Package 'risk.assessr'

Title: Assessing Package Risk Metrics
Description: A reliable and validated tool that captures detailed risk metrics such as R 'CMD' check, test coverage, traceability matrix, documentation, dependencies, reverse dependencies, suggested dependency analysis, repository data, and enhanced reporting for R packages that are local or stored on remote repositories such as GitHub, CRAN, and Bioconductor.
Authors: Edward Gillian [cre, aut] (ORCID: <https://orcid.org/0000-0003-2732-5107>), Hugo Bottois [aut] (ORCID: <https://orcid.org/0000-0003-4674-0875>), Paulin Charliquart [aut], Andre Couturier [aut], Sanofi [cph, fnd]
Maintainer: Edward Gillian <[email protected]>
License: GPL (>= 2)
Version: 4.1.0
Built: 2026-06-11 18:26:26 UTC
Source: https://github.com/cran/risk.assessr

Help Index

Assess an R package by name (deprecated)

Description

Use [risk_assess_pkg()] with 'package' instead.

Usage

assess_pkg_r_package(package_name, version = NA, repos = getOption("repos"))

Arguments

package_name

Package name.
version

Package version. Default 'NA' uses latest.
repos

Repository URLs. Default 'getOption("repos")'.

Value

Assessment results or 'NULL'.

Calculate Average Time to Close GitHub Issues

Description

This function uses the GitHub API to retrieve closed issues from a repository and calculates the average time (in hours) it took to close them, excluding pull requests.

Usage

average_issue_close_time(
  owner,
  repo,
  max_pages = 10,
  per_page = 100,
  headers = c(Accept = "application/vnd.github.v3+json")
)

Arguments

owner

Character. GitHub organization or username.
repo

Character. Repository name.
max_pages

Integer. Maximum number of API result pages to query. Each page can contain up to 'per_page' issues. Default is 10.
per_page

Integer. Number of issues to request per page (max 100). Default is 100.
headers

Named character vector of HTTP headers to send with the API request. Default sets GitHub API version.

Value

Numeric. Average time in hours to close issues, or 'NA' if no closed issues were found.

Examples

## Not run: 
average_issue_close_time("tidyverse", "ggplot2")

## End(Not run)

Find Bioconductor Package Reverse Dependencies

Description

This function returns the reverse dependencies for a given Bioconductor package.

Usage

bioconductor_reverse_deps(
  pkg,
  which = "Imports",
  only.bioc = FALSE,
  version = BiocManager::version(),
  db = NULL,
  biocdb = NULL
)

Arguments

pkg

Character string. The name of the package for which to find reverse dependencies.
which

Character vector. The dependency categories to check. One or more of "Depends", "Imports", "LinkingTo", "Suggests", or "Enhances". Defaults to "Imports".
only.bioc

Logical. If TRUE (default), only reverse dependencies that are Bioconductor packages are returned.
version

Bioconductor version to use. Defaults to the current version.
db

Optional. A pre-loaded package database to use for lookups.
biocdb

Optional. A pre-loaded Bioconductor package database.

Value

A named list of reverse dependency package names.

Examples

## Not run: 
# Get reverse Imports dependencies as a list:
bioconductor_reverse_deps("limma")

# Get multiple categories:
bioconductor_reverse_deps("limma", which = c("Depends", "Suggests"))

## End(Not run)

Build a Dependency Tree for an R Package

Description

This function constructs a nested list representing the dependency tree of a specified R package. The recursion stops at the specified maximum depth level (default: 3) or until a base package is reached.

Usage

build_dependency_tree(
  package_name,
  level = 1,
  get_license = FALSE,
  max_level = 3
)

Arguments

package_name

A character string specifying the name of the package.
level

An integer indicating the current recursion depth (default: 1).
get_license

A logical value indicating whether to extract and include license information from DESCRIPTION files (default: 'FALSE').
max_level

An integer specifying the maximum depth level for dependency recursion (default: 3). Set to a higher value to explore deeper dependency layers.

Value

A nested list representing the dependency tree, where base packages are marked as "base". If 'get_license' is 'TRUE', each package entry in the tree includes a 'license' field containing that specific package's license (extracted from its DESCRIPTION file). Each package's license is independent - the license of a parent package does not imply the licenses of its dependencies.

Examples

## Not run: 
build_dependency_tree("ggplot2")
build_dependency_tree("ggplot2", get_license = TRUE)
build_dependency_tree("ggplot2", max_level = 5)  # Deeper dependency exploration

## 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

package_name

A character string specifying the name of the package to check and fetch.
package_version

An optional character string specifying the version of the package to fetch. Defaults to 'NULL'.

Value

A list with one of the following structures:

package_url

Character string; the URL to download the package tarball.

last_version

A named list with version and date for the latest available version.

version

Character string; the requested version (or NULL if not specified).

all_versions

A list of named lists, each with version and date, representing all available versions.

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

package_name

A character string specifying the name of the package to check.

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)

Count Commits in the Last Months

Description

Counts the total number of commits from the last 'months' months using a data frame with weekly commit data (column 'week_start').

Usage

count_commits_last_months(df, months = 1, today = Sys.Date())

Arguments

df

A data frame with 'week_start' (Date) and 'n_commits' (int) columns.
months

Integer. Number of months to look back (default is 1).
today

today's date.default is Sys.Date()

Value

Integer. Total number of commits in the time window.

Examples

## Not run: 
df <- get_commits_since("tidyverse", "ggplot2", years = 1)
count_commits_last_months(df, months = 3)

## End(Not run)

Retrieve the List of CRAN Packages (Internal)

Description

Downloads and caches the current list of packages available on CRAN.

Usage

cran_packages(cache = TRUE)

Arguments

cache

Logical. If TRUE (default), the result is cached using memoise::memoise() with a timeout of 30 minutes to avoid repeated downloads. If FALSE, the metadata is fetched directly from CRAN each time the function is called.

Details

The function downloads the packages.rds file from the CRAN website, which contains metadata about all available packages. The result is cached using memoise::memoise() with a timeout of 30 minutes.

Value

A matrix of package metadata similar to the output of utils::available.packages(), with package names as row names.

Examples

## Not run: 
# Downloads packages.rds from CRAN (needs network).
pkgs <- cran_packages()
head(rownames(pkgs))

## End(Not run)

Find Reverse Dependencies of a CRAN Package

Description

This function finds the reverse dependencies of a CRAN package, i.e., packages that depend on the specified package.

Usage

cran_revdep(
  pkg,
  dependencies = c("Depends", "Imports", "Suggests", "LinkingTo"),
  recursive = FALSE,
  ignore = NULL,
  installed = NULL
)

Arguments

pkg

A character string representing the name of the package.
dependencies

A character vector specifying the types of dependencies to consider. Default is c("Depends", "Imports", "Suggests", "LinkingTo").
recursive

A logical value indicating whether to find dependencies recursively. Default is FALSE.
ignore

A character vector of package names to ignore. Default is NULL.
installed

A matrix of installed packages.

Value

deps - A sorted character vector of package names that depend on the specified package.

Examples

## Not run: 
cran_revdep("ggplot2")

## End(Not run)

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 = NULL,
  verbose = FALSE,
  execute_coverage = TRUE
)

Arguments

pkg_name

name of package
pkg_source_path

path to a source package
func_covr

function coverage
verbose

Logical ('TRUE'/'FALSE'). If 'TRUE', show any warnings/messages per function.
execute_coverage

Logical ('TRUE'/'FALSE'). If 'TRUE', execute test coverage.

Value

a nested list with fine grained traceability matrices

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)

dp <- system.file("test-data", "here-1.0.1.tar.gz", 
   package = "risk.assessr")

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

# 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)

# Get package name and version
pkg_desc <- get_pkg_desc(pkg_source_path, 
                         fields = c("Package", 
                                    "Version"))
pkg_name <- pkg_desc$Package
package_installed <- TRUE
covr_list <- test.assessr::get_package_coverage(
  pkg_source_path,
  package_installed
)
# run without test coverage   
tm_list_no_covr <- create_traceability_matrix(pkg_name, 
                                      pkg_source_path,
                                      execute_coverage = FALSE)   
                                      
# run with test coverage                                         
tm_list_covr <- create_traceability_matrix(pkg_name, 
                                      pkg_source_path,
                                      covr_list$res_cov)
                                      
# run with test coverage parameter but no test coverage list                                        
tm_list_no_covr_list <- create_traceability_matrix(pkg_name, 
                                      pkg_source_path)   
                                         
options(old)

## End(Not run)

Determine Packages that Depend on Given Packages

Description

This function identifies packages that depend on the specified packages, considering various types of dependencies (e.g., strong, most, all).

Usage

dependsOnPkgs(
  pkgs,
  dependencies = "most",
  recursive = TRUE,
  lib.loc = NULL,
  installed = NULL
)

Arguments

pkgs

A character vector of package names to check dependencies for.
dependencies

A character string specifying the types of dependencies to consider. Can be "strong", "most", "all", or a custom vector of dependency types.
recursive

A logical value indicating whether to recursively check dependencies.
lib.loc

A character vector of library locations to search for installed packages.
installed

A matrix of installed packages, obtained from cran_packages function. .

Value

A character vector of package names that depend on the specified packages.

Examples

## Not run: 
installed <- cran_packages()
dependsOnPkgs("here", installed = installed)

## End(Not run)

Detect Version Conflicts from dependency tree

Description

This function identifies duplicate version packages and reports conflicts.

Usage

detect_version_conflicts(pkg_list)

Arguments

pkg_list

A nested list structure from fetch_all_dependencies function

Value

A list of strings describing package version conflicts such as "Conflict in package cli: versions found - 3.6.2, 3.6.1" 'NULL' if no conflicts are found.

Examples

pkg_list <- list(
  ggplot2 = list(
    version = "3.5.1",
    cli = list(version = "3.6.2"),
    gtable = list(
      version = "0.3.4",
      cli = list(version = "3.6.1")
    )
  )
)
detect_version_conflicts(pkg_list)

Download and Parse Dependencies of an R Package

Description

Downloads a package from a repository, extracts it, and parses dependencies from the DESCRIPTION file.

Usage

download_and_parse_dependencies(
  package_name,
  version = NA,
  get_license = FALSE
)

Arguments

package_name

Name of the package to download.
version

Package version to download (default: 'NA' for latest).
get_license

Whether to extract license information (default: 'FALSE').

Details

The 'license' field refers only to the package specified by 'package_name', not its dependencies. Use 'build_dependency_tree()' or 'fetch_all_dependencies()' with 'get_license = TRUE' for full license information.

Value

When 'get_license = FALSE', a data frame with columns 'package', 'type', and 'parent_package'. When 'get_license = TRUE', a list with: - 'dependencies': Data frame of direct dependencies. - 'license': License of the specified package only (not dependencies). Returns 'NA' if not found.

Examples

## Not run: 
download_and_parse_dependencies("dplyr")
download_and_parse_dependencies("dplyr", get_license = TRUE)

## End(Not run)

Extract the Installed Version of a Package

Description

This function retrieves the installed version of a specified R package. If the package is not installed, returns 'NA'.

Usage

extract_package_version(package_name)

Arguments

package_name

A character string specifying the name of the package.

Value

A character string representing the installed package version, or 'NA' if the package is not found.

Examples

## Not run: 
extract_package_version("dplyr")
# 1.1.4

## End(Not run)

Extract risk thresholds by id

Description

Extract risk thresholds by id

Usage

extract_thresholds_by_id(risk_rule, id_value)

Arguments

risk_rule

- list containing all risk rules
id_value

- character vector containing risk rule choice

Value

list containing specific risk rules

Extract risk thresholds by key

Description

Extract risk thresholds by key

Usage

extract_thresholds_by_key(risk_rule, key_value)

Arguments

risk_rule

- list containing all risk rules
key_value

- character vector containing risk rule choice

Value

list containing specific risk rules

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

path

A character string specifying the file path or URL.
package_name

A character string specifying the name of the package.

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 All Dependencies for a Package

Description

This function builds and retrieves the full dependency tree for a given R package.

Usage

fetch_all_dependencies(package_name, get_license = FALSE, max_level = 3)

Arguments

package_name

A character string specifying the name of the package.
get_license

A logical value indicating whether to extract and include license information from DESCRIPTION files (default: 'FALSE').
max_level

An integer specifying the maximum depth level for dependency recursion (default: 3). Set to a higher value to explore deeper dependency layers.

Value

A nested list representing the dependency tree of the package. If 'get_license' is 'TRUE', each package in the tree (including the root package and all dependencies) will have a ‘license' field containing that package’s license extracted from its DESCRIPTION file.

Examples

## Not run: 
fetch_all_dependencies("ggplot2")
fetch_all_dependencies("ggplot2", get_license = TRUE)
fetch_all_dependencies("ggplot2", max_level = 5)  # Deeper dependency exploration

## 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

bioconductor_version

A character string specifying the Bioconductor version (e.g., "3.14").
package_name

A character string specifying the name of the package.

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: 
info <- fetch_bioconductor_package_info("3.14", "GenomicRanges")
print(info)

## 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)

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 = NULL)

Arguments

assessment_results

List containing the results from risk_assess_pkg function.
output_dir

Character string indicating the directory where the report will be saved.

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)

Assess an R Package traceability matrix from package name and version

Description

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

Usage

generate_traceability_matrix(
  package_name,
  version = NA,
  repos = getOption("repos"),
  execute_coverage = FALSE
)

Arguments

package_name

A character string specifying the name of the package to assess.
version

A character string specifying the version of the package to assess. Default is 'NA', which assesses the latest version.
repos

A character string specifying the repo directly. Default is getOption("repos")
execute_coverage

Logical ('TRUE'/'FALSE'). If 'TRUE', execute test coverage.

Value

The function returns package traceability_matrix If the package cannot be downloaded or installed, an error message is returned.

Examples

## Not run: 

results_no_test_covr <- generate_traceability_matrix(
 "here", 
 version = "1.0.1", 
 execute_coverage = FALSE
)

results_test_covr <- generate_traceability_matrix(
 "here", 
 version = "1.0.1", 
 execute_coverage = TRUE
)


print(results_no_test_covr)

print(results_test_covr)

## End(Not run)

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.

Usage

get_bioconductor_package_url(
  package_name,
  package_version = NULL,
  release_data
)

Arguments

package_name

A character string specifying the name of the Bioconductor package.
package_version

(Optional) A character string specifying the package version. Defaults to 'NULL', which retrieves the latest version.
release_data

A list containing Bioconductor release information.

Value

A list containing:

url

The URL of the source package (if available).
version

The specified or latest available package version.
last_version

A list with version, date, and Bioconductor version.
all_versions

A list of all discovered versions with version, date, and Bioconductor version.
bioconductor_version_package

The Bioconductor version matched to the selected version.
archived

A logical value indicating whether the package is archived.

Examples

## Not run: 
release_data <- list(
  list(release = "3.17", date = "October 14, 2005"),
  list(release = "3.18", date = "October 4, 2006"),
  list(release = "3.19", date = "October 8, 2007")
)

get_bioconductor_package_url("GenomicRanges", release_data = release_data)


## End(Not run)

Retrieve GitHub Commits as Weekly Counts (using curl)

Description

This function fetches all commits from a specified GitHub repository using the GitHub API and returns a data frame with weekly commit counts.

Usage

get_commits_since(owner, repo, years = 1)

Arguments

owner

Character. The GitHub username or organization that owns the repository.
repo

Character. The name of the GitHub repository.
years

Numeric. Number of years to look back from today's date (default is 1).

Value

A data frame with four columns:

week_start

Start date of the week (class Date).

year

Year of the commits.

month

Month of the commits.

n_commits

Number of commits during the week.

Examples

## Not run: 
# Get commit counts for the past year
get_commits_since(owner = "tidyverse", repo = "ggplot2")

## 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

package_name

A character string specifying the name of the package.
version

An optional character string specifying the version of the package. If 'NULL', the latest version is assumed.
last_version

A named list with elements version and date, representing the latest available version and its publication date.
all_versions

A list of named lists, each with elements version and date, representing all known versions of the package and their publication dates.

Value

A character string containing the URL to download the package tarball, or "No valid URL found" if the version is not found in the list of available versions.

Examples

## Not run: 
# Example data structure
last_version <- list(version = "1.0.10", date = "2024-01-01")
all_versions <- list(
  list(version = "1.0.0", date = "2023-01-01"),
  list(version = "1.0.10", date = "2024-01-01")
)

# Get the URL for the latest version of "dplyr"
url <- get_cran_package_url("dplyr", NULL, last_version, all_versions)
print(url)

## End(Not run)

Get CRAN Total or Recent Downloads for a Package

Description

Retrieves either all-time total downloads or the total from the last 'n' full months for a given CRAN package.

Usage

get_cran_total_downloads(pkg, months = NULL)

Arguments

pkg

Character string, the name of the CRAN package.
months

Integer. If NULL, returns all-time total; otherwise, returns total from the last 'months' full months (excluding current).

Details

Similar data can be obtained via:

https://cranlogs.r-pkg.org/badges/grand-total/ggplot2 https://cranlogs.r-pkg.org/badges/last-month/ggplot2

Value

An integer: total number of downloads.

Examples

## Not run: 
  get_cran_total_downloads("ggplot2")        # all-time total
  # 160776616

  get_cran_total_downloads("ggplot2", 3)     # last 3 full months
  # 4741707

  get_cran_total_downloads("ggplot2", 12)    # last 12 full months
  # 19878885

## End(Not run)

list all package exports

Description

list all package exports

Usage

get_exports(pkg_source_path)

Arguments

pkg_source_path

a file path pointing to an unpacked/untarred package directory

Value

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

Examples

## Not run: 
tmpdir <- tempdir()

# Locate the package source tarball bundled with risk.assessr
dp <- system.file("test-data", "test.package.0001_0.1.0.tar.gz",
                  package = "risk.assessr")

# Extract the source package into the temporary directory
utils::untar(dp, exdir = tmpdir)

# Find the extracted package directory (it should contain DESCRIPTION)
pkg_dirs <- list.dirs(tmpdir, full.names = TRUE, recursive = FALSE)
desc_dir <- pkg_dirs[file.exists(file.path(pkg_dirs, "DESCRIPTION"))]
stopifnot(length(desc_dir) == 1L)
pkg_source_path <- desc_dir

# Now operate on the *source* (no installation)
exports_df <- get_exports(pkg_source_path)

# Optional: inspect result (kept simple for examples)
head(exports_df)

# Clean up the extracted sources
unlink(pkg_source_path, recursive = TRUE, force = TRUE)

## End(Not run)

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

owner

A character string specifying the owner of the repository.
repo

A character string specifying the name of the repository.

A GitHub Personal Access Token (PAT) will be needed for some requests or to help with the rate limit. Use Sys.setenv(GITHUB_TOKEN = "personal_access_token") or store your token in a .Renviron file. The token is passed via the 'Authorization' header only if 'Sys.getenv("GITHUB_TOKEN")' is non-empty.

Details

Repository data is fetched using the GitHub API via 'curl' and 'jsonlite'.

Value

A list containing: - 'created_at': Creation date of the repository. - 'stars': Number of stars. - 'forks': Number of forks. - 'date': Acquisition date (YYYY-MM-DD). - 'recent_commits_count': Number of commits in the last 30 days. - 'open_issues': Number of open issues.

Examples

## Not run: 
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

pkg_name

Character. The name of the package.
pkg_version

Character. The version of the package.
pkg_source_path

Character. The file path to the package source directory containing the DESCRIPTION file.

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.

Examples

## Not run: 
result <- get_host_package(pkg_name, pkg_version, pkg_source_path)
print(result)

## End(Not run)

Get Internal Package URL

Description

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

Usage

get_internal_package_url(package_name, version = NULL, base_url = NULL)

Arguments

package_name

A character string specifying the name of the package.
version

An optional character string specifying the version of the package. Defaults to 'NULL', in which case the latest version will be used.
base_url

A character string specifying the base URL of the internal package manager.

Value

A list containing: - 'url': A character string of the package URL (or 'NULL' if not found). - 'last_version': A list with 'version' and 'date' of the latest version (or 'NULL'). - 'version': The version used to generate the URL (or 'NULL'). - 'all_versions': A list of all available versions, each as a list with 'version' and 'date'.

Examples

## Not run: 
result <- get_internal_package_url("internalpackage", version = "1.0.1")
print(result)

## End(Not run)

Get Bioconductor Package Download Statistics

Description

Downloads and processes monthly download statistics for a Bioconductor package from the Bioconductor package statistics archive. Returns the full history, the total downloads over the last 6 full months (current month excluded), and the all-time total downloads.

Usage

get_package_download_bioconductor(pkg)

Arguments

pkg

Character string. The name of a Bioconductor package (e.g. "GenomicRanges").

Value

A list with three elements:

all_data

A data.frame of the full cleaned dataset with dates and cumulative counts.

total_6_months

Total downloads in the last 6 complete months.

total_download

Total all-time downloads.

Examples

## Not run: 
  result <- get_package_download_bioconductor("bioconductorpackage")
  print(result$total_6_months)
  head(result$all_data)
  
#$all_data
#Date Year Month Nb_of_distinct_IPs Nb_of_downloads Cumulative_downloads
#1   2009-01-01 2009   Jan               3341            7053                 7053
#2   2009-02-01 2009   Feb               3229            6681                13734
#3   2009-03-01 2009   Mar               3753            8021                21755
  
  #$total_6_months
  #[1] 547560
  
  #$total_download
  #[1] 7318550

## End(Not run)

Get CRAN Daily Downloads for a Package

Description

Retrieves daily CRAN download counts over the past years for a given package, including cumulative downloads.

Usage

get_package_download_cran(pkg, years = 1)

Arguments

pkg

Character string, name of the CRAN package.
years

integer, number of past years (default 1) for historical

Value

A data frame with columns: date, count, and cumulative_downloads.

Examples

## Not run: 
  get_package_download_cran("ggplot2")
  # Example output:
  #          date  count cumulative_downloads
  # 1 2025-04-22  78379           20073615
  # 2 2025-04-21  63195           19995236
  # 3 2025-04-20  42119           19932041
  # 4 2025-04-19  40848           19889922
  # 5 2025-04-18  54914           19849074
  # 6 2025-04-17  86273           19794160
  # 7 2025-04-16  80201           19707887

## End(Not run)

Download R Package Source Tarball

Description

Downloads the source tarball (.tar.gz) for a specified R package from CRAN, Bioconductor, or an internal repository fallback.

Usage

get_package_tarfile(package_name, version = NULL, repos = getOption("repos"))

Arguments

package_name

Character string specifying the name of the package to download.
version

Optional character string specifying the version of the package. If NULL (default), the latest available version will be downloaded.
repos

Optional character vector of repository URLs to use. If NULL (default), the current repositories set in options() will be used.

Value

Character string with the path to the downloaded tarball file, or NULL if the download was unsuccessful.

Examples

## Not run: 
# Download the latest version of dplyr
tarball_path <- get_package_tarfile("dplyr")

# Download a specific version
tarball_path <- get_package_tarfile("dplyr", version = "1.0.0")

# Use a specific repository
tarball_path <- get_package_tarfile("dplyr", repos = "https://cloud.r-project.org")

## End(Not run)

get package name for display

Description

get package name for display

Usage

get_pkg_name(input_string)

Arguments

input_string

- string containing package name

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 Annual PubMed Article Counts for a Search Term

Description

This function queries the NCBI E-utilities API to retrieve the number of PubMed articles published each year over a specified number of past years for a given search term or package name.

Usage

get_pubmed_by_year(
  package_name,
  years_back = 10,
  api_key = getOption("pubmed.api_key", NULL)
)

Arguments

package_name

A character string representing the search term (e.g., an R package name).
years_back

An integer specifying how many years back to query. Defaults to 10.
api_key

Optional. A character string with an NCBI API key. If not supplied, it will attempt to use the option getOption("pubmed.api_key").

Value

A data frame with two columns:

Year

The publication year (integer).

Count

The number of articles published in that year (integer).

Returns an empty data frame if no valid data is retrieved.

Examples

## Not run: 
get_pubmed_by_year("ggplot2", years_back = 5)

## End(Not run)

Get Total Number of PubMed Articles for a Search Term

Description

This function queries the NCBI E-utilities API to retrieve the total number of PubMed articles that match a given search term or R package name.

Usage

get_pubmed_count(package_name, api_key = getOption("pubmed.api_key", NULL))

Arguments

package_name

A character string representing the search term (e.g., an R package name).
api_key

Optional. A character string with an NCBI API key. If not supplied, it will attempt to use the option getOption("pubmed.api_key").

Value

An integer representing the total number of PubMed articles matching the search term, or NA if the request fails.

Examples

## Not run: 
get_pubmed_count("ggplot2")

## End(Not run)

Get Risk Analysis

Description

Compute risk levels for the package metadata.

Usage

get_risk_analysis(data)

Arguments

data

The nested package metadata.

Value

A named list of computed risk levels.

Examples

# Minimal mock input for demonstration
mock_data <- list(
  dependencies_count = 5,
  later_version = 2,
  code_coverage = 0.75,
  last_month_download = 150000,
  license = "MIT",
  reverse_dependencies_count = 10,
  documentation_score = 2,
  has_examples = list(
    data = data.frame(
      function_name          = "somefunction",
      documentation_name     = "No documentation found",
      documentation_location = 0,
      example                = "no Rd file",
      stringsAsFactors       = FALSE
    ),
    example_score = 0.20   
  ),
  has_docs = list(
    data = data.frame(
      function_name    = "somefunction",
      stringsAsFactors = FALSE
    ),
    has_docs_score = 0.30  
  ),
  cmd_check = 0
)

get_risk_analysis(mock_data)

Get Risk Definition

Description

Load risk definition config from options, JSON file, or fallback to bundled file.

Usage

get_risk_definition()

Value

A list of risk configuration items.

Examples

risk_rule <- get_risk_definition()
print(risk_rule)

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

deps_list

A data frame containing the dependency information of the package (provided by calc_dependencies function)

Value

A list with two elements:

imports

A named list of packages in the "Imports" section along with their corresponding versions

suggests

A named list of packages in the "Suggests" section along with their corresponding versions

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

data

- all packages listed in the DESCRIPTION file

Value

- data with package names and exported functions

Get Package Versions

Description

This function retrieves all available versions of a package, including the latest version, by parsing the provided version table and querying the RStudio Package Manager.

Usage

get_versions(table, package_name)

Arguments

table

A list of parsed package data (e.g., from 'parse_html_version()'), where each element contains package details such as 'package_version' and 'date'.
package_name

A character string specifying the name of the package to fetch versions for.

Value

A list with the following elements:

all_versions

A list of named lists, each containing:

version

The version number of the package.

date

The associated publication date as a string.

last_version

A named list containing the latest version of the package with:

version

The latest version number.

date

The publication date of the latest version.

May be NULL if the API call fails.

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"
  )
)

result <- get_versions(table, "here")
print(result)

## End(Not run)

Install package locally

Description

Install package locally

Usage

install_package_local(pkg_source_path)

Arguments

pkg_source_path

- source path for install local

Value

logical - package_installed

Examples

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

## End(Not run)

Check if a Package is a Base or Recommended R Package

Description

This function determines whether a given package is a base or recommended package using CRAN metadata.

Usage

is_base(pkg)

Arguments

pkg

A character string representing the name of the package.

Value

A logical value: 'TRUE' if the package is a base or recommended package, 'FALSE' otherwise.

Examples

## Not run: 
is_base("stats")     # TRUE
is_base("ggplot2")   # FALSE

## End(Not run)

List badges image URLs from a local README

Description

Scans a local README (Markdown) and returns badge image URLs.

Usage

list_badges(path)

Arguments

path

Character scalar; path to a local README file (e.g., "README.md").

Value

data.frame with badge info

Examples

## Not run: 
tmp <- tempfile(fileext = ".md")
writeLines(c(
  "# MyPkg",
  "![build](build-status.svg)",
  "![cov](coverage.svg)"
), tmp)
out <- list_badges(tmp)
print(out)

## End(Not run)

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

tar_file

A string representing the path to the '.tar.gz' file that contains the R package.

Value

A string containing the path to the newly created modified '.tar.gz' file, or the original 'tar_file' path unchanged if modification was unnecessary or failed.

Examples

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

## 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

html_content

The parsed HTML document from 'fetch_bioconductor_releases'.

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)
print(release_data)

## 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

name

A character string specifying the name of the package to fetch information for.

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"
parse_package_info("dplyr")


## End(Not run)

Print a Package Dependency Tree

Description

This function prints a hierarchical representation of a package's dependencies, including version and base status

Usage

print_tree(tree, prefix = "", last = TRUE, show_version = TRUE)

Arguments

tree

A nested list representing the package dependency tree, where each package has a 'version' field and potentially sub-dependencies.
prefix

A character string used for formatting tree branches (default: "").
last

A logical value indicating if the current package is the last in the tree level (default: 'TRUE').
show_version

A logical value indicating whether to display package versions if available (default: 'TRUE').

Value

Prints the dependency tree to the console.

Examples

## Not run: 
db <- list(
  stringr = list(
    version = "1.5.1",
    cli = list(version = "3.6.2", utils = "base"),
    glue = list(version = "1.7.0", methods = "base"),
    lifecycle = list(
      version = "1.0.4",
      cli = list(version = "3.6.2", utils = "base"),
      glue = list(version = "1.7.0", methods = "base"),
      rlang = list(version = "1.1.3", utils = "base")
    ),
    magrittr = list(version = "2.0.3"),
    rlang = list(version = "1.1.3", utils = "base"),
    stringi = list(version = "1.8.3", tools = "base", utils = "base", stats = "base"),
    vctrs = list(
      version = "0.6.5",
      cli = list(version = "3.6.2", utils = "base"),
      glue = list(version = "1.7.0", methods = "base"),
      lifecycle = list(version = "1.0.4"),
      rlang = list(version = "1.1.3", utils = "base")
    )
  )
)
print_tree(db)

## End(Not run)

Assess package for risk metrics

Description

Assess an R package for risk metrics. Use exactly one of: * 'path' – path to a local .tar.gz archive, or * 'package' – package name to fetch (optionally with 'version'), or * neither – opens an interactive file chooser.

Usage

risk_assess_pkg(
  path = NULL,
  package = NULL,
  version = NA,
  repos = getOption("repos")
)

Arguments

path

Path to a local .tar.gz package archive. Use only when not providing 'package'.
package

Package name to fetch from CRAN, Bioconductor, or internal repos. Use only when not providing 'path'.
version

(optional) Package version when using 'package'. Default 'NA' uses the latest available.
repos

Repository URLs when fetching by 'package'. Default is 'getOption("repos")'.

Value

List containing results (metrics, covr, trace matrix, R CMD check), or 'NULL' if the package cannot be assessed.

Examples

## Not run: 
# Local package (path or file chooser)
results <- risk_assess_pkg()
results <- risk_assess_pkg(path = "path/to/package.tar.gz")

# Package by name from repositories
results <- risk_assess_pkg(package = "here")
results <- risk_assess_pkg(package = "here", version = "1.0.1")
results <- risk_assess_pkg(package = "here", repos = "https://cloud.r-project.org")

## 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

input_data

- path to a lock file

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)

Creates information on package installation

Description

Creates information on package installation

Usage

set_up_pkg(package_path, check_type = "1")

Arguments

package_path

Path to the package tarball (.tar.gz).
check_type

Type of R CMD check: "1" for basic, "2" for CRAN-like.

Value

list with local package install

Examples

## Not run: 
set_up_pkg("path/to/tarball")

## End(Not run)

Write the risk assessment summary report

Description

Renders the package risk assessment report ('summary.Rmd') to a chosen format and writes it to disk. The output file path can be inferred or explicitly set. You can specify the output format directly via 'output_format' or let it be inferred from the extension of 'output_file'. If 'output_dir' is not provided, the current working directory is used.

Usage

write_summary_report(
  results,
  output_file = NULL,
  output_format = NULL,
  output_dir = NULL
)

Arguments

results

A results object containing the risk assessment results. It is expected to include 'results$results$pkg_name' and 'results$results$pkg_version', which are used to construct default file names and report parameters.
output_file

'character(1)' or 'NULL'. The output file path **or** a directory. - If 'NULL', a default name is generated: '"summary_report_<pkg_name>_<pkg_version>.html"' in 'output_dir'. - If it is a directory, the default name is composed inside it. - If it is a relative path, it is resolved against 'output_dir'.
output_format

'character(1)' or 'NULL'. Explicit output format to render: one of '"html"' or '"md"' (case-insensitive; do **not** include a leading dot). If 'NULL', the format is inferred from the extension of 'output_file'. Unknown values trigger a warning and default to HTML.
output_dir

'character(1)' or 'NULL'. Base directory used when 'output_file' is 'NULL' or a relative path. If 'NULL', defaults to the current working directory ('getwd()'), with an informational message.

Details

The function calls [rmarkdown::render()] on an internal template: 'system.file("report_templates", "summary.Rmd", package = "risk.assessr")'.

The format mapping is: - '"html"' -> [rmarkdown::html_document()] - '"md"' -> [rmarkdown::md_document()]

If 'output_format' is provided, it takes precedence for rendering even if 'output_file' has a different extension; in that case the filename is adjusted to match the format. If 'output_format' is not provided, the function infers the format from ‘output_file'’s extension. For unknown extensions, it warns and rewrites the extension to '.html'.

Value

(Invisibly) the absolute path to the written report file.

Behavior

- If 'output_dir' is 'NULL', it defaults to 'getwd()' and a message is printed. - If 'output_file' is 'NULL', a file name is auto-generated as '"summary_report_<pkg>_<version>.html"' inside 'output_dir'. - If 'output_file' points to an existing directory (or ends with a path separator), a file name is composed inside that directory as '"summary_report_<pkg>_<version>.html"'. - If 'output_file' is a relative path, it is resolved against 'output_dir'. - If 'output_format' is provided, it determines the render format (and the 'output_file' name is adjusted to match the format). - If 'output_format' is not provided, the render format is inferred from the extension of 'output_file'. Unknown extensions trigger a warning and the extension is changed to '.html'.

Examples

## Not run: 
# generate assessment_results
results <- risk_assess_pkg()

# Basic usage: auto-name in the working directory (HTML)
write_summary_report(results)

# Specify output directory (auto-name inside that directory)
write_summary_report(results, output_dir = "artifacts")

# Provide an explicit filename (relative to output_dir)
write_summary_report(results, output_file = "reports/summary.html")

# Provide a directory as output_file: auto-name inside that directory
write_summary_report(results, output_file = "reports/")

# Render to Markdown explicitly
write_summary_report(results, output_format = "md")

# Let the extension drive the format (md)
write_summary_report(results, output_file = "reports/summary.md")

# Case-insensitive formats work; avoid leading dots (".md" is not valid)
write_summary_report(results, output_format = "MD")

## End(Not run)