Package {risk.assessr}

Title:	Assessing Package Risk Metrics
Version:	4.1.0
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.
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	https://pharmaverse.github.io/risk.assessr/
BugReports:	https://github.com/pharmaverse/risk.assessr/issues
Depends:	R (≥ 4.1.0)
Imports:	remotes, test.assessr (≥ 2.1.0), checkmate, desc, dplyr, fs, methods, purrr, rmarkdown, rcmdcheck, rlang, xml2, stringr (≥ 1.5.0), tidyr, utils, curl, jsonlite, memoise, BiocManager, glue
Suggests:	devtools, forcats, here, htmltools, htmlwidgets, kableExtra (≥ 1.4.0), knitr, magrittr, openxlsx, pkgload, R6, S7, readr, roxygen2, testthat (≥ 3.0.0), tibble, tidyselect, tools, withr, mockery, ggplot2, DT
Encoding:	UTF-8
Config/testthat/edition:	3
Config/build/clean-inst-doc:	false
VignetteBuilder:	knitr
Config/roxygen2/version:	8.0.0
RoxygenNote:	7.3.3
NeedsCompilation:	no
Packaged:	2026-06-11 12:46:24 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:	2026-06-11 14:10:07 UTC

risk.assessr: 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.

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://pharmaverse.github.io/risk.assessr/

• Report bugs at https://github.com/pharmaverse/risk.assessr/issues

Convert input to ISO 8601 date (YYYY-MM-DD)

Description

Formats inputs as ISO 8601 calendar dates ('"YYYY-MM-DD"').

Usage

as_iso_date(x)

Arguments

Details

Coercion uses [base::as.Date()], so time-of-day and timezone information are dropped. For 'POSIXct' inputs, the date is computed by 'as.Date.POSIXct' (which uses 'tz = "UTC"' by default). Be aware that ambiguous character dates (e.g., '"01/02/2024"') depend on your R locale/format unless you specify a format before calling this function.

Value

A character vector the same length as 'x' (or 'NULL' if 'x' is 'NULL') with dates formatted as '"YYYY-MM-DD"'. Unparseable elements or 'NA's become 'NA_character_'.

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 examples (exported functions only)

Description

Scans the package Rd database at 'pkg_source_path' and reports whether each **exported function** has examples. Resolution supports shared topics via roxygen '@rdname' (multiple functions documented on the same Rd page) and multiple '\alias' entries.

Usage

assess_examples(pkg_name, pkg_source_path)

Arguments

Value

A list with:

data

A data.frame with columns 'function_name', 'documentation_name', 'documentation_location', and 'example'.

example_score

Numeric; percentage of exported functions with examples.

Examples

## Not run: 
  res <- assess_examples("stringr", "<path-to-stringr-source>")
  head(res$data)
  res$example_score

## End(Not run)

assess_export_help

Description

assess_export_help

Usage

assess_export_help(pkg_name, pkg_source_path)

Arguments

Value

- export_help - variable with score

Assess documentation coverage for exported functions

Description

Scans the package Rd database at 'pkg_source_path' and resolves exported functions to their Rd pages to determine whether documentation exists. Resolution supports shared topics and multiple '\alias' entries, and the returned data includes only 'function_name', 'documentation_name', and 'documentation_location', together with a score representing the fraction of exported functions that have any Rd documentation.

Usage

assess_exported_functions_docs(pkg_name, pkg_source_path)

Arguments

Value

A list with:

data

A 'data.frame' with columns 'function_name', 'documentation_name', and 'documentation_location'.

has_docs_score

Numeric in \[0, 1\]; fraction of exported functions that have an Rd page.

Assess exported functions to namespace

Description

Returns 1L if the package's NAMESPACE declares any exports ('export', 'exportClasses', 'exportMethods', 'exportPattern' or 'exportClassPatterns'), 0L otherwise.

Usage

assess_exports(data)

Arguments

Value

integer scalar: 1L if any exports are declared, 0L otherwise.

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

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

Value

Assessment results or 'NULL'.

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 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

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

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

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)

Build a lookup from normalized R script keys to actual R/ paths

Description

Build a lookup from normalized R script keys to actual R/ paths

Usage

build_r_script_lookup(pkg_source_path)

Arguments

Value

Named character vector: normalized key -> "R/<file>".

Build a fast lookup index for an Rd database

Description

Provides (1) an alias index, mapping 'alias -> filename', and (2) a topic index, mapping 'filename -> \name' (topic).

Usage

build_rd_index(db)

Arguments

Value

A list with elements 'alias_index' (environment) and 'topic_by_file' (named character vector).

Convert CamelCase identifiers to kebab-case

Description

Convert CamelCase identifiers to kebab-case

Usage

camel_to_kebab(x)

Arguments

Value

Character scalar, e.g. "geom-alluvium".

Capture CRAN URL warnings and errors

Description

This internal function attempts to open a CRAN URL and read its contents. It captures and classifies warnings and errors related to network issues, such as timeouts or inaccessible URLs.

Usage

capture_cran_warning(cran_url, path)

Arguments

Value

A list with two elements:

status

Character string indicating the result type: "success", "url_error", "timeout", "error", "url_warning", "timeout_warning", or "warning".

message

Character string with the captured warning or error message, or NULL if successful.

Examples

## Not run: 
  capture_cran_warning("http://cran.us.r-project.org", "src/contrib/Meta/archive.rds")

## 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 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

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)

Reclassify Forbidden Notes as Errors in rcmdcheck Results

Description

This internal helper function scans the 'notes' field of an 'rcmdcheck' result object for specific patterns that indicate more serious issues. If any of these patterns are found, the corresponding notes are reclassified as errors by moving them from the 'notes' field to the 'errors' field.

Usage

check_forbidden_notes(res_check, pkg_name)

Arguments

Value

A modified version of 'res_check' where certain notes matching forbidden patterns are moved to the 'errors' field.

function to check value of ggproto

Description

function to check all classes of a ggproto function

Usage

check_ggproto(value)

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

classify_function_body

Description

This function gets the function bodies for exported functions

Usage

classify_function_body(row, package_name)

Arguments

Value

row - row with the function details plus function body

Clean and normalize license names

Description

Splits a license string on commas, plus signs, or pipes, trims whitespace, removes trailing noise like "file LICENSE", and normalizes each part to uppercase letters only.

Usage

clean_license(x)

Arguments

Value

A character vector of normalized license names.

Clean Up Dependencies

Description

Cleans up a list of dependency strings by extracting unique package names.

Usage

clean_up_dependencies(x)

Arguments

Value

A character vector of unique package names.

Compute Risk Level

Description

Apply risk thresholds to compute risk level for a single metric.

Usage

compute_risk(value, risk)

Arguments

Value

The computed risk level (e.g. "low", "medium", "high").

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.

Convert number to abbreviation

Description

Convert number to abbreviation

Usage

convert_number_to_abbreviation(value)

Arguments

Convert number to percent

Description

Convert number to percent

Usage

convert_number_to_percent(value)

Arguments

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

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

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

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 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

Combine example/docs scores into a single metric (sum).

Description

Combine example/docs scores into a single metric (sum).

Usage

create_has_ex_docs_score(example_score, has_docs_score)

Arguments

Value

Numeric vector: example_score + has_docs_score in [0, 2], with NA where both inputs are NA at that position.

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 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

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

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

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)

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

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

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)

Evaluate Risk Highlighting for Rejection and Mitigation

Description

This function analyzes risk levels for key metrics ("CMD Check" and "Code Coverage") and other metrics to determine whether a report should be highlighted for rejection or mitigation based on predefined rules.

Usage

evaluate_risk_highlighting(risk_analysis_output)

Arguments

Details

**Rejection Logic:** - Reject if BOTH key metrics ("CMD Check" and "Code Coverage") are medium/high. - OR if there are severe other risks (greater equal to 2 high OR greater equal to 3 medium) - AND at least one key metric is not low.

**Mitigation Logic:** - Mitigate if only one key metric is medium/high OR other risks are significant (greater equal to 1 high OR greater equal to 2 medium), provided the report is not rejected.

Value

status - 3 possible values - "Accepted", "Mitigation Needed", "Rejected"

Expand Dependency Type Specification

Description

Expands a dependency type specification into a character vector of dependency types.

Usage

expand_dependency_type_spec(x)

Arguments

Value

A character vector of dependency types.

Build a file-coverage data frame from a single res_cov object

Description

Build a file-coverage data frame from a single res_cov object

Usage

extract_coverage_df(res_cov, pkg_name)

Arguments

Extract Package Names from a Dependency String

Description

Parses a single package dependency string and extracts valid package names, excluding "R" and ignoring version constraints or comments.

Usage

extract_dependency_package_names(x)

Arguments

Value

A character vector of package names extracted from the input string. The result excludes "R" and any version information.

Extract examples text from an Rd document

Description

Supports both '\examples' and '\example' sections. If multiple sections exist, their contents are concatenated with blank lines.

Usage

extract_examples_text(rd_doc)

Arguments

Value

Character scalar of combined examples text, or 'NULL' if none/non‑informative.

Extract Exported Function Metadata from an R Package

Description

This internal utility function analyzes the namespace of an R package and extracts metadata about its exported functions, including classification into S3, S4, S7, and regular functions.

Usage

extract_exported_function_info(.pkg_source_path, package_name)

Arguments

Value

A tibble with columns: 'exported_function', 'class', 'function_type', 'function_body', and 'where'.

function to extract ggproto methods

Description

function to get all the methods of a ggproto function

Usage

extract_ggproto_methods(obj)

Arguments

Extract License from Package DESCRIPTION File

Description

This function extracts the license information from a package's DESCRIPTION file.

Usage

extract_license_from_description(path)

Arguments

Value

A character string representing the package license, or 'NA' if not found.

Helper to create maintainer

Description

Helper to create maintainer

Usage

extract_maintainer_info(person_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 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

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 Inputs

Description

Compute intermediate risk input values from flattened package data.

Usage

extract_risk_inputs(flat_data)

Arguments

Value

A list of computed values required for risk scoring.

Helper to extract "R/<file>" from any path by taking the last two components

Description

Helper to extract "R/<file>" from any path by taking the last two components

Usage

extract_short_path(long_file_name)

Arguments

Value

A character string composed of the last two path components, e.g., "R/add.R"

Extract risk thresholds by id

Description

Extract risk thresholds by id

Usage

extract_thresholds_by_id(risk_rule, id_value)

Arguments

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

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

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

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

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)

Paths to NEWS files for a package source tree

Description

Searches the same locations and basenames that utils::news uses for an installed package (via tools:::.build_news_db): NEWS.Rd, NEWS.md, and extensionless NEWS. For a source checkout, those files are collected from the package root, doc/, vignettes/, and under inst/ (recursively, including inst/NEWS as in tools::news2Rd).

Usage

find_news_files(pkg_source_path)

Arguments

Value

Character vector of absolute file paths (possibly empty).

Find an Rd document for a function using an index

Description

Tries 'fun.Rd', then alias-based resolution via the index, and as a last resort matches the topic name if it equals the function name.

Usage

find_rd_for_fun(fun, db, idx = NULL)

Arguments

Value

'NULL' if not found, otherwise a list with 'rd' (the Rd object) and 'filename' (the Rd filename).

Create fine grained traceability matrices

Description

Create fine grained traceability matrices

Usage

fine_grained_tms(tm, pkg_name)

Arguments

Value

- nested list with fine grained tms

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. For single-framework packages returns a data frame; for multi-framework packages returns a named list of data frames (one per framework).

Usage

generate_coverage_section(assessment_results, pkg_name)

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 Fine grained Trace Matrices Section

Description

Generates the Trace Matrices section for the HTML report.

Usage

generate_fg_trace_matrix_section(tm_type, tm_df)

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 = NULL)

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 Popularity Metrics Section

Description

Generates the popularity section for the HTML report.

Usage

generate_pop_metrics_section(assessment_results)

Arguments

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 Analysis

Description

Generates the Risk Analysis table for the HTML report.

Usage

generate_risk_analysis(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(total_coverage, file_coverage, tm_df)

Arguments

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

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)

Extract all S4 methods

Description

Extract all S4 methods

Usage

get_all_s4_methods(generic_name)

Arguments

Value

list with method_strings, generic, and methods

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

Value

A list containing:

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

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

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

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)

Get dependencies

Description

Get dependencies

Usage

get_dependencies(pkg_source_path)

Arguments

Get exported function names with a NAMESPACE-source fallback.

Description

Attempts to obtain exported function names from the installed namespace. If the namespace is not available - for example when 'R CMD INSTALL' failed because the package has no 'R/' folder on stricter R versions - falls back to parsing 'NAMESPACE' from 'pkg_source_path' via [get_exports_from_source()]. In the fallback path the result includes every declared export, because function-ness cannot be verified without a loaded namespace.

Usage

get_exported_function_names(pkg_name, pkg_source_path)

Arguments

Value

Character vector of exported names (possibly empty).

list all package exports

Description

list all package exports

Usage

get_exports(pkg_source_path)

Arguments

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)

Parse exported names from a package's NAMESPACE on disk.

Description

Used as a fallback when the package is not loaded as a namespace (for example when 'R CMD INSTALL' failed because the package has no R/ folder on stricter R versions).

Usage

get_exports_from_source(pkg_source_path)

Arguments

Value

Character vector of exported names (possibly empty).

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

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

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

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 License Levels from Thresholds

Description

This internal utility function processes a list of license thresholds and returns a named list of license values grouped by their risk level (e.g., "high", "medium", "low").

Usage

get_license_thresholds(thresholds)

Arguments

Value

A named list with elements '"high"', '"medium"', and '"low"', each containing a character vector of license names.

Extract Maximum Thresholds for Code Coverage Levels

Description

This internal function retrieves the 'max' values for '"high"','"medium"', and '"low"' levels from a list of code coverage thresholds.

Usage

get_max_thresholds(thresholds)

Arguments

Value

A list with three elements:

high_max

The maximum threshold value for the '"high"' level.

medium_max

The maximum threshold value for the '"medium"' level.

medium_max

The maximum threshold value for the '"low"' level.

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

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

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

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)

Assess Authors

Description

Assess Authors

Usage

get_pkg_author(pkg_name, pkg_source_path)

Arguments

Value

- Authors related variable

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

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 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

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

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)

function to get R6 methods

Description

function to get R6 methods from class

Usage

get_r6_methods_details(class_name)

Arguments

Get the first Rd section by tag

Description

Depth-first search returning the first node whose 'Rd_tag' equals 'paste0("\\", section)'.

Usage

get_rd_section(rd, section)

Arguments

Value

The first matching Rd node or 'NULL' if not found.

Get all Rd sections by tag

Description

Recursively collects all nodes whose 'Rd_tag' matches a given section name, e.g., "alias", "examples", "example", "name".

Usage

get_rd_sections(rd, section)

Arguments

Value

A list of Rd nodes matching the section (possibly empty).

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 Analysis

Description

Compute risk levels for the package metadata.

Usage

get_risk_analysis(data)

Arguments

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 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

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

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)

Helper function to replace NULL with "N/A"

Description

Helper function to replace NULL with "N/A"

Usage

handle_null(x)

Arguments

Install package locally

Description

Install package locally

Usage

install_package_local(pkg_source_path)

Arguments

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

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

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

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)

Normalize an R source path for coverage join keys

Description

Strips directory/extension and ignores hyphen, underscore, and case differences so man/geom_alluvium.Rd (R/geom_alluvium.R) matches covr keys like R/geom-alluvium.r.

Usage

normalize_code_script_key(path)

Arguments

Value

Normalized basename without separators, or NA_character_.

Normalize Nested Package Data

Description

Flattens nested package metadata into a flat list for further processing.

Usage

normalize_data(results)

Arguments

Value

A list with flattened package information.

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)
print(release_data)

## End(Not run)

Parse DCF of description file

Description

Parse DCF of description file

Usage

parse_dcf_dependencies(path)

Arguments

Parse Dependencies from a Package DESCRIPTION File

Description

This function extracts and returns the dependencies from the DESCRIPTION file of an R package, focusing on the 'Imports' field.

Usage

parse_dcf_dependencies_version(path)

Arguments

Value

A data frame with columns: - 'package': The name of the imported package. - 'type': The type of dependency (e.g., "Imports").

Examples

## Not run: 
parse_dcf_dependencies_version("/path/to/package")

## End(Not run)

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)
## Not run: 
html_content <- parse_package_info("dplyr")
parse_html_version(html_content, "dplyr")

## 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"
parse_package_info("dplyr")


## 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

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

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)

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

Extract all aliases from an Rd document

Description

Collects text from **all** '\alias' nodes, trimming whitespace and de-duplicating.

Usage

rd_aliases(rd)

Arguments

Value

A character vector of aliases (possibly empty).

Flatten example nodes to a text block

Description

Recursively collects example text from nodes that carry R code or text, unwrapping containers such as '\dontrun', '\donttest', and '\dontshow'.

Usage

rd_examples_to_text(node)

Arguments

Value

Character scalar containing example text or '""' if none.

Flatten an Rd node to plain text

Description

Recursively flattens a node (or list of nodes) into a character string.

Usage

rd_flatten_text(node)

Arguments

Value

Character scalar containing the concatenated text.

Extract the topic name from an Rd document

Description

Returns the '\name' (roxygen '@rdname') of the Rd document.

Usage

rd_name(rd)

Arguments

Value

A length-1 character scalar (topic name) or 'NA_character_' if missing.

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 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

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

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 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 expanded from [riskmetric::metric_score.pkg_metric_r_cmd_check()] by including forbidden notes,

Helper to conditionally apply handle_null or abbreviation

Description

Helper to conditionally apply handle_null or abbreviation

Usage

safe_value(x)

Arguments

Creates information on package installation

Description

Creates information on package installation

Usage

set_up_pkg(package_path, check_type = "1")

Arguments

Value

list with local package install

Examples

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

## 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

Untar package and return installation directory

Description

Untar package and return installation directory

Usage

unpack_tarball(pkg_tar, temp_file_name = "temp_file_")

Arguments

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

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)