diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000..81b960f --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/r_app/extract_current_versions.R b/r_app/extract_current_versions.R new file mode 100644 index 0000000..f98cea2 --- /dev/null +++ b/r_app/extract_current_versions.R @@ -0,0 +1,200 @@ +#' Version Extractor for SmartCane Project +#' +#' This script scans your R scripts to find all used packages and extracts +#' the currently installed versions. Use this to populate the package_manager.R +#' with your actual working versions. +#' +#' Usage: +#' source("extract_current_versions.R") +#' +#' Author: SmartCane Team +#' Date: 2025-06-24 + +# ============================================================================= +# PACKAGE DISCOVERY +# ============================================================================= + +#' Extract packages from R scripts +extract_packages_from_scripts <- function(script_dir = ".") { + # Find all R files + r_files <- list.files(script_dir, pattern = "\\.(R|Rmd)$", recursive = TRUE, full.names = TRUE) + + packages <- c() + + for (file in r_files) { + cat("Scanning:", file, "\n") + + tryCatch({ + content <- readLines(file, warn = FALSE) + + # Find library() calls + library_matches <- regmatches(content, regexpr('library\\(["\']?([^"\'\\)]+)["\']?\\)', content)) + library_packages <- gsub('library\\(["\']?([^"\'\\)]+)["\']?\\)', '\\1', library_matches) + library_packages <- library_packages[library_packages != ""] + + # Find require() calls + require_matches <- regmatches(content, regexpr('require\\(["\']?([^"\'\\)]+)["\']?\\)', content)) + require_packages <- gsub('require\\(["\']?([^"\'\\)]+)["\']?\\)', '\\1', require_matches) + require_packages <- require_packages[require_packages != ""] + + # Find package::function calls + namespace_matches <- regmatches(content, gregexpr('[a-zA-Z][a-zA-Z0-9.]*::', content)) + namespace_packages <- unique(unlist(lapply(namespace_matches, function(x) gsub('::', '', x)))) + namespace_packages <- namespace_packages[namespace_packages != ""] + + packages <- c(packages, library_packages, require_packages, namespace_packages) + + }, error = function(e) { + cat("Error reading", file, ":", e$message, "\n") + }) + } + + # Clean and deduplicate + packages <- unique(packages) + packages <- packages[!packages %in% c("", "base", "stats", "utils", "graphics", "grDevices")] + + return(sort(packages)) +} + +#' Get current version of installed packages +get_current_versions <- function(packages) { + versions <- list() + + cat("\nChecking installed versions...\n") + cat("===============================\n") + + for (pkg in packages) { + if (pkg %in% rownames(installed.packages())) { + version <- as.character(packageVersion(pkg)) + versions[[pkg]] <- version + cat(sprintf("✓ %-20s %s\n", pkg, version)) + } else { + cat(sprintf("✗ %-20s NOT INSTALLED\n", pkg)) + } + } + + return(versions) +} + +#' Generate package manager configuration +generate_package_config <- function(versions) { + cat("\n\nGenerating REQUIRED_PACKAGES configuration...\n") + cat("=============================================\n\n") + + config_lines <- c( + "# Package requirements with your current working versions", + "REQUIRED_PACKAGES <- list(" + ) + + # Group packages by category + categories <- list( + "Core data manipulation" = c("here", "dplyr", "tidyr", "readr", "readxl", "magrittr", "lubridate", "stringr"), + "Spatial data" = c("sf", "terra", "exactextractr", "raster", "sp", "sf", "rgdal", "rgeos"), + "Visualization" = c("tmap", "ggplot2", "RColorBrewer", "viridis", "scales"), + "Statistical analysis" = c("lme4", "nlme", "mgcv", "survival", "cluster"), + "Reporting" = c("knitr", "rmarkdown", "officedown", "officer", "flextable"), + "Tidyverse" = c("tidyverse", "purrr", "forcats", "tibble"), + "Other packages" = c() + ) + + # Categorize packages + categorized <- list() + uncategorized <- names(versions) + + for (category in names(categories)) { + cat_packages <- intersect(names(versions), categories[[category]]) + if (length(cat_packages) > 0) { + categorized[[category]] <- cat_packages + uncategorized <- setdiff(uncategorized, cat_packages) + } + } + + # Add uncategorized packages + if (length(uncategorized) > 0) { + categorized[["Other packages"]] <- uncategorized + } + + # Generate config + for (category in names(categorized)) { + config_lines <- c(config_lines, paste0(" # ", category)) + + packages_in_cat <- categorized[[category]] + for (i in seq_along(packages_in_cat)) { + pkg <- packages_in_cat[i] + version <- versions[[pkg]] + comma <- if (i == length(packages_in_cat) && category == names(categorized)[length(categorized)]) "" else "," + + # Add special comment for critical packages + comment <- "" + if (pkg == "tmap") comment <- " # CRITICAL: for tm_scale_continuous() syntax" + if (pkg == "terra") comment <- " # CRITICAL: for raster processing" + + config_lines <- c(config_lines, sprintf(' "%s" = "%s"%s%s', pkg, version, comma, comment)) + } + + if (category != names(categorized)[length(categorized)]) { + config_lines <- c(config_lines, "") + } + } + + config_lines <- c(config_lines, ")") + + # Print to console + cat(paste(config_lines, collapse = "\n")) + + # Save to file + writeLines(config_lines, "generated_package_config.R") + cat("\n\n📁 Configuration saved to: generated_package_config.R\n") + + return(config_lines) +} + +# ============================================================================= +# MAIN EXECUTION +# ============================================================================= + +main <- function() { + cat("🔍 SmartCane Package Version Extractor\n") + cat("======================================\n\n") + + # Step 1: Find all packages used in scripts + cat("Step 1: Scanning R scripts for package usage...\n") + packages <- extract_packages_from_scripts() + + cat("\nFound packages:\n") + cat(paste(packages, collapse = ", "), "\n") + cat("\nTotal packages found:", length(packages), "\n") + + # Step 2: Get current versions + cat("\nStep 2: Checking installed versions...\n") + versions <- get_current_versions(packages) + + installed_count <- length(versions) + missing_count <- length(packages) - installed_count + + cat(sprintf("\n📊 Summary: %d installed, %d missing\n", installed_count, missing_count)) + + if (missing_count > 0) { + missing_packages <- setdiff(packages, names(versions)) + cat("\n⚠️ Missing packages:\n") + cat(paste(missing_packages, collapse = ", "), "\n") + cat("\nYou may want to install these first, then re-run this script.\n") + } + + # Step 3: Generate configuration + if (length(versions) > 0) { + cat("\nStep 3: Generating package manager configuration...\n") + config <- generate_package_config(versions) + + cat("\n✅ Next steps:\n") + cat("1. Review generated_package_config.R\n") + cat("2. Copy the REQUIRED_PACKAGES list to package_manager.R\n") + cat("3. Adjust any versions as needed\n") + cat("4. Run package_manager.R\n") + } else { + cat("\n❌ No installed packages found. Install packages first.\n") + } +} + +# Run the extraction +main() diff --git a/r_app/package_manager.R b/r_app/package_manager.R new file mode 100644 index 0000000..84d021d --- /dev/null +++ b/r_app/package_manager.R @@ -0,0 +1,315 @@ +#' Package Manager for SmartCane Project +#' +#' This script manages R package versions across development, testing, and production environments. +#' It uses renv for reproducible environments and ensures consistent package versions. +#' +#' Usage: +#' source("package_manager.R") +#' +#' Author: SmartCane Team +#' Date: 2025-06-24 + +# ============================================================================= +# CONFIGURATION +# ============================================================================= + +# Package requirements with your current working versions +REQUIRED_PACKAGES <- list( + # Core data manipulation + "dplyr" = "1.1.4", + "here" = "1.0.1", + "lubridate" = "1.9.4", + "readr" = "2.1.5", + "readxl" = "1.4.5", + "stringr" = "1.5.1", + "tidyr" = "1.3.1", + "purrr" = "1.0.2", + "magrittr" = "2.0.0", # Adding this as it's commonly used + + # Spatial data + "exactextractr" = "0.10.0", + "raster" = "3.6.32", + "sf" = "1.0.19", + "terra" = "1.8.43", # CRITICAL: for raster processing + + # Visualization - CRITICAL: tmap v4 for new syntax + "ggplot2" = "3.5.1", + "tmap" = "4.0", # CRITICAL: for tm_scale_continuous() syntax + "gridExtra" = "2.3", + # Reporting + "knitr" = "1.50", + "rmarkdown" = "2.21.0", # Adding this as it's needed for reports + + # Tidyverse meta-package + "tidyverse" = "2.0.0", + + # Machine Learning & Statistics + "caret" = "7.0.1", + "CAST" = "1.0.3", + "randomForest" = "4.7.1.2", + "rsample" = "1.3.0", + + # Parallel processing + "furrr" = "0.3.1", + "future" = "1.40.0", + "progressr" = "0.15.1", + + # Other utilities + "reshape2" = "1.4.4", + "zoo" = "1.8.13" +) + +# Log file setup +LOG_FILE <- file.path(getwd(), "package_manager.log") +START_TIME <- Sys.time() + +# ============================================================================= +# UTILITY FUNCTIONS +# ============================================================================= + +#' Log message to both console and file +log_message <- function(message, level = "INFO") { + timestamp <- format(Sys.time(), "%Y-%m-%d %H:%M:%S") + formatted_msg <- sprintf("[%s] %s - %s", level, timestamp, message) + + # Print to console + cat(formatted_msg, "\n") + + # Write to log file + cat(formatted_msg, "\n", file = LOG_FILE, append = TRUE) +} + +#' Check if package is installed +is_package_installed <- function(package) { + package %in% rownames(installed.packages()) +} + +#' Get installed package version +get_package_version <- function(package) { + if (is_package_installed(package)) { + as.character(packageVersion(package)) + } else { + NULL + } +} + +#' Compare version strings (returns TRUE if installed >= required) +version_meets_requirement <- function(installed, required) { + if (is.null(installed)) return(FALSE) + utils::compareVersion(installed, required) >= 0 +} + +#' Install or update package to minimum version +install_or_update_package <- function(package, required_version) { + current_version <- get_package_version(package) + + if (is.null(current_version)) { + log_message(sprintf("Installing %s (required: >= %s)", package, required_version)) + tryCatch({ + install.packages(package, dependencies = TRUE, quiet = TRUE) + new_version <- get_package_version(package) + log_message(sprintf("✓ Installed %s version %s", package, new_version), "SUCCESS") + return(TRUE) + }, error = function(e) { + log_message(sprintf("✗ Failed to install %s: %s", package, e$message), "ERROR") + return(FALSE) + }) + } else if (!version_meets_requirement(current_version, required_version)) { + log_message(sprintf("Updating %s from %s to >= %s", package, current_version, required_version)) + tryCatch({ + install.packages(package, dependencies = TRUE, quiet = TRUE) + new_version <- get_package_version(package) + if (version_meets_requirement(new_version, required_version)) { + log_message(sprintf("✓ Updated %s to version %s", package, new_version), "SUCCESS") + return(TRUE) + } else { + log_message(sprintf("⚠ %s updated to %s but still below required %s", package, new_version, required_version), "WARNING") + return(FALSE) + } + }, error = function(e) { + log_message(sprintf("✗ Failed to update %s: %s", package, e$message), "ERROR") + return(FALSE) + }) + } else { + log_message(sprintf("✓ %s version %s meets requirement (>= %s)", package, current_version, required_version)) + return(TRUE) + } +} + +# ============================================================================= +# MAIN PACKAGE MANAGEMENT FUNCTIONS +# ============================================================================= + +#' Initialize renv if not already initialized +initialize_renv <- function() { + log_message("Checking renv initialization...") + + if (!file.exists("renv.lock")) { + log_message("Initializing renv for the first time...") + if (!requireNamespace("renv", quietly = TRUE)) { + log_message("Installing renv...") + install.packages("renv") + } + renv::init() + log_message("✓ renv initialized", "SUCCESS") + } else { + log_message("✓ renv already initialized") + # Check if renv is already active by looking at the library path + if (!requireNamespace("renv", quietly = TRUE)) { + install.packages("renv") + } + # Check if we're already using the renv project library + lib_paths <- .libPaths() + + if (!any(grepl("renv", lib_paths))) { + log_message("Activating renv...") + renv::activate() + log_message("✓ renv activated") + } else { + log_message("✓ renv already active") + } + } +} + +#' Check and install all required packages +manage_packages <- function() { + log_message("=== PACKAGE MANAGEMENT STARTED ===") + log_message(sprintf("R version: %s", R.version.string)) + + success_count <- 0 + failure_count <- 0 + + for (package in names(REQUIRED_PACKAGES)) { + required_version <- REQUIRED_PACKAGES[[package]] + + if (install_or_update_package(package, required_version)) { + success_count <- success_count + 1 + } else { + failure_count <- failure_count + 1 + } + } + + log_message(sprintf("Package management complete: %d success, %d failures", success_count, failure_count)) + + if (failure_count > 0) { + log_message("Some packages failed to install/update. Check log for details.", "WARNING") + } + + return(failure_count == 0) +} + +#' Update renv lockfile with current package versions +update_lockfile <- function() { + log_message("Updating renv lockfile...") + tryCatch({ + renv::snapshot(prompt = FALSE) + log_message("✓ renv lockfile updated", "SUCCESS") + }, error = function(e) { + log_message(sprintf("✗ Failed to update lockfile: %s", e$message), "ERROR") + }) +} + +#' Generate package report +generate_package_report <- function() { + log_message("=== PACKAGE REPORT ===") + + # Check each required package + for (package in names(REQUIRED_PACKAGES)) { + required_version <- REQUIRED_PACKAGES[[package]] + current_version <- get_package_version(package) + + if (is.null(current_version)) { + status <- "❌ NOT INSTALLED" + } else if (version_meets_requirement(current_version, required_version)) { + status <- "✅ OK" + } else { + status <- "⚠️ VERSION TOO OLD" + } + + log_message(sprintf("%-20s | Required: >= %-8s | Installed: %-8s | %s", + package, required_version, + ifelse(is.null(current_version), "NONE", current_version), + status)) + } + + log_message("=== END PACKAGE REPORT ===") +} + +#' Main function to run complete package management +run_package_manager <- function() { + # Initialize log + cat("", file = LOG_FILE) # Clear log file + log_message("SmartCane Project - Package Manager Started") + log_message(sprintf("Working directory: %s", getwd())) + + # Step 1: Initialize renv + initialize_renv() + + # Step 2: Generate initial report + log_message("\n=== INITIAL STATE ===") + generate_package_report() + + # Step 3: Manage packages + log_message("\n=== PACKAGE INSTALLATION/UPDATES ===") + success <- manage_packages() + + # Step 4: Update lockfile if successful + if (success) { + update_lockfile() + } + + # Step 5: Generate final report + log_message("\n=== FINAL STATE ===") + generate_package_report() + + # Summary + end_time <- Sys.time() + duration <- round(as.numeric(difftime(end_time, START_TIME, units = "secs")), 2) + + log_message(sprintf("Package management completed in %s seconds", duration)) + log_message(sprintf("Log saved to: %s", LOG_FILE)) + + if (success) { + log_message("🎉 All packages successfully managed!", "SUCCESS") + log_message("📋 Next steps:") + log_message(" 1. Test your R scripts to ensure everything works") + log_message(" 2. Commit renv.lock to version control") + log_message(" 3. Share this script with your team") + } else { + log_message("⚠️ Some issues occurred. Check the log for details.", "WARNING") + log_message("💡 You may need to:") + log_message(" 1. Update R to a newer version") + log_message(" 2. Install system dependencies") + log_message(" 3. Check your internet connection") + } + + return(success) +} + +# ============================================================================= +# EXECUTION +# ============================================================================= + +# Only run if script is sourced directly (not when loaded as module) +if (!exists("PACKAGE_MANAGER_LOADED")) { + PACKAGE_MANAGER_LOADED <- TRUE + + cat("🚀 SmartCane Package Manager\n") + cat("============================\n") + cat("This will check and install/update all required R packages.\n") + cat("Log file:", LOG_FILE, "\n\n") + + # Ask for confirmation + response <- readline("Continue? (y/N): ") + if (tolower(substr(response, 1, 1)) == "y") { + result <- run_package_manager() + + if (result) { + cat("\n✅ Package management completed successfully!\n") + } else { + cat("\n❌ Package management completed with errors. Check the log.\n") + } + } else { + cat("❌ Package management cancelled.\n") + } +} diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000..4607526 --- /dev/null +++ b/renv.lock @@ -0,0 +1,7385 @@ +{ + "R": { + "Version": "4.4.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://packagemanager.posit.co/cran/latest" + } + ] + }, + "Packages": { + "CAST": { + "Package": "CAST", + "Version": "1.0.3", + "Source": "Repository", + "Type": "Package", + "Title": "'caret' Applications for Spatial-Temporal Models", + "Authors@R": "c(person(\"Hanna\", \"Meyer\", email = \"hanna.meyer@uni-muenster.de\", role = c(\"cre\", \"aut\")), person(\"Carles\", \"Milà\", role = c(\"aut\")), person(\"Marvin\", \"Ludwig\", role = c(\"aut\")), person(\"Jan\", \"Linnenbrink\", role = c(\"aut\")), person(\"Fabian\", \"Schumacher\", role = c(\"aut\")), person(\"Philipp\", \"Otto\", role = c(\"ctb\")), person(\"Chris\", \"Reudenbach\", role = c(\"ctb\")), person(\"Thomas\", \"Nauss\", role = c(\"ctb\")), person(\"Edzer\", \"Pebesma\", role = c(\"ctb\")), person(\"Jakub\", \"Nowosad\", role = c(\"ctb\")))", + "Author": "Hanna Meyer [cre, aut], Carles Milà [aut], Marvin Ludwig [aut], Jan Linnenbrink [aut], Fabian Schumacher [aut], Philipp Otto [ctb], Chris Reudenbach [ctb], Thomas Nauss [ctb], Edzer Pebesma [ctb], Jakub Nowosad [ctb]", + "Maintainer": "Hanna Meyer ", + "Description": "Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) ; Meyer et al. (2019) ; Meyer and Pebesma (2021) ; Milà et al. (2022) ; Meyer and Pebesma (2022) ; Linnenbrink et al. (2023) ; Schumacher et al. (2024) . The package is described in detail in Meyer et al. (2024) .", + "License": "GPL (>= 2)", + "URL": "https://github.com/HannaMeyer/CAST, https://hannameyer.github.io/CAST/", + "Encoding": "UTF-8", + "LazyData": "false", + "Depends": [ + "R (>= 4.1.0)" + ], + "BugReports": "https://github.com/HannaMeyer/CAST/issues/", + "Imports": [ + "caret", + "stats", + "utils", + "ggplot2", + "graphics", + "FNN", + "plyr", + "zoo", + "methods", + "grDevices", + "data.table", + "sf", + "forcats", + "twosamples", + "terra", + "sp" + ], + "Suggests": [ + "doParallel", + "lubridate", + "randomForest", + "knitr", + "geodata", + "mapview", + "rmarkdown", + "scales", + "parallel", + "gridExtra", + "viridis", + "stars", + "scam", + "rnaturalearth", + "MASS", + "RColorBrewer", + "tmap", + "PCAmixdata", + "gower", + "clustMixType", + "testthat (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.3", + "Source": "Repository", + "Title": "R Database Interface", + "Date": "2024-06-02", + "Authors@R": "c( person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\") )", + "Description": "A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.", + "License": "LGPL (>= 2.1)", + "URL": "https://dbi.r-dbi.org, https://github.com/r-dbi/DBI", + "BugReports": "https://github.com/r-dbi/DBI/issues", + "Depends": [ + "methods", + "R (>= 3.0.0)" + ], + "Suggests": [ + "arrow", + "blob", + "covr", + "DBItest", + "dbplyr", + "downlit", + "dplyr", + "glue", + "hms", + "knitr", + "magrittr", + "nanoarrow (>= 0.3.0.1)", + "RMariaDB", + "rmarkdown", + "rprojroot", + "RSQLite (>= 1.1-2)", + "testthat (>= 3.0.0)", + "vctrs", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "false", + "Config/Needs/check": "r-dbi/DBItest", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Config/Needs/website": "r-dbi/DBItest, r-dbi/dbitemplate, adbi, AzureKusto, bigrquery, DatabaseConnector, dittodb, duckdb, implyr, lazysf, odbc, pool, RAthena, IMSMWU/RClickhouse, RH2, RJDBC, RMariaDB, RMySQL, RPostgres, RPostgreSQL, RPresto, RSQLite, sergeant, sparklyr, withr", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "R Special Interest Group on Databases (R-SIG-DB) [aut], Hadley Wickham [aut], Kirill Müller [aut, cre] (), R Consortium [fnd]", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "FNN": { + "Package": "FNN", + "Version": "1.1.4.1", + "Source": "Repository", + "Date": "2023-12-31", + "Title": "Fast Nearest Neighbor Search Algorithms and Applications", + "Authors@R": "c(person(\"Alina\", \"Beygelzimer\", role = \"aut\", comment = \"cover tree library\"), person(\"Sham\", \"Kakadet\", role = \"aut\", comment = \"cover tree library\"), person(\"John\", \"Langford\", role = \"aut\", comment = \"cover tree library\"), person(\"Sunil\", \"Arya\", role = \"aut\", comment = \"ANN library 1.1.2 for the kd-tree approach\"), person(\"David\", \"Mount\", role = \"aut\", comment = \"ANN library 1.1.2 for the kd-tree approach\"), person(\"Shengqiao\", \"Li\", role = c(\"aut\", \"cre\"), email = \"lishengqiao@yahoo.com\"))", + "Copyright": "ANN Copyright (c) 1997-2010 University of Maryland and Sunil Arya and David Mount. All Rights Reserved.", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "chemometrics", + "mvtnorm" + ], + "Description": "Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.", + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Author": "Alina Beygelzimer [aut] (cover tree library), Sham Kakadet [aut] (cover tree library), John Langford [aut] (cover tree library), Sunil Arya [aut] (ANN library 1.1.2 for the kd-tree approach), David Mount [aut] (ANN library 1.1.2 for the kd-tree approach), Shengqiao Li [aut, cre]", + "Maintainer": "Shengqiao Li " + }, + "KernSmooth": { + "Package": "KernSmooth", + "Version": "2.23-24", + "Source": "Repository", + "Priority": "recommended", + "Date": "2024-05-16", + "Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)", + "Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"Matt.Wand@uts.edu.au\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"ripley@stats.ox.ac.uk\", comment = \"R port and updates\"))", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Depends": [ + "R (>= 2.5.0)", + "stats" + ], + "Suggests": [ + "MASS", + "carData" + ], + "Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. 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This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "License": "MIT + file LICENSE", + "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", + "BugReports": "https://github.com/tidymodels/broom/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "backports", + "cli", + "dplyr (>= 1.0.0)", + "generics (>= 0.0.2)", + "glue", + "lifecycle", + "purrr", + "rlang (>= 1.1.0)", + "stringr", + "tibble (>= 3.0.0)", + "tidyr (>= 1.0.0)" + ], + "Suggests": [ + "AER", + "AUC", + "bbmle", + "betareg (>= 3.2-1)", + "biglm", + "binGroup", + "boot", + "btergm (>= 1.10.6)", + "car (>= 3.1-2)", + "carData", + "caret", + 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Capabilities include: date-time parsing, formatting, arithmetic, extraction and updating of components, and rounding.", + "License": "MIT + file LICENSE", + "URL": "https://clock.r-lib.org, https://github.com/r-lib/clock", + "BugReports": "https://github.com/r-lib/clock/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "cli (>= 3.6.4)", + "lifecycle (>= 1.0.4)", + "rlang (>= 1.1.5)", + "tzdb (>= 0.5.0)", + "vctrs (>= 0.6.5)" + ], + "Suggests": [ + "covr", + "knitr", + "magrittr", + "pillar", + "rmarkdown", + "slider (>= 0.3.2)", + "testthat (>= 3.0.0)", + "withr" + ], + "LinkingTo": [ + "cpp11 (>= 0.5.2)", + "tzdb (>= 0.5.0)" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "lubridate, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" + ], + "Maintainer": "Luke Tierney ", + "URL": "https://gitlab.com/luke-tierney/codetools", + "License": "GPL", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-1", + "Source": "Repository", + "Date": "2024-07-26", + "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", + "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", + "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ + "graphics", + "grDevices", + "stats" + ], + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + }, + "cols4all": { + "Package": "cols4all", + "Version": "0.8", + "Source": "Repository", + "License": "GPL-3", + "Title": "Colors for all", + "Type": "Package", + "LazyLoad": "yes", + "Authors@R": "c( person(\"Martijn\", \"Tennekes\", email = \"mtennekes@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Marco\", \"Puts\", email = \"mputs@acm.org\", role = \"ctb\"), person(\"Achim\", \"Zeileis\", email = \"Achim.Zeileis@R-project.org\", role = \"ctb\"), person(\"Jakub\", \"Nowosad\", email = \"nowosad.jakub@gmail.com\", role = \"ctb\"), person(\"Robin\", \"Lovelace\", email = \"rob00x@gmail.com\", role = \"ctb\"), person(\"Helgasoft\", email = \"contact@helgasoft.com\", role = \"ctb\"), person(\"Matthew\", \"Petroff\", email = \"matthew@mpetroff.net\", role = \"ctb\"), person(\"Olivier\", \"Roy\", role = \"ctb\") )", + "Description": "Color palettes for all people, including those with color vision deficiency. Popular color palette series have been organized by type and have been scored on several properties such as color-blind-friendliness and fairness (i.e. do colors stand out equally?). Own palettes can also be loaded and analysed. Besides the common palette types (categorical, sequential, and diverging) it also includes cyclic and bivariate color palettes. Furthermore, a color for missing values is assigned to each palette.", + "Date": "2024-10-16", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "methods", + "grDevices", + "stats", + "abind", + "png", + "stringdist", + "colorspace (>= 2.1)", + "spacesXYZ" + ], + "Suggests": [ + "colorblindcheck", + "kableExtra", + "knitr", + "shiny", + "shinyjs", + "ggplot2", + "scales", + "rmarkdown", + "bookdown", + "bibtex", + "plotly" + ], + "URL": "https://mtennekes.github.io/cols4all/, https://github.com/mtennekes/cols4all", + "BugReports": "https://github.com/mtennekes/cols4all/issues", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Martijn Tennekes [aut, cre], Marco Puts [ctb], Achim Zeileis [ctb], Jakub Nowosad [ctb], Robin Lovelace [ctb], Helgasoft [ctb], Matthew Petroff [ctb], Olivier Roy [ctb]", + "Maintainer": "Martijn Tennekes ", + "Repository": "CRAN" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.5", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance CommonMark and Github Markdown Rendering in R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", + "Description": "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.", + "License": "BSD_2_clause + file LICENSE", + "URL": "https://docs.ropensci.org/commonmark/ https://ropensci.r-universe.dev/commonmark", + "BugReports": "https://github.com/r-lib/commonmark/issues", + "Suggests": [ + "curl", + "testthat", + "xml2" + ], + "RoxygenNote": "7.3.2", + "Language": "en-US", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), John MacFarlane [cph] (Author of cmark)", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "conflicted": { + "Package": "conflicted", + "Version": "1.2.0", + "Source": "Repository", + "Title": "An Alternative Conflict Resolution Strategy", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.", + "License": "MIT + file LICENSE", + "URL": "https://conflicted.r-lib.org/, https://github.com/r-lib/conflicted", + "BugReports": "https://github.com/r-lib/conflicted/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "memoise", + "rlang (>= 1.0.0)" + ], + "Suggests": [ + "callr", + "covr", + "dplyr", + "Matrix", + "methods", + "pkgload", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.2", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.", + "License": "MIT + file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "jsonlite", + "lazyeval", + "R6" + ], + "Suggests": [ + "shiny", + "ggplot2", + "testthat (>= 2.1.0)", + "sass", + "bslib" + ], + "URL": "https://rstudio.github.io/crosstalk/, https://github.com/rstudio/crosstalk", + "BugReports": "https://github.com/rstudio/crosstalk/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (), Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library)", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" + }, + "curl": { + "Package": "curl", + "Version": "6.2.2", + "Source": "Repository", + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Posit Software, PBC\", role = \"cph\"))", + "Description": "Bindings to 'libcurl' for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "data.table": { + "Package": "data.table", + "Version": "1.16.4", + "Source": "Repository", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), 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Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Ivan Krylov [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "CRAN" + }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.0", + "Source": "Repository", + "Type": "Package", + "Title": "A 'dplyr' Back End for Databases", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Edgar\", \"Ruiz\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.", + "License": "MIT + file LICENSE", + "URL": "https://dbplyr.tidyverse.org/, https://github.com/tidyverse/dbplyr", + "BugReports": "https://github.com/tidyverse/dbplyr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "blob (>= 1.2.0)", + "cli (>= 3.6.1)", + "DBI (>= 1.1.3)", + "dplyr (>= 1.1.2)", + "glue (>= 1.6.2)", + "lifecycle (>= 1.0.3)", + "magrittr", + "methods", + "pillar (>= 1.9.0)", + "purrr (>= 1.0.1)", + "R6 (>= 2.2.2)", + "rlang (>= 1.1.1)", + "tibble (>= 3.2.1)", + "tidyr (>= 1.3.0)", + "tidyselect (>= 1.2.1)", + "utils", + "vctrs (>= 0.6.3)", + "withr (>= 2.5.0)" + ], + "Suggests": [ + "bit64", + "covr", + "knitr", + "Lahman", + "nycflights13", + "odbc (>= 1.4.2)", + "RMariaDB (>= 1.2.2)", + "rmarkdown", + "RPostgres (>= 1.4.5)", + "RPostgreSQL", + "RSQLite (>= 2.3.1)", + "testthat (>= 3.1.10)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Encoding": "UTF-8", + "Language": "en-gb", + "RoxygenNote": "7.3.1", + "Collate": "'db-sql.R' 'utils-check.R' 'import-standalone-types-check.R' 'import-standalone-obj-type.R' 'utils.R' 'sql.R' 'escape.R' 'translate-sql-cut.R' 'translate-sql-quantile.R' 'translate-sql-string.R' 'translate-sql-paste.R' 'translate-sql-helpers.R' 'translate-sql-window.R' 'translate-sql-conditional.R' 'backend-.R' 'backend-access.R' 'backend-hana.R' 'backend-hive.R' 'backend-impala.R' 'verb-copy-to.R' 'backend-mssql.R' 'backend-mysql.R' 'backend-odbc.R' 'backend-oracle.R' 'backend-postgres.R' 'backend-postgres-old.R' 'backend-redshift.R' 'backend-snowflake.R' 'backend-spark-sql.R' 'backend-sqlite.R' 'backend-teradata.R' 'build-sql.R' 'data-cache.R' 'data-lahman.R' 'data-nycflights13.R' 'db-escape.R' 'db-io.R' 'db.R' 'dbplyr.R' 'explain.R' 'ident.R' 'import-standalone-s3-register.R' 'join-by-compat.R' 'join-cols-compat.R' 'lazy-join-query.R' 'lazy-ops.R' 'lazy-query.R' 'lazy-select-query.R' 'lazy-set-op-query.R' 'memdb.R' 'optimise-utils.R' 'pillar.R' 'progress.R' 'sql-build.R' 'query-join.R' 'query-select.R' 'query-semi-join.R' 'query-set-op.R' 'query.R' 'reexport.R' 'remote.R' 'rows.R' 'schema.R' 'simulate.R' 'sql-clause.R' 'sql-expr.R' 'src-sql.R' 'src_dbi.R' 'table-name.R' 'tbl-lazy.R' 'tbl-sql.R' 'test-frame.R' 'testthat.R' 'tidyeval-across.R' 'tidyeval.R' 'translate-sql.R' 'utils-format.R' 'verb-arrange.R' 'verb-compute.R' 'verb-count.R' 'verb-distinct.R' 'verb-do-query.R' 'verb-do.R' 'verb-expand.R' 'verb-fill.R' 'verb-filter.R' 'verb-group_by.R' 'verb-head.R' 'verb-joins.R' 'verb-mutate.R' 'verb-pivot-longer.R' 'verb-pivot-wider.R' 'verb-pull.R' 'verb-select.R' 'verb-set-ops.R' 'verb-slice.R' 'verb-summarise.R' 'verb-uncount.R' 'verb-window.R' 'zzz.R'", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Maximilian Girlich [aut], Edgar Ruiz [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "diagram": { + "Package": "diagram", + "Version": "1.6.5", + "Source": "Repository", + "Title": "Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams", + "Author": "Karline Soetaert ", + "Maintainer": "Karline Soetaert ", + "Depends": [ + "R (>= 2.01)", + "shape" + ], + "Imports": [ + "stats", + "graphics" + ], + "Description": "Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book \"A practical guide to ecological modelling - using R as a simulation platform\" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. 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This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. 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It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.", + "License": "MIT + file LICENSE", + "URL": "https://readr.tidyverse.org, https://github.com/tidyverse/readr", + "BugReports": "https://github.com/tidyverse/readr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.2.0)", + "clipr", + "crayon", + "hms (>= 0.4.1)", + "lifecycle (>= 0.2.0)", + "methods", + "R6", + "rlang", + "tibble", + "utils", + "vroom (>= 1.6.0)" + ], + "Suggests": [ + "covr", + "curl", + "datasets", + "knitr", + "rmarkdown", + "spelling", + "stringi", + "testthat (>= 3.2.0)", + "tzdb (>= 0.1.1)", + "waldo", + "withr", + "xml2" + ], + "LinkingTo": [ + "cpp11", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], Posit Software, PBC [cph, fnd], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.5", + "Source": "Repository", + "Title": "Read Excel Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = \"Copyright holder of all R code and all C/C++ code without explicit copyright attribution\"), person(\"Marcin\", \"Kalicinski\", role = c(\"ctb\", \"cph\"), comment = \"Author of included RapidXML code\"), person(\"Komarov Valery\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Christophe Leitienne\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Bob Colbert\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"David Hoerl\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Evan Miller\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\") )", + "Description": "Import excel files into R. Supports '.xls' via the embedded 'libxls' C library and '.xlsx' via the embedded 'RapidXML' C++ library . Works on Windows, Mac and Linux without external dependencies.", + "License": "MIT + file LICENSE", + "URL": "https://readxl.tidyverse.org, https://github.com/tidyverse/readxl", + "BugReports": "https://github.com/tidyverse/readxl/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cellranger", + "tibble (>= 2.0.1)", + "utils" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.1.6)", + "withr" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.0)", + "progress" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate, tidyverse", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Note": "libxls v1.6.3 c199d13", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Posit, PBC [cph, fnd] (Copyright holder of all R code and all C/C++ code without explicit copyright attribution), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Komarov Valery [ctb, cph] (Author of included libxls code), Christophe Leitienne [ctb, cph] (Author of included libxls code), Bob Colbert [ctb, cph] (Author of included libxls code), David Hoerl [ctb, cph] (Author of included libxls code), Evan Miller [ctb, cph] (Author of included libxls code)", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "recipes": { + "Package": "recipes", + "Version": "1.2.1", + "Source": "Repository", + "Title": "Preprocessing and Feature Engineering Steps for Modeling", + "Authors@R": "c( person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = \"aut\"), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A recipe prepares your data for modeling. 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Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. 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Calculate Correlated Color Temperature (CCT) and the Planckian and daylight loci. The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included. Three standard color difference metrics are included, plus the forward direction of the 'CIECAM02' color appearance model.", + "License": "GPL (>= 3)", + "LazyLoad": "yes", + "LazyData": "yes", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "logger" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "microbenchmark" + ], + "Enhances": [ + "colorSpec" + ], + "Repository": "CRAN", + "VignetteBuilder": "knitr", + "BuildVignettes": "yes", + "NeedsCompilation": "no", + "Author": "Glenn Davis [aut, cre]" + }, + "sparsevctrs": { + "Package": "sparsevctrs", + "Version": "0.3.2", + "Source": "Repository", + "Title": "Sparse Vectors for Use in Data Frames", + "Authors@R": "c( person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0679-1945\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides sparse vectors powered by ALTREP (Alternative Representations for R Objects) that behave like regular vectors, and can thus be used in data frames. Also provides tools to convert between sparse matrices and data frames with sparse columns and functions to interact with sparse vectors.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/sparsevctrs, https://r-lib.github.io/sparsevctrs/", + "BugReports": "https://github.com/r-lib/sparsevctrs/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "rlang (>= 1.1.0)", + "vctrs" + ], + "Suggests": [ + "knitr", + "Matrix", + "methods", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate, rmarkdown, lobstr, ggplot2, bench, tidyr, ggbeeswarm", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Emil Hvitfeldt [aut, cre] (), Davis Vaughan [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Emil Hvitfeldt ", + "Repository": "CRAN" + }, + "stars": { + "Package": "stars", + "Version": "0.6-8", + "Source": "Repository", + "Title": "Spatiotemporal Arrays, Raster and Vector Data Cubes", + "Authors@R": "c(person(given = \"Edzer\", family = \"Pebesma\", role = c(\"aut\", \"cre\"), email = \"edzer.pebesma@uni-muenster.de\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(given = \"Michael\", family = \"Sumner\", role = \"ctb\", comment=c(ORCID = \"0000-0002-2471-7511\")), person(given = \"Etienne\", family = \"Racine\", role = \"ctb\"), person(given = \"Adriano\", family = \"Fantini\", role = \"ctb\"), person(given = \"David\", family = \"Blodgett\", role = \"ctb\"), person(given = \"Krzysztof\", family = \"Dyba\", role = \"ctb\", comment=c(ORCID = \"0000-0002-8614-3816\")))", + "Description": "Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.", + "License": "Apache License", + "URL": "https://r-spatial.github.io/stars/, https://github.com/r-spatial/stars/", + "BugReports": "https://github.com/r-spatial/stars/issues/", + "Additional_repositories": "https://cran.uni-muenster.de/pebesma/", + "LazyData": "true", + "Depends": [ + "R (>= 3.3.0)", + "abind", + "sf (>= 1.0-19)" + ], + "Imports": [ + "methods", + "parallel", + "classInt (>= 0.4-1)", + "rlang", + "units" + ], + "Suggests": [ + "Cairo", + "OpenStreetMap", + "PCICt", + "RNetCDF (>= 1.8-2)", + "clue", + "covr", + "cubble (>= 0.3.0)", + "cubelyr", + "digest", + "dplyr (>= 0.7-0)", + "exactextractr", + "FNN", + "future.apply", + "ggforce", + "ggplot2", + "ggthemes", + "gstat", + "httr", + "jsonlite", + "knitr", + "lwgeom", + "maps", + "mapdata", + "ncdfgeom", + "ncmeta (>= 0.0.3)", + "pbapply", + "plm", + "randomForest", + "raster", + "rmarkdown", + "sp", + "spacetime", + "spatstat (>= 2.0-1)", + "spatstat.geom", + "starsdata", + "terra (>= 1.4-22)", + "testthat", + "tibble", + "tidyr", + "tsibble", + "viridis", + "xts", + "zoo" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aggregate.R' 'cubble.R' 'datasets.R' 'dimensions.R' 'extract.R' 'factors.R' 'geom.R' 'gt.R' 'init.R' 'intervals.R' 'mdim.R' 'mosaic.R' 'ncdf.R' 'ncproxy.R' 'OpenStreetMap.R' 'ops.R' 'plot.R' 'prcomp.R' 'proxy.R' 'rasterize.R' 'raster.R' 'read.R' 'rotate.R' 'sample.R' 'sf.R' 'spacetime.R' 'spatstat.R' 'sp.R' 'stars.R' 'subset.R' 'tidyverse.R' 'tile.R' 'transform.R' 'values.R' 'warp.R' 'write.R' 'xts.R'", + "NeedsCompilation": "no", + "Author": "Edzer Pebesma [aut, cre] (), Michael Sumner [ctb] (), Etienne Racine [ctb], Adriano Fantini [ctb], David Blodgett [ctb], Krzysztof Dyba [ctb] ()", + "Maintainer": "Edzer Pebesma ", + "Repository": "CRAN" + }, + "stringdist": { + "Package": "stringdist", + "Version": "0.9.15", + "Source": "Repository", + "Maintainer": "Mark van der Loo ", + "License": "GPL-3", + "Title": "Approximate String Matching, Fuzzy Text Search, and String Distance Functions", + "Type": "Package", + "LazyLoad": "yes", + "Authors@R": "c( person(\"Mark\", \"van der Loo\", role=c(\"aut\",\"cre\") , email=\"mark.vanderloo@gmail.com\" , comment= c(ORCID=\"0000-0002-9807-4686\")) , person(\"Jan\", \"van der Laan\", role=\"ctb\") , person(\"R Core Team\",\"\" , role=\"ctb\") , person(\"Nick\",\"Logan\" , role=\"ctb\") , person(\"Chris\",\"Muir\" , role=\"ctb\") , person(\"Johannes\", \"Gruber\" , role=\"ctb\") , person(\"Brian\",\"Ripley\" , role=\"ctb\"))", + "Description": "Implements an approximate string matching version of R's native 'match' function. Also offers fuzzy text search based on various string distance measures. Can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences. This package is built for speed and runs in parallel by using 'openMP'. An API for C or C++ is exposed as well. Reference: MPJ van der Loo (2014) .", + "Depends": [ + "R (>= 2.15.3)" + ], + "URL": "https://github.com/markvanderloo/stringdist", + "BugReports": "https://github.com/markvanderloo/stringdist/issues", + "Suggests": [ + "tinytest" + ], + "Imports": [ + "parallel" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Mark van der Loo [aut, cre] (), Jan van der Laan [ctb], R Core Team [ctb], Nick Logan [ctb], Chris Muir [ctb], Johannes Gruber [ctb], Brian Ripley [ctb]", + "Repository": "CRAN" + }, + "stringi": { + "Package": "stringi", + "Version": "1.8.4", + "Source": "Repository", + "Date": "2024-05-06", + "Title": "Fast and Portable Character String Processing Facilities", + "Description": "A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. Documentation about 'stringi' is provided via its website at and the paper by Gagolewski (2022, ).", + "URL": "https://stringi.gagolewski.com/, https://github.com/gagolews/stringi, https://icu.unicode.org/", + "BugReports": "https://github.com/gagolews/stringi/issues", + "SystemRequirements": "ICU4C (>= 61, optional)", + "Type": "Package", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "tools", + "utils", + "stats" + ], + "Biarch": "TRUE", + "License": "file LICENSE", + "Author": "Marek Gagolewski [aut, cre, cph] (), Bartek Tartanus [ctb], and others (stringi source code); Unicode, Inc. and others (ICU4C source code, Unicode Character Database)", + "Maintainer": "Marek Gagolewski ", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "License_is_FOSS": "yes", + "Repository": "CRAN" + }, + "stringr": { + "Package": "stringr", + "Version": "1.5.1", + "Source": "Repository", + "Title": "Simple, Consistent Wrappers for Common String Operations", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with \"NA\"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.", + "License": "MIT + file LICENSE", + "URL": "https://stringr.tidyverse.org, https://github.com/tidyverse/stringr", + "BugReports": "https://github.com/tidyverse/stringr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli", + "glue (>= 1.6.1)", + "lifecycle (>= 1.0.3)", + "magrittr", + "rlang (>= 1.0.0)", + "stringi (>= 1.5.3)", + "vctrs (>= 0.4.0)" + ], + "Suggests": [ + "covr", + "dplyr", + "gt", + "htmltools", + "htmlwidgets", + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre, cph], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "survival": { + "Package": "survival", + "Version": "3.7-0", + "Source": "Repository", + "Title": "Survival Analysis", + "Priority": "recommended", + "Date": "2024-06-01", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "Matrix", + "methods", + "splines", + "stats", + "utils" + ], + "LazyData": "Yes", + "LazyDataCompression": "xz", + "ByteCompile": "Yes", + "Authors@R": "c(person(c(\"Terry\", \"M\"), \"Therneau\", email=\"therneau.terry@mayo.edu\", role=c(\"aut\", \"cre\")), person(\"Thomas\", \"Lumley\", role=c(\"ctb\", \"trl\"), comment=\"original S->R port and R maintainer until 2009\"), person(\"Atkinson\", \"Elizabeth\", role=\"ctb\"), person(\"Crowson\", \"Cynthia\", role=\"ctb\"))", + "Description": "Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.", + "License": "LGPL (>= 2)", + "URL": "https://github.com/therneau/survival", + "NeedsCompilation": "yes", + "Author": "Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009), Atkinson Elizabeth [ctb], Crowson Cynthia [ctb]", + "Maintainer": "Terry M Therneau ", + "Repository": "CRAN" + }, + "sys": { + "Package": "sys", + "Version": "3.4.3", + "Source": "Repository", + "Type": "Package", + "Title": "Powerful and Reliable Tools for Running System Commands in R", + "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"ctb\"))", + "Description": "Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/sys", + "BugReports": "https://github.com/jeroen/sys/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.1.1", + "Suggests": [ + "unix (>= 1.4)", + "spelling", + "testthat" + ], + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Gábor Csárdi [ctb]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.2.2", + "Source": "Repository", + "Type": "Package", + "Title": "System Native Font Finding", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Jeroen\", \"Ooms\", , \"jeroen@berkeley.edu\", role = \"aut\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Devon\", \"Govett\", role = \"aut\", comment = \"Author of font-manager\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries on Windows, macOS and Linux for finding font files that can then be used further by e.g. graphic devices. The main use is intended to be from compiled code but 'systemfonts' also provides access from R.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/systemfonts, https://systemfonts.r-lib.org", + "BugReports": "https://github.com/r-lib/systemfonts/issues", + "Depends": [ + "R (>= 3.2.0)" + ], + "Suggests": [ + "covr", + "farver", + "graphics", + "knitr", + "rmarkdown", + "testthat (>= 2.1.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.1)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "fontconfig, freetype2", + "Config/Needs/website": "tidyverse/tidytemplate", + "Imports": [ + "grid", + "jsonlite", + "lifecycle", + "tools", + "utils" + ], + "Config/build/compilation-database": "true", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [aut, cre] (), Jeroen Ooms [aut] (), Devon Govett [aut] (Author of font-manager), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "terra": { + "Package": "terra", + "Version": "1.8-43", + "Source": "Repository", + "Type": "Package", + "Title": "Spatial Data Analysis", + "Date": "2025-04-03", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "parallel", + "tinytest", + "ncdf4", + "sf (>= 0.9-8)", + "deldir", + "XML", + "leaflet (>= 2.2.1)", + "htmlwidgets" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "methods", + "Rcpp (>= 1.0-10)" + ], + "SystemRequirements": "C++17, GDAL (>= 2.2.3), GEOS (>= 3.4.0), PROJ (>= 4.9.3), TBB, sqlite3", + "Encoding": "UTF-8", + "Language": "en-US", + "Maintainer": "Robert J. Hijmans ", + "Description": "Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).", + "License": "GPL (>=3)", + "URL": "https://rspatial.org/, https://rspatial.github.io/terra/", + "BugReports": "https://github.com/rspatial/terra/issues/", + "LazyLoad": "yes", + "Authors@R": "c( person(\"Robert J.\", \"Hijmans\", role=c(\"cre\", \"aut\"), email=\"r.hijmans@gmail.com\", comment=c(ORCID=\"0000-0001-5872-2872\")),\t\t\t person(\"Márcia\", \"Barbosa\", role=\"ctb\"), person(\"Roger\", \"Bivand\", role=\"ctb\", comment=c(ORCID=\"0000-0003-2392-6140\")), person(\"Andrew\", \"Brown\", role=\"ctb\"), person(\"Michael\", \"Chirico\", role=\"ctb\"), person(\"Emanuele\", \"Cordano\", role=\"ctb\",comment=c(ORCID=\"0000-0002-3508-5898\")), person(\"Krzysztof\", \"Dyba\", role=\"ctb\", comment=c(ORCID=\"0000-0002-8614-3816\")), person(\"Edzer\", \"Pebesma\", role=\"ctb\", comment=c(ORCID=\"0000-0001-8049-7069\")), person(\"Barry\", \"Rowlingson\", role=\"ctb\"), person(\"Michael D.\", \"Sumner\", role=\"ctb\"))", + "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev", + "Repository": "https://rspatial.r-universe.dev", + "RemoteUrl": "https://github.com/rspatial/terra", + "RemoteRef": "HEAD", + "RemoteSha": "de8828a3a6c418b6e8f435291171a817a512cb8a", + "NeedsCompilation": "yes", + "Author": "Robert J. 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Testing the hypothesis that two samples come from the same distribution using randomization to create p-values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, Anderson-Darling, Wasserstein, and DTS. The default test (two_sample) is based on the DTS test statistic, as it is the most powerful, and thus most useful to most users. The DTS test statistic builds on the Wasserstein distance by using a weighting scheme like that of Anderson-Darling. See the companion paper at or for details of that test statistic, and non-standard uses of the package (parallel for big N, weighted observations, one sample tests, etc). We also include the permutation scheme to make test building simple for others.", + "License": "GPL (>= 2)", + "Encoding": "UTF-8", + "LinkingTo": [ + "cpp11" + ], + "RoxygenNote": "7.2.3", + "URL": "https://twosampletest.com, https://github.com/cdowd/twosamples", + "BugReports": "https://github.com/cdowd/twosamples/issues", + "Suggests": [ + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Connor Dowd [aut, cre] ()", + "Maintainer": "Connor Dowd ", + "Repository": "CRAN" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.4.0", + "Source": "Repository", + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "units": { + "Package": "units", + "Version": "0.8-5", + "Source": "Repository", + "Title": "Measurement Units for R Vectors", + "Authors@R": "c(person(\"Edzer\", \"Pebesma\", role = c(\"aut\", \"cre\"), email = \"edzer.pebesma@uni-muenster.de\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(\"Thomas\", \"Mailund\", role = \"aut\", email = \"mailund@birc.au.dk\"), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"James\", \"Hiebert\", role = \"ctb\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", email = \"iucar@fedoraproject.org\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Thomas Lin\", \"Pedersen\", role = \"ctb\") )", + "Depends": [ + "R (>= 3.0.2)" + ], + "Imports": [ + "Rcpp" + ], + "LinkingTo": [ + "Rcpp (>= 0.12.10)" + ], + "Suggests": [ + "NISTunits", + "measurements", + "xml2", + "magrittr", + "pillar (>= 1.3.0)", + "dplyr (>= 1.0.0)", + "vctrs (>= 0.3.1)", + "ggplot2 (> 3.2.1)", + "testthat (>= 3.0.0)", + "vdiffr", + "knitr", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "Description": "Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion. Documentation about 'units' is provided in the paper by Pebesma, Mailund & Hiebert (2016, ), included in this package as a vignette; see 'citation(\"units\")' for details.", + "SystemRequirements": "udunits-2", + "License": "GPL-2", + "URL": "https://r-quantities.github.io/units/, https://github.com/r-quantities/units", + "BugReports": "https://github.com/r-quantities/units/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Edzer Pebesma [aut, cre] (), Thomas Mailund [aut], Tomasz Kalinowski [aut], James Hiebert [ctb], Iñaki Ucar [aut] (), Thomas Lin Pedersen [ctb]", + "Maintainer": "Edzer Pebesma ", + "Repository": "CRAN" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository", + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8", + "BugReports": "https://github.com/patperry/r-utf8/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. [cph, dtc] (Unicode Character Database)", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "uuid": { + "Package": "uuid", + "Version": "1.2-1", + "Source": "Repository", + "Title": "Tools for Generating and Handling of UUIDs", + "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.org, ), Theodore Ts'o [aut, cph] (libuuid)", + "Maintainer": "Simon Urbanek ", + "Authors@R": "c(person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.org\", ORCID=\"0000-0003-2297-1732\")), person(\"Theodore\",\"Ts'o\", email=\"tytso@thunk.org\", role=c(\"aut\",\"cph\"), comment=\"libuuid\"))", + "Depends": [ + "R (>= 2.9.0)" + ], + "Description": "Tools for generating and handling of UUIDs (Universally Unique Identifiers).", + "License": "MIT + file LICENSE", + "URL": "https://www.rforge.net/uuid", + "BugReports": "https://github.com/s-u/uuid/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository", + "Title": "Vector Helpers", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"data.table team\", role = \"cph\", comment = \"Radix sort based on data.table's forder() and their contribution to R's order()\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.", + "License": "MIT + file LICENSE", + "URL": "https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs", + "BugReports": "https://github.com/r-lib/vctrs/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "glue", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "bit64", + "covr", + "crayon", + "dplyr (>= 0.8.5)", + "generics", + "knitr", + "pillar (>= 1.4.4)", + "pkgdown (>= 2.0.1)", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble (>= 3.1.3)", + "waldo (>= 0.2.0)", + "withr", + "xml2", + "zeallot" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-GB", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Lionel Henry [aut], Davis Vaughan [aut, cre], data.table team [cph] (Radix sort based on data.table's forder() and their contribution to R's order()), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.", + "License": "MIT + file LICENSE", + "URL": "https://vroom.r-lib.org, https://github.com/tidyverse/vroom", + "BugReports": "https://github.com/tidyverse/vroom/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bit64", + "cli (>= 3.2.0)", + "crayon", + "glue", + "hms", + "lifecycle (>= 1.0.3)", + "methods", + "rlang (>= 0.4.2)", + "stats", + "tibble (>= 2.0.0)", + "tidyselect", + "tzdb (>= 0.1.1)", + "vctrs (>= 0.2.0)", + "withr" + ], + "Suggests": [ + "archive", + "bench (>= 1.1.0)", + "covr", + "curl", + "dplyr", + "forcats", + "fs", + "ggplot2", + "knitr", + "patchwork", + "prettyunits", + "purrr", + "rmarkdown", + "rstudioapi", + "scales", + "spelling", + "testthat (>= 2.1.0)", + "tidyr", + "utils", + "waldo", + "xml2" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.0)", + "progress (>= 1.2.1)", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "nycflights13, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Copyright": "file COPYRIGHTS", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3.9000", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "warp": { + "Package": "warp", + "Version": "0.2.1", + "Source": "Repository", + "Title": "Group Dates", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tooling to group dates by a variety of periods including: yearly, monthly, by second, by week of the month, and more. The groups are defined in such a way that they also represent the distance between dates in terms of the period. This extracts valuable information that can be used in further calculations that rely on a specific temporal spacing between observations.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/DavisVaughan/warp, https://davisvaughan.github.io/warp/", + "BugReports": "https://github.com/DavisVaughan/warp/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "withr": { + "Package": "withr", + "Version": "3.0.2", + "Source": "Repository", + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" + }, + "wk": { + "Package": "wk", + "Version": "0.9.4", + "Source": "Repository", + "Title": "Lightweight Well-Known Geometry Parsing", + "Authors@R": "c( person(given = \"Dewey\", family = \"Dunnington\", role = c(\"aut\", \"cre\"), email = \"dewey@fishandwhistle.net\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(given = \"Edzer\", family = \"Pebesma\", role = c(\"aut\"), email = \"edzer.pebesma@uni-muenster.de\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(given = \"Anthony\", family = \"North\", email = \"anthony.jl.north@gmail.com\", role = c(\"ctb\")) )", + "Maintainer": "Dewey Dunnington ", + "Description": "Provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are useful in R only if the information they contain can be accessed in R, for which high-performance functions are provided here.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Suggests": [ + "testthat (>= 3.0.0)", + "vctrs (>= 0.3.0)", + "sf", + "tibble", + "readr" + ], + "URL": "https://paleolimbot.github.io/wk/, https://github.com/paleolimbot/wk", + "BugReports": "https://github.com/paleolimbot/wk/issues", + "Config/testthat/edition": "3", + "Depends": [ + "R (>= 2.10)" + ], + "LazyData": "true", + "NeedsCompilation": "yes", + "Author": "Dewey Dunnington [aut, cre] (), Edzer Pebesma [aut] (), Anthony North [ctb]", + "Repository": "CRAN" + }, + "xfun": { + "Package": "xfun", + "Version": "0.52", + "Source": "Repository", + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "grDevices", + "stats", + "tools" + ], + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown (>= 0.4)", + "commonmark", + "knitr (>= 1.50)", + "remotes", + "pak", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (, https://yihui.org), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository", + "Title": "Parse XML", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Foundation\", role = \"ctb\", comment = \"Copy of R-project homepage cached as example\") )", + "Description": "Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org/, https://github.com/r-lib/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "cli", + "methods", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Jim Hester [aut], Jeroen Ooms [aut], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Date": "2019-04-08", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott ", + "Imports": [ + "stats", + "utils" + ], + "Suggests": [ + "knitr", + "plm", + "zoo", + "survival" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "CRAN", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-13", + "Source": "Repository", + "Date": "2025-02-20", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.0.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + } + } +} diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..90b251c --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1334 @@ + +local({ + + # the requested version of renv + version <- "1.1.4" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix_default <- function() { + + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() + + # build list of path components + components <- c(version, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + + expected <- description[["RemoteSha"]] + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(project, libpath, version) + } + + renv_bootstrap_run <- function(project, libpath, version) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = project)) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + + # arrays + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + + # maps + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + + } + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) + } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) + renv_json_read_remap(result, patterns) + + } + + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000..ffdbb32 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +}