Title:	Assessing Package Risk Metrics
Version:	2.0.0
Description:	Provides a structured approach to assess the quality and trustworthiness of R packages (documentation, testing, popularity, dependencies), supporting informed decisions in production or research by highlighting strengths and potential risks in adoption or development.
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	https://sanofi-public.github.io/risk.assessr/
BugReports:	https://github.com/Sanofi-Public/risk.assessr/issues
Depends:	R (≥ 4.1.0)
Imports:	remotes, callr, checkmate, covr, desc, devtools, dplyr, fs, methods, purrr, rcmdcheck, rlang, xml2, stringr, tidyr, utils, curl, gh, jsonlite
Suggests:	forcats, glue, here, htmltools, kableExtra, knitr, magrittr, openxlsx, readr, roxygen2, testthat (≥ 3.0.0), tidyselect, tools, rmarkdown, withr, mockery
Encoding:	UTF-8
RoxygenNote:	7.3.2
Config/testthat/edition:	3
Config/build/clean-inst-doc:	false
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2025-07-07 14:25:15 UTC; u1004798
Author:	Edward Gillian [cre, aut], Hugo Bottois [aut], Paulin Charliquart [aut], Andre Couturier [aut], Sanofi [cph, fnd]
Maintainer:	Edward Gillian <edward.gillian-ext@sanofi.com>
Repository:	CRAN
Date/Publication:	2025-07-10 15:20:02 UTC

risk.assessr: Assessing Package Risk Metrics

Description

Provides a structured approach to assess the quality and trustworthiness of R packages (documentation, testing, popularity, dependencies), supporting informed decisions in production or research by highlighting strengths and potential risks in adoption or development.

Author(s)

Maintainer: Edward Gillian edward.gillian-ext@sanofi.com (ORCID)

Authors:

• Hugo Bottois hugo.bottois@sanofi.com (ORCID)

• Paulin Charliquart paulin.charliquart@sanofi.com

• Andre Couturier andre.couturier@sanofi.com

Other contributors:

• Sanofi [copyright holder, funder]

See Also

Useful links:

• https://sanofi-public.github.io/risk.assessr/

• Report bugs at https://github.com/Sanofi-Public/risk.assessr/issues

Set the default weight of each metric to 1.

Description

Set the default weight of each metric to 1.

Usage

add_default_risk_weights(data)

Arguments

Assess dependencies for sigmoid point

Description

This function calculates average number of dependencies to determine the dependency sigmoid point

Usage

assess_dep_for_sigmoid(riskdata_results)

Arguments

Value

nested list with dependencies, Import count mean, and all dependency count and mean

assess_description_file_elements

Description

assess_description_file_elements

Usage

assess_description_file_elements(pkg_name, pkg_source_path)

Arguments

Value

- list - list with scores for description file elements

Assess Rd files for example or examples

Description

Assess Rd files for example or examples

Usage

assess_examples(pkg_name, pkg_source_path)

Arguments

Value

has_examples - variable with score

assess_export_help

Description

assess_export_help

Usage

assess_export_help(pkg_name, pkg_source_path)

Arguments

Value

- export_help - variable with score

Assess exported functions to namespace

Description

Assess exported functions to namespace

Usage

assess_exports(data)

Arguments

Assess Rd files for news

Description

Assess Rd files for news

Usage

assess_news(pkg_name, pkg_source_path)

Arguments

Value

has_news - variable with score

Assess Rd files for news

Description

Assess Rd files for news

Usage

assess_news_current(pkg_name, pkg_ver, pkg_source_path)

Arguments

Value

news_current - variable with score

Assess package

Description

assess package for risk metrics

Usage

assess_pkg(pkg_source_path, rcmdcheck_args, covr_timeout = Inf)

Arguments

Value

list containing results - list containing metrics, covr, tm - trace matrix, and R CMD check

Examples

## Not run: 
# set CRAN repo to enable running of reverse dependencies
r = getOption("repos")
r["CRAN"] = "http://cran.us.r-project.org"
old <- options(repos = r)

pkg_source_path <- system.file("test-data", "here-1.0.1.tar.gz", 
   package = "risk.assessr")
pkg_name <- sub("\\.tar\\.gz$", "", basename(pkg_source_path)) 
modified_tar_file <- modify_description_file(pkg_source_path)

# Set up the package using the temporary file
install_list <- set_up_pkg(modified_tar_file)

# Extract information from the installation list
build_vignettes <- install_list$build_vignettes
package_installed <- install_list$package_installed
pkg_source_path <- install_list$pkg_source_path
rcmdcheck_args <- install_list$rcmdcheck_args

# check if the package needs to be installed locally
package_installed <- install_package_local(pkg_source_path)

# Check if the package was installed successfully
if (package_installed == TRUE) {
  # Assess the package
  assess_package <- assess_pkg(pkg_source_path, rcmdcheck_args)
  # Output the assessment result
} else {
  message("Package installation failed.")
}
options(old)

## End(Not run)

Assess an R Package riskmetric with package name and version

Description

This function use 'risk.assessr::assess_pkg' assessment function with only the package name and version

Usage

assess_pkg_r_package(package_name, version = NA, repos = NULL)

Arguments

Details

This function follows these steps:

1. Downloads the specified R package

2. Installs the downloaded package in a temporary location.

3. Runs the 'risk.assessr::assess_pkg' function to assess the package for risks and issues.

4. Returns the results of the assessment.

Value

The function returns a list of assessment results generated by the 'risk.assessr::assess_pkg' function. If the package cannot be downloaded or installed, an error message is returned.

Examples

## Not run: 
# Example usage of assess_pkg_r_package
results <- assess_pkg_r_package("here", version = "1.0.1")
print(results)

## End(Not run)

assess codebase size

Description

Scores packages based on its codebase size, as determined by number of lines of code.

Usage

assess_size_codebase(pkg_source_path)

Arguments

Value

- size_codebase - numeric value between 0 (for small codebase) and 1 (for large codebase)

Assess vignettes

Description

Assess vignettes

Usage

assess_vignettes(pkg_name, pkg_source_path)

Arguments

Value

- has_vignettes - variable with score

Calculate dependency score

Description

Calculate dependency score

Usage

calc_dependencies(pkg_source_path)

Arguments

Calculate overall package risk scores

Description

Calculate overall package risk scores

Usage

calc_overall_risk_score(data, default_weights = FALSE)

Arguments

Value

pkg_score

Examples

data <- list(
  pkg_name = "synapser",
  pkg_version = "0.2.1",
  pkg_source_path = "/tmp/RtmpNpDlUz/temp_file_1fe56774aacc/synapser",
  has_bug_reports_url = 1, 
  has_examples = 1,
  has_maintainer = 1,
  size_codebase = 0.06702413,
  has_news = 0,
  has_source_control = 0,
  has_vignettes = 1,
  has_website = 1,
  news_current = 0,
  export_help = 1,
  export_calc = 0.586281,
  check = .7,
  covr = .1084,
  dep_score = .9706878,
  revdep_score = .1260338
  )
  overall_risk_score <- 
    calc_overall_risk_score(data, 
                            default_weights = TRUE)

Calculate reverse dependency score

Description

Calculate reverse dependency score

Usage

calc_reverse_dependencies(pkg_source_path)

Arguments

Calculate package risk profile

Description

Calculate package risk profile

Usage

calc_risk_profile(risk_data)

Arguments

Value

risk_profile

Examples

## Not run: 
# Toy dataset
toy_data <- data.frame(score = c(0.1, 0.2, 0.3, 0.4, 0.8, 1.2))

calc_risk_profile(toy_data)

## End(Not run)

Check and Fetch CRAN Package

Description

This function checks if a package exists on CRAN and retrieves the corresponding package URL and version details. If a specific version is not provided, the latest version is used.

Usage

check_and_fetch_cran_package(package_name, package_version = NULL)

Arguments

Value

A list containing: - 'package_url': URL to download the package tarball. - 'last_version': Latest version available - 'version': The requested version of the package (or 'NULL' if not specified). - 'all_versions': A character vector of all available package versions - 'error': If the package or version is not found, an error message is included.

Examples

## Not run: 
# Check and fetch a specific version of "ggplot2"
result <- check_and_fetch_cran_package("ggplot2", package_version = "3.3.5")
print(result)

## End(Not run)

Check if a Package Exists on CRAN

Description

This function checks if a given package is available on CRAN.

Usage

check_cran_package(package_name)

Arguments

Value

A logical value: 'TRUE' if the package exists on CRAN, 'FALSE' otherwise.

Examples

## Not run: 
# Check if the package "ggplot2" exists on CRAN
check_cran_package("ggplot2")

## End(Not run)

function to check value of ggproto

Description

function to check all classes of a ggproto function

Usage

check_ggproto(value)

Arguments

Check that the provided weights are numeric and non-negative.

Description

Check that the provided weights are numeric and non-negative.

Usage

check_risk_weights(weights)

Arguments

Function to check suggested exported functions

Description

This function checks the exported functions of target package against the exported functions of Suggested dependencies to see if any Suggested packages should be in Imports in the DESCRIPTION file

Usage

check_suggested_exp_funcs(pkg_name, pkg_source_path, suggested_deps)

Arguments

Value

- data frame with results of Suggests check

Check for Vignette Folder and .Rmd Files in a .tar File

Description

This function checks if a given .tar file contains a 'vignettes' folder and if there is at least one .Rmd file within that folder. If both 'vignettes' and 'inst/doc' folders exist, the function will return FALSE.

Usage

contains_r_folder(package_dir)

Arguments

Details

The function checks if the specified folder exists. If 'R' folder does not exist, the function returns FALSE. If the R folder exists, the function returns TRUE.

Value

A logical value: TRUE if the 'R' folder exists, FALSE otherwise.

Check for Vignette Folder and .Rmd Files in a .tar File

Description

This function checks if a given .tar file contains a 'vignettes' folder and if there is at least one .Rmd file within that folder. If both 'vignettes' and 'inst/doc' folders exist, the function will return FALSE.

Usage

contains_vignette_folder(tar_file)

Arguments

Details

The function checks if the specified file exists and has a valid .tar extension using utils::untar. If the file is empty or any error occurs during the extraction, the function stops and returns an error message. If both 'vignettes' and 'inst/doc' folders exist, the function returns FALSE. If the 'vignettes' folder exists and contains at least one .Rmd file, the function returns TRUE. Otherwise, it returns FALSE.

Value

A logical value: TRUE if the 'vignettes' folder exists and contains at least one .Rmd file, and neither 'vignettes' nor 'inst/doc' folders are present, FALSE otherwise.

Examples

## Not run: 
  tar_file <- system.file("test-data", "here-1.0.1.tar.gz", 
   package = "risk.assessr")
  result <- contains_vignette_folder(tar_file)
  print(result)

## End(Not run)

Convert Abbreviated Numbers to Integers

Description

Converts a string containing a number with optional 'K' or 'M' abbreviation into an integer.

Usage

convert_abbreviation_to_number(value)

Arguments

Value

An integer representation of the numeric value.

Create empty results

Description

This creates an empty results list for all risk metrics

Usage

create_empty_results(pkg_name, pkg_ver, pkg_source_path, metadata)

Arguments

Value

- list with empty risk profile values

create empty tm

Description

create empty tm

Usage

create_empty_tm(pkg_name)

Arguments

Value

empty_tm - list with no tm

Generate file coverage df

Description

Generates file coverage df when errors list created.

Usage

create_file_coverage_df(file_names, file_coverage, errors, notes)

Arguments

Create items matched

Description

create a df with functions that match exported functions from a suggested package

Usage

create_items_matched(extracted_functions, suggested_exp_func)

Arguments

Create risk profile

Description

This creates a risk profile for all risk metrics

Usage

create_risk_profile()

Value

- list with risk profile values

Create a Traceability Matrix

Description

Returns a table that links all exported functions and their aliases to their documentation ('man' files), the R scripts containing them, and the test scripts that reference them.

Usage

create_traceability_matrix(
  pkg_name,
  pkg_source_path,
  func_covr,
  verbose = FALSE
)

Arguments

Value

a tibble with traceability matrix

Create weights profile

Description

This creates a specific weights profile for all risk metrics

Usage

create_weights_profile()

Value

- numeric vector with weights profile

Examples

create_weights_profile()

Run all relevant documentation riskmetric checks

Description

Run all relevant documentation riskmetric checks

Usage

doc_riskmetric(pkg_name, pkg_ver, pkg_source_path)

Arguments

Value

raw riskmetric outputs

Extract aria-label from SVG data

Description

Extracts the aria-label attribute value from SVG data badge.

Usage

extract_aria_label(svg_data)

Arguments

Value

A character string containing the extracted aria-label value, or NULL if not found.

function to extract ggproto methods

Description

function to get all the methods of a ggproto function

Usage

extract_ggproto_methods(obj)

Arguments

Extract package name from package source path

Description

Extract package name from package source path

Usage

extract_package_name(pkg_source_path)

Arguments

Value

package_name

Extract Package Version from File Path

Description

This function extracts the version number from a package source file name based on the package name and expected file pattern.

Usage

extract_version(path, package_name)

Arguments

Value

A character string representing the extracted version number, or 'NULL' if no match is found.

Examples

## Not run: 
link <- "https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicRanges_1.42.0.tar.gz"
extract_version(link, "GenomicRanges")

## End(Not run)

Fetch Bioconductor Package Information

Description

This function retrieves information about a specific Bioconductor package for a given Bioconductor version. It fetches the package details, such as version, source package URL, and archived versions if available.

Usage

fetch_bioconductor_package_info(bioconductor_version, package_name)

Arguments

Value

A list containing package details, including the latest version, package URL, source package link, and any archived versions if available. Returns 'FALSE' if the package does not exist or cannot be retrieved.

Examples

## Not run: 
fetch_bioconductor_package_info("3.14", "GenomicRanges")


## End(Not run)

Fetch Bioconductor Release Announcements

Description

This function retrieves the Bioconductor release announcements page and returns its HTML content for further processing.

Usage

fetch_bioconductor_releases()

Value

An XML document from bioconductor version page.

Examples

## Not run: 
html_content <- fetch_bioconductor_releases()

## End(Not run)

Remove specific symbols from vector of functions

Description

adapted from mpn.scorecard

adapted from mpn.scorecard

Usage

filter_symbol_functions(funcs)

filter_symbol_functions(funcs)

Arguments

find reverse dependencies

Description

find reverse dependencies

Usage

find_reverse_dependencies(path)

Arguments

function to check value of ggproto

Description

function to check if first argument inherits from any of the classes specified

Usage

function_is_ggproto(x)

Arguments

Generate Coverage Section

Description

Generates the Coverage section for the HTML report.

Usage

generate_coverage_section(assessment_results)

Arguments

Generate Dependencies Section

Description

Generates the dependencies section for the HTML report.

Usage

generate_deps_section(assessment_results)

Arguments

Generate Doc Metrics Section

Description

Generates the documentation section for the HTML report.

Usage

generate_doc_metrics_section(assessment_results)

Arguments

Generate HTML Report for Package Assessment

Description

Generates an HTML report for the package assessment results using rmarkdown.

Usage

generate_html_report(assessment_results, output_dir)

Arguments

Value

Path to the generated HTML report.

Examples

## Not run: 
assessment_results <- risk_assess_pkg()
generate_html_report(assessment_results, output_dir = "path/to/save/report")

## End(Not run)

Generate RCMD Check Metrics Section

Description

Generates the RCMD Check Metrics HTML table for the HTML report.

Usage

generate_rcmd_check_section(assessment_results)

Arguments

Generate Reverse Dependencies Section

Description

Generates the reverse dependencies section for the HTML report.

Usage

generate_rev_deps_section(assessment_results)

Arguments

Generate Risk Details

Description

Generates the Risk Details table for the HTML report.

Usage

generate_risk_details(assessment_results)

Arguments

Generate Risk Summary

Description

Generates the Risk Summary table for the HTML report.

Usage

generate_risk_summary(assessment_results)

Arguments

Generate Trace Matrix Section

Description

Generates the Trace Matrix section for the HTML report.

Usage

generate_trace_matrix_section(assessment_results)

Arguments

Retrieve Bioconductor Package URL

Description

This function fetches the source package URL for a given Bioconductor package. If no version is specified, it retrieves the latest available version. Currently, this function is not able to fetch archived package version for a bioconductor version

Usage

get_bioconductor_package_url(
  package_name,
  package_version = NULL,
  release_data
)

Arguments

Value

A list containing the following elements:

Examples

## Not run: 
release_data <- list(
  list(release = "3.12"),
  list(release = "3.13"),
  list(release = "3.14")
)

get_bioconductor_package_url("GenomicRanges", release_data = release_data)




## End(Not run)

Get CRAN Package URL

Description

This function constructs the CRAN package URL for a specified package and version.

Usage

get_cran_package_url(package_name, version, last_version, all_versions)

Arguments

Value

A character string containing the URL to download the package tarball, or 'NULL' if the version is not found in the list of available versions.

Examples

url_result <- get_cran_package_url("dplyr", NULL, "1.0.10", c("1.0.0", "1.0.10"))

list all package exports

Description

adapted from mpn.scorecard

adapted from mpn.scorecard

Usage

get_exports(pkg_source_path)

get_exports(pkg_source_path)

Arguments

Value

data.frame, with one column 'exported_function', that can be passed to all downstream map_* helpers

data.frame, with one column 'exported_function', that can be passed to all downstream map_* helpers

Get function descriptions

Description

get descriptions of exported functions

Usage

get_func_descriptions(pkg_name)

Arguments

Fetch GitHub Repository Data

Description

This function retrieves metadata about a GitHub repository, including creation date, stars, forks, and the number of recent commits within the last 30 days.

Usage

get_github_data(owner, repo)

Arguments

Details

If the 'owner' parameter is 'NA' or empty, the function returns an empty response object. Repository data is fetched using the GitHub API via the 'gh' package.

Value

A list containing: - 'created_at': Creation date of the repository. - 'stars': Number of stars the repository - 'forks': Number of forks of the repository. - 'date': acquisition date in the format "YYYY-MM-DD". - 'recent_commits_count': count of commits in the last 30 days (from acquisition date).

Examples

## Not run: 
# Fetch data for the "ggplot2" repository owned by "tidyverse"
result <- get_github_data("tidyverse", "ggplot2")
print(result)

## End(Not run)

Extract and Validate Package Hosting Information

Description

This function retrieves hosting links for an R package from various sources such as GitHub, CRAN, internal repositories, or Bioconductor.

Usage

get_host_package(pkg_name, pkg_version, pkg_source_path)

Arguments

Details

The function extracts hosting links by: 1. Parsing the 'DESCRIPTION' file for GitHub and BugReports URLs. 2. Checking if the package is valid on CRAN and others host repository

If no links are found in the 'DESCRIPTION' file, returns 'NULL'

Value

A list containing the following elements:

- 'github_links': GitHub links related to the package. - 'cran_links': CRAN links - 'internal_links': internal repository links. - 'bioconductor_links': Bioconductor links

If links are found, return empty or NULL.

Get Internal Package URL

Description

This function retrieves the URL of an internal package on your internal Mirror, its latest version, and a list of all available versions.

Usage

get_internal_package_url(
  package_name,
  version = NULL,
  base_url = "http://cran.us.r-project.org",
  internal_path = "/src/contrib/"
)

Arguments

Value

A list containing: - 'url': A character string of the package URL (or 'NULL' if not found). - 'last_version': A character string of the latest version of the package. - 'all_versions': A character vector of all available package versions.

Examples

## Not run: 

# Retrieve a specific version URL of a package
result <- get_internal_package_url("internalpackage", version = "1.0.1")
print(result) 

## End(Not run)

Get CRAN Package Download Count

Description

Retrieves the download count for a given CRAN package from the CRAN logs API.

Usage

get_package_download(package_name, timeline = "grand-total")

Arguments

Value

An integer representing the total number of downloads.

Examples

## Not run: 
total_download_result <- get_package_download('ggplot2')

month_download_result <- get_package_download('dplyr', 'last-month')

## End(Not run)

Assess Authors

Description

Assess Authors

Usage

get_pkg_author(pkg_name, pkg_source_path)

Arguments

Value

- Authors related variable

check for package creator

Description

check for package creator

Usage

get_pkg_creator_info(pkg_name, pkg_source_path)

Arguments

Value

- logical - package creator exists - 'FALSE'

Read Description file and parse the package name and version

Description

Read Description file and parse the package name and version

Usage

get_pkg_desc(pkg_source_path, fields = NULL)

Arguments

Value

list with package description

Assess License

Description

Assess License

Usage

get_pkg_license(pkg_name, pkg_source_path)

Arguments

Value

- Authors related variable

get package name for display

Description

get package name for display

Usage

get_pkg_name(input_string)

Arguments

Value

pkg_disp - package name for display

Examples

pkg_source_path <- "/home/user/R/test.package.0001_0.1.0.tar.gz"
pkg_disp_1 <- get_pkg_name(pkg_source_path)
print(pkg_disp_1)

pkg <- "TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz"
pkg_disp_2 <- get_pkg_name(pkg)
print(pkg_disp_2)

get regular function bodies

Description

create a tibble with regular function bodies

Usage

get_regular_function_body(pkg_name, func_name)

Arguments

Extract GitHub repository owner from links

Description

Given a vector of GitHub links and a package name, this function finds the link corresponding to the package and extracts the GitHub repository owner.

Usage

get_repo_owner(links, pkg_name)

Arguments

Value

A string containing the GitHub repository owner, or NA if not found.

Assign output file path for various outputs during scorecard rendering

Description

Assign output file path for various outputs during scorecard rendering

Usage

get_result_path(
  out_dir,
  ext = c("check.rds", "covr.rds", "tm_doc.rds", "tm_doc.xlsx")
)

Arguments

Details

The basename of 'out_dir' should be the package name and version pasted together

Get risk metadata

Description

Get risk metadata

Usage

get_risk_metadata(executor = NULL)

Arguments

Value

list with metadata

function to get S3 method

Description

function to get S3 method from generic

Usage

get_s3_method(generic, class, package)

Arguments

Get Dependencies

Description

This function extracts the version information of imported and suggested packages for a given package from the current R session.

Usage

get_session_dependencies(deps_list)

Arguments

Value

A list with two elements:

Examples

deps_list <- data.frame(
  package = c("dplyr", "ggplot2", "testthat", "knitr"),
  type = c("Imports", "Imports", "Suggests", "Suggests")
)
get_session_dependencies(deps_list)

Function to get suggested exported functions

Description

This function gets exported functions for all packages in the Suggests section of the target package's DESCRIPTION file

Usage

get_suggested_exp_funcs(data)

Arguments

Value

- data with package names and exported functions

list all top-level objects defined in the package code

Description

adapted from mpn.scorecard

adapted from mpn.scorecard

Usage

get_toplevel_assignments(pkg_source_path)

get_toplevel_assignments(pkg_source_path)

Arguments

Details

This is primarily for getting all _functions_, but it also returns top-level declarations, regardless of type. This is intentional, because we also want to capture any global variables or anything else that could be potentially exported by the package.

This is primarily for getting all _functions_, but it also returns top-level declarations, regardless of type. This is intentional, because we also want to capture any global variables or anything else that could be potentially exported by the package.

Value

A data.frame with the columns 'function' and 'code_script' with a row for every top-level object defined in the package.

A data.frame with the columns 'function' and 'code_script' with a row for every top-level object defined in the package.

Get Package Versions

Description

This function retrieves all available versions including last version from parse_html_version function'

Usage

get_versions(table, package_name)

Arguments

Value

A list containing: - 'all_versions': A character vector of all unique package versions. - 'last_version': A character string of the latest version fetched from the RStudio Package Manager, or 'NULL' if not available.

Examples

## Not run: 
# Define the input table
table <- list(
  list(
    package_name = "here",
    package_version = "0.1",
    link = "here_0.1.tar.gz",
    date = "2017-05-28 08:13",
    size = "3.5K"
  ),
  list(
    package_name = "here",
    package_version = "1.0.0",
    link = "here_1.0.0.tar.gz",
    date = "2020-11-15 18:10",
    size = "32K"
  )
)

# Use the get_versions function
result <- get_versions(table, "here")

# Example output
print(result)

## End(Not run)

Install package locally

Description

Install package locally

Usage

install_package_local(pkg_source_path)

Arguments

Value

logical. Returns 'TRUE' if the package was successfully installed, 'FALSE' otherwise.

Examples

## Not run: 
results <- install_package_local("pkg_source_path")
print(results)

## End(Not run)

Map all Rd files to the functions they describe

Description

adapted from mpn.scorecard

Usage

map_functions_to_docs(exports_df, pkg_source_path, verbose)

Value

Returns the data.frame passed to 'exports_df', with a 'documentation' column appended. This column will contain the path to the '.Rd' files in 'man/' that document the associated exported functions.

Get all exported functions and map them to R script where they are defined

Description

adapted from mpn.scorecard

adapted from mpn.scorecard

Usage

map_functions_to_scripts(exports_df, pkg_source_path, verbose)

map_functions_to_scripts(exports_df, pkg_source_path, verbose)

Arguments

Value

A data.frame with the columns 'exported_function' and 'code_script'.

A data.frame with the columns 'exported_function' and 'code_script'.

Modify the DESCRIPTION File in a R Package Tarball

Description

This function recreate a '.tar.gz' R package file after modifying its 'DESCRIPTION' file by appending Config/build/clean-inst-doc: false parameter.

Usage

modify_description_file(tar_file)

Arguments

Value

A string containing the path to the newly created modified '.tar.gz' file.

Examples

## Not run: 
  modified_tar <- modify_description_file("path/to/mypackage.tar.gz")
  print(modified_tar)

## End(Not run)

Parse Bioconductor Release Announcements

Description

This function extracts Bioconductor release details such as version number, release date, number of software packages, and required R version from the release announcements HTML page.

Usage

parse_bioconductor_releases(html_content)

Arguments

Value

A list of lists containing Bioconductor release details: release version, date, number of software packages, and corresponding R version.

Examples

## Not run: 
html_content <- fetch_bioconductor_releases()
release_data <- parse_bioconductor_releases(html_content)


## End(Not run)

Parse DCF of description file

Description

Parse DCF of description file

Usage

parse_dcf_dependencies(path)

Arguments

Parse HTML Content for Package Versions

Description

This function extracts version information from an HTML page listing available versions of a Bioconductor package.

This function extracts version information from the HTML content of a CRAN archive page.

Usage

parse_html_version(html_content, package_name)

parse_html_version(html_content, package_name)

Arguments

Value

A list of lists containing package details such as package name, version, link, date, and size. Returns an empty list if no versions are found.

A list of lists, where each sublist contains: - 'package_name': package name. - 'package_version': package version. - 'link': link to the package tarball. - 'date': The date associated with the package version. - 'size': The size of the package tarball.

Examples

## Not run: 
parse_html_version(html_content, "GenomicRanges")

## End(Not run)

Parse Package Information from CRAN Archive

Description

This function retrieves the package archive information from the CRAN Archive.

Usage

parse_package_info(name)

Arguments

Value

A character string containing the raw HTML content of the package archive page, or 'NULL' if the request fails or the package is not found.

Examples

## Not run: 
# Fetch package archive information for "dplyr"
result <- parse_package_info("dplyr")

print(result)


## End(Not run)

function to preprocess func_full_name

Description

function to extract package, class, and generic

Usage

preprocess_func_full_name(func_full_name)

Arguments

process items matched

Description

create a df with functions that match exported functions from a suggested package

Usage

process_items_matched(items_matched, suggested_exp_func)

Arguments

Details

This function extracts all the functions from the function body and filters them to keep only function calls It also extracts all the valid function names, matches with the source package and writes a message

Re-calculate package risk scores

Description

Use this function to re-calculate risk scores and risk profile

Usage

recalc_risk_scores(riskdata_results, update_comments)

Arguments

Details

Use cases: if the weighting profile and/or risk profile thresholds have changed and the risk metrics have not changed, then use this function to re-calculate the risk scores and profile without running the whole risk assessment process again

Value

A dataframe containing both the original and newly calculated risk scores, profiles, and comments.

Helper function to remove base and recommended packages

Description

Helper function to remove base and recommended packages

Usage

remove_base_packages(df)

Arguments

Assess package - simplified

Description

simplified input to assess package for risk metrics

Usage

risk_assess_pkg(path = NULL)

Arguments

Value

list containing results - list containing metrics, covr, tm - trace matrix, and R CMD check

Examples

## Not run: 
risk_assess_package <- risk_assess_pkg()

OR

risk_assess_package <- risk_assess_pkg(path/to/package.tar.gz)

## End(Not run)

Process lock files

Description

This function processes 'renv.lock' and 'pak.lock' files to produce risk metric data

Usage

risk_assess_pkg_lock_files(input_data)

Arguments

Value

assessment_results - nested list containing risk metric data

Examples

## Not run: 
  input_data <- ("path/to/mypak.lock")
  pak_results <- risk_assess_pkg_lock_files(input_data) 
  print(pak_results)
 
## End(Not run) 

Run covr and potentially save results to disk

Description

Run covr and potentially save results to disk

Usage

run_coverage(pkg_source_path, timeout = Inf)

Arguments

Value

list with total coverage and function coverage

Run covr in subprocess with timeout

Description

Run covr in subprocess with timeout

Usage

run_covr(path, timeout)

Arguments

Run R CMD CHECK

Description

Run R CMD CHECK

Usage

run_rcmdcheck(pkg_source_path, rcmdcheck_args)

Arguments

Details

rcmdcheck takes either a tarball or an installation directory.

The basename of 'pkg_source_path' should be the package name and version pasted together

The returned score is calculated via a weighted sum of notes (0.10), warnings (0.25), and errors (1.0). It has a maximum score of 1 (indicating no errors, notes or warnings) and a minimum score of 0 (equal to 1 error, 4 warnings, or 10 notes). This scoring methodology is taken directly from [riskmetric::metric_score.pkg_metric_r_cmd_check()].

Score a package for dependencies

Description

Calculates a regularized score based on the number of dependencies a package has. Convert the number of dependencies NROW(x) into a validation score [0,1]

1 / (1 + exp(-0.5 * (NROW(x) + 19)))

Usage

score_dependencies(x)

Arguments

Details

removed - 1 from the formula e.g.

1 - 1 / (1 + exp(NROW(x)- 19))

to reverse the return value e.g. 0 - low; 1 - high

The scoring function is the classic logistic curve

/ (1 + exp(-k(x-x[0]))

x = NROW(x), sigmoid midpoint is 20 reverse dependencies, ie. x[0] = 19, and logistic growth rate of k = 0.5.

1 / (1 + exp(NROW(x)- 19))

Value

numeric value between 0 (low number of dependencies) and 1 (high number of dependencies)

Scoring method for number of reverse dependencies a package has

Description

Score a package for the number of reverse dependencies it has; regularized Convert the number of reverse dependencies length(x) into a validation score [0,1]

1 / (1 + exp(-0.5 * (sqrt(length(x)) + sqrt(20))))

Usage

score_reverse_dependencies(x)

Arguments

Details

The scoring function is the classic logistic curve

1 / (1 + exp(-k(x-x[0]))

with a square root scale for the number of reverse dependencies x = sqrt(length(x)), sigmoid midpoint is 20 reverse dependencies, ie. x[0] = sqrt(15), and logistic growth rate of k = 0.5.

1 / (1 + -0.5 * exp(sqrt(length(x)) - sqrt(20)))

Value

numeric value between 1 (high number of reverse dependencies) and 0 (low number of reverse dependencies)

Creates information on package installation

Description

Creates information on package installation

Usage

set_up_pkg(dp, check_type = "1")

Arguments

Value

list with local package install

Examples

## Not run: 
set_up_pkg(path/to/package, "mypackage")

## End(Not run)

set up rcmdcheck arguments

Description

This sets up rcmdcheck arguments

Usage

setup_rcmdcheck_args(check_type = "1", build_vignettes)

Arguments

Details

Some packages need to have build vignettes as a build argument as their vignettes structure is inst/doc or inst/docs

Value

- list with rcmdcheck arguments

Check weights values and standardize them.

Description

Check weights values and standardize them.

Usage

standardize_risk_weights(data, weights)

Arguments

Untar package and return installation directory

Description

Untar package and return installation directory

Usage

unpack_tarball(pkg_tar, temp_file_name = "temp_file_")

Arguments

update pscore results

Description

This updates results list for pscore risk metrics

Usage

update_pscore_results(results, pscore)

Arguments

Value

- list with updated risk result values

update results doc_metrics

Description

This updates results list for documentation risk metrics

Usage

update_results_doc_scores(results, doc_scores)

Arguments

Value

- list with updated risk result values