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/.github/workflows/quarto.yaml b/.github/workflows/quarto.yaml new file mode 100644 index 0000000..ac28956 --- /dev/null +++ b/.github/workflows/quarto.yaml @@ -0,0 +1,54 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help + +on: + workflow_dispatch: + push: + branches: main + +name: quarto + +jobs: + quarto: + # run on mac - generally faster + runs-on: ubuntu-latest + timeout-minutes: 120 + permissions: + contents: write + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + RSPM: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" + steps: + - uses: actions/checkout@v3 + - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - name: Install spatial dependencies + run: sudo apt-get install libgdal-dev libproj-dev libgeos-dev libudunits2-dev netcdf-bin + + - name: Install dependencies + run: | + install.packages("renv") + renv::restore() + shell: Rscript {0} + + - name: Set up Quarto + uses: quarto-dev/quarto-actions/setup@v2 + + - name: Render Quarto Project + uses: quarto-dev/quarto-actions/render@v2 + with: + path: ./book/ + + - name: Render and Publish + uses: quarto-dev/quarto-actions/publish@v2 + with: + path: ./book/ + target: gh-pages + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..83ff7c2 --- /dev/null +++ b/.gitignore @@ -0,0 +1,7 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata + +/.quarto/ +_book/ \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..8e73bad --- /dev/null +++ b/LICENSE @@ -0,0 +1,26 @@ +All contents are Copyright (c) to BlueGreen Labs (BV) 2023. + +For the WebR dynamic R tooling we relied on community input by +Ethan White under an MIT license as specified below. + +MIT License + +Copyright (c) 2023 Ethan White + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000..07f21e9 --- /dev/null +++ b/README.md @@ -0,0 +1,3 @@ +# R book template + +A quarto project template to use for courses and other documentation produced by the GECO group. Based on the BlueGreen Labs template by Koen Hufkens. diff --git a/R_book_template.Rproj b/R_book_template.Rproj new file mode 100644 index 0000000..8e3c2eb --- /dev/null +++ b/R_book_template.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000..29cfdeb --- /dev/null +++ b/renv.lock @@ -0,0 +1,2039 @@ +{ + "R": { + "Version": "4.3.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "DBI": { + "Package": "DBI", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "065ae649b05f1ff66bb0c793107508f5", + "Requirements": [] + }, + "KernSmooth": { + "Package": "KernSmooth", + "Version": "2.23-22", + "Source": "Repository", + "Repository": "CRAN", 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"stringr", + "tibble", + "tidyselect", + "vctrs" + ] + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "829f27b9c4919c16b593794a6344d6c0", + "Requirements": [ + "cli", + "glue", + "lifecycle", + "rlang", + "vctrs", + "withr" + ] + }, + "tidyverse": { + "Package": "tidyverse", + "Version": "2.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c328568cd14ea89a83bd4ca7f54ae07e", + "Requirements": [ + "broom", + "cli", + "conflicted", + "dbplyr", + "dplyr", + "dtplyr", + "forcats", + "ggplot2", + "googledrive", + "googlesheets4", + "haven", + "hms", + "httr", + "jsonlite", + "lubridate", + "magrittr", + "modelr", + "pillar", + "purrr", + "ragg", + "readr", + "readxl", + "reprex", + "rlang", + "rstudioapi", + "rvest", + "stringr", + "tibble", + "tidyr", + "xml2" + ] + }, + "timeDate": { + "Package": "timeDate", + "Version": "4041.110", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c5e48e8ac24d4472ddb122bcdeb011ad", + "Requirements": [] + }, + "timechange": { + "Package": "timechange", + "Version": "0.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c5f3c201b931cd6474d17d8700ccb1c8", + "Requirements": [ + "cpp11" + ] + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.48", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8f96d229b7311beb32b94cf413b13f84", + "Requirements": [ + "xfun" + ] + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f561504ec2897f4d46f0c7657e488ae1", + "Requirements": [ + "cpp11" + ] + }, + "units": { + "Package": "units", + "Version": "0.8-5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "119d19da480e873f72241ff6962ffd83", + "Requirements": [ + "Rcpp" + ] + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "62b65c52671e6665f803ff02954446e9", + "Requirements": [] + }, + "uuid": { + "Package": "uuid", + "Version": "1.2-1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "34e965e62a41fcafb1ca60e9b142085b", + "Requirements": [] + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "266c1ca411266ba8f365fcc726444b87", + "Requirements": [ + "cli", + "glue", + "lifecycle", + "rlang" + ] + }, + "vip": { + "Package": "vip", + "Version": "0.4.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4bfee1f7181f71d552a4b63485f8fc25", + "Requirements": [ + "foreach", + "ggplot2", + "tibble", + "yardstick" + ] + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c826c7c4241b6fc89ff55aaea3fa7491", + "Requirements": [] + }, + "visdat": { + "Package": "visdat", + "Version": "0.6.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "aa0c558f21cab0196eea9b51433f2c0e", + "Requirements": [ + "cli", + "dplyr", + "forcats", + "ggplot2", + "glue", + "magrittr", + "purrr", + "readr", + "scales", + "tibble", + "tidyr" + ] + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "390f9315bc0025be03012054103d227c", + "Requirements": [ + "bit64", + "cli", + "cpp11", + "crayon", + "glue", + "hms", + "lifecycle", + "progress", + "rlang", + "tibble", + "tidyselect", + "tzdb", + "vctrs", + "withr" + ] + }, + "warp": { + "Package": "warp", + "Version": "0.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fea474d578b1cbcb696ae6ac8bdcc439", + "Requirements": [] + }, + "withr": { + "Package": "withr", + "Version": "2.5.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4b25e70111b7d644322e9513f403a272", + "Requirements": [] + }, + "wk": { + "Package": "wk", + "Version": "0.9.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9ca478d7cb1450b42dcb8af2ea5681cc", + "Requirements": [] + }, + "xfun": { + "Package": "xfun", + "Version": "0.41", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "460a5e0fe46a80ef87424ad216028014", + "Requirements": [] + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61", + "Requirements": [ + "cli", + "rlang" + ] + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0d0056cc5383fbc240ccd0cb584bf436", + "Requirements": [] + }, + "yardstick": { + "Package": "yardstick", + "Version": "1.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9ce4117141b326c4fffc7c42e56e0f88", + "Requirements": [ + "cli", + "dplyr", + "generics", + "hardhat", + "lifecycle", + "rlang", + "tibble", + "tidyselect", + "vctrs", + "withr" + ] + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..019b5a6 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,994 @@ + +local({ + + # the requested version of renv + version <- "0.16.0" + + # the project directory + project <- getwd() + + # 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) + + # next, check environment variables + # TODO: 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 + + }) + + if (!enabled) + 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 + `%||%` <- function(x, y) { + if (is.environment(x) || length(x)) x else y + } + + bootstrap <- function(version, library) { + + # attempt to download renv + tarball <- tryCatch(renv_bootstrap_download(version), error = identity) + if (inherits(tarball, "error")) + stop("failed to download renv ", version) + + # now attempt to install + status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) + if (inherits(status, "error")) + stop("failed to install renv ", version) + + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) + return(repos) + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # if we're testing, re-use the test repositories + if (renv_bootstrap_tests_running()) + return(getOption("renv.tests.repos")) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- getOption( + "renv.repos.cran", + "https://cloud.r-project.org" + ) + + # 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$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + # if the renv version number has 4 components, assume it must + # be retrieved via github + nv <- numeric_version(version) + components <- unclass(nv)[[1]] + + # if this appears to be a development version of 'renv', we'll + # try to restore from github + dev <- length(components) == 4L + + # begin collecting different methods for finding renv + methods <- c( + renv_bootstrap_download_tarball, + if (dev) + renv_bootstrap_download_github + else c( + renv_bootstrap_download_cran_latest, + renv_bootstrap_download_cran_archive + ) + ) + + for (method in methods) { + path <- tryCatch(method(version), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("failed to download renv ", version) + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + args$headers <- renv_bootstrap_download_custom_headers(url) + + 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 + + message("* Downloading renv ", version, " ... ", appendLF = FALSE) + + 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")) { + message("FAILED") + return(FALSE) + } + + # report success and return + message("OK (downloaded ", type, ")") + 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$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + message("* Downloading renv ", version, " ... ", appendLF = FALSE) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) { + message("OK") + return(destfile) + } + + } + + message("FAILED") + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + info <- file.info(tarball, extra_cols = FALSE) + if (identical(info$isdir, TRUE)) { + 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() + + } + + fmt <- "* Bootstrapping with tarball at path '%s'." + msg <- sprintf(fmt, tarball) + message(msg) + + tarball + + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + 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(pat)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + 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) + } + + message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) + + 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)) { + message("FAILED") + return(FALSE) + } + + message("OK") + return(destfile) + + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + message("* Installing renv ", version, " ... ", appendLF = FALSE) + dir.create(library, showWarnings = FALSE, recursive = TRUE) + + # 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)) + ) + + output <- system2(r, args, stdout = TRUE, stderr = TRUE) + message("Done!") + + # check for successful install + status <- attr(output, "status") + if (is.numeric(status) && !identical(status, 0L)) { + header <- "Error installing renv:" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- c(header, lines, output) + writeLines(text, con = stderr()) + } + + status + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # 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) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$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) { + + loadedversion <- utils::packageDescription("renv", fields = "Version") + if (version == loadedversion) + return(TRUE) + + # assume four-component versions are from GitHub; three-component + # versions are from CRAN + components <- strsplit(loadedversion, "[.-]")[[1]] + remote <- if (length(components) == 4L) + paste("rstudio/renv", loadedversion, sep = "@") + else + paste("renv", loadedversion, sep = "@") + + fmt <- paste( + "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.", + sep = "\n" + ) + + msg <- sprintf(fmt, loadedversion, version, remote) + warning(msg, call. = FALSE) + + FALSE + + } + + 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) + + # 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_json_read <- function(file = NULL, text = NULL) { + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) + renv_json_read_jsonlite(file, text) + else + renv_json_read_default(file, text) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% read(file), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% read(file), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_remap(json[[i]], map)) + } + } + + json + + } + + # 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) + + # attempt to load + if (renv_bootstrap_load(project, libpath, version)) + return(TRUE) + + # load failed; inform user we're about to bootstrap + prefix <- paste("# Bootstrapping renv", version) + postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") + header <- paste(prefix, postfix) + message(header) + + # 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)) { + message("* Successfully installed and loaded renv ", version, ".") + return(renv::load()) + } + + # 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) + +}) diff --git a/renv/settings.dcf b/renv/settings.dcf new file mode 100644 index 0000000..169d82f --- /dev/null +++ b/renv/settings.dcf @@ -0,0 +1,10 @@ +bioconductor.version: +external.libraries: +ignored.packages: +package.dependency.fields: Imports, Depends, LinkingTo +r.version: +snapshot.type: implicit +use.cache: TRUE +vcs.ignore.cellar: TRUE +vcs.ignore.library: TRUE +vcs.ignore.local: TRUE diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000..2472d63 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": [], + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": [], + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +}