame containing lintr messages. See lintRepo.

Value

(tibble)

type

(character) Type of message.

pct

(double) Score.

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  messages <- lintRepo(repo = repo)

  # Run lintScore on the Repository object.
  lintScore(repo = repo, messages = messages)
}

makeGraph

Description

Makes the graph

Usage

makeGraph(funsPerDefFun, pkgName, expFuns, ...)

Arguments

funsPerDefFun

(data.frame)
Functions per defined function data.frame.

pkgName

(character)
Name of package.

expFuns

(data.frame)
Exported functinos data.frame.

...

Optional other parameters for grViz.

Value

(htmlwidget)
Diagram of the package. See grViz.

makeReport

Description

Uses rmarkdown's render function to render a html-report of the given package.

Usage

makeReport(repo, outputFile, showCode = FALSE, nThreads = 1)

Arguments

repo

(Repository)
Repository object.

outputFile

(character)
Path to html-file.

showCode

(logical: FALSE)
Logical to show code or not in the report.

nThreads

(numeric(1): 1) Number of threads to use to fetch permitted packages

Value

(NULL)

Examples


fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/darwin-eu/IncidencePrevalence.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run makeReport on the Repository object.
  makeReport(repo = repo, outputFile = tempfile())
}

pkgDiagram

Description

Creates a diagram of all defined functions in a package.

Usage

pkgDiagram(repo, verbose = FALSE, ...)

Arguments

repo

(Repository)
Repository object.

verbose

(logical)
Turn verbose messages on or off.

...

Optional other parameters for grViz.

Value

(htmlwidget)
Diagram htmlwidget object. See createWidget

Examples

fetchedRepo <- tryCatch(
  {
    # Set dir to clone repository to.
    tempDir <- tempdir()
    pathToRepo <- file.path(tempDir, "glue")

    # Clone repo
    git2r::clone(
      url = "https://github.com/tidyverse/glue.git",
      local_path = pathToRepo
    )

    # Create instance of Repository object.
    repo <- PaRe::Repository$new(path = pathToRepo)

    # Set fetchedRepo to TRUE if all goes well.
    TRUE
  },
  error = function(e) {
    # Set fetchedRepo to FALSE if an error is encountered.
    FALSE
  },
  warning = function(w) {
    # Set fetchedRepo to FALSE if a warning is encountered.
    FALSE
  }
)

if (fetchedRepo) {
  # Run pkgDiagram on the Repository object.
  pkgDiagram(repo = repo)
}

whiteList

Description

data.frame containing links to csv-files which should be used to fetch white-listed dependencies.

Usage

whiteList

Format

An object of class tbl_df (inherits from tbl, data.frame) with 3 rows and 4 columns.

Details

By default three csv's are listed:

  1. darwin

  2. hades

  3. tidyverse

The data.frame is locally fetched under: system.file(package = "PaRe", "whiteList.csv")

Manual insertions into this data.frame can be made, or the data.frame can be overwritten entirely.

The data.frame itself has the following structure:

column data type description
source character name of the source
link character link or path to the csv-file
package character columnname of the package name column in the csv-file being linked to
version character columnname of the version column in the csv-file being linked to

The csv-files that are being pointed to should have the following structure:

Examples

if (interactive()) {
  # Dropping tidyverse
  whiteList <- whiteList %>%
    dplyr::filter(source != "tidyverse")

  # getDefaultPermittedPackages will now only use darwin and hades
  getDefaultPermittedPackages()
}