diff --git a/.Rprofile b/.Rprofile index 2c3ad5185..b574ba4d7 100644 --- a/.Rprofile +++ b/.Rprofile @@ -18,3 +18,16 @@ options( renv.config.sandbox.enabled = FALSE, renv.config.auto.snapshot = FALSE ) + +if(interactive()){ + cat( + "", + "This project uses different renv profiles for different operations", + "You should be on the default profile if you are contributing a blogpost", + " - `renv::activate('json')` enables profile with packages for json validation", + " - `renv::activate('production')` enables profile with packages needed to build the website", + " - `renv::activate('dev')` enables profile with all packages working locally on the website", + "", + sep="\n" + ) +} diff --git a/.github/workflows/build.yaml b/.github/workflows/build-preview.yaml similarity index 97% rename from .github/workflows/build.yaml rename to .github/workflows/build-preview.yaml index 379ea7d98..319c236a5 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build-preview.yaml @@ -38,7 +38,7 @@ env: jobs: build: name: Build site - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest env: hugobd: public on_fork: ${{ github.event.pull_request.head.repo.fork == true }} @@ -72,10 +72,12 @@ jobs: uses: r-lib/actions/setup-r@v2 with: r-version: '4.3.0' - + + - name: Serup renv + uses: r-lib/actions/setup-renv@v2 + - name: Populate untranslated pages run: | - rm .Rprofile # avoid starting renv Rscript scripts/missing_translations.R - name: Site data - Clean folders @@ -160,7 +162,7 @@ jobs: run: | npm install netlify-cli -g netlify deploy \ - --alias ${{ env.netalias }} \ + --alias=${{ env.netalias }} \ --dir=${{ env.hugobd }} - uses: actions/github-script@v6 diff --git a/.github/workflows/build_production.yaml b/.github/workflows/build-production.yaml similarity index 89% rename from .github/workflows/build_production.yaml rename to .github/workflows/build-production.yaml index 2ceeedf7e..fbeb5c2f0 100644 --- a/.github/workflows/build_production.yaml +++ b/.github/workflows/build-production.yaml @@ -15,9 +15,9 @@ concurrency: jobs: build: name: Build site - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest env: - RENV_PROFILE: "dev" + RENV_PROFILE: "production" RENV_CONFIG_SANDBOX_ENABLED: FALSE hugobd: public steps: @@ -27,7 +27,7 @@ jobs: echo "hugovr=$ver" >> $GITHUB_ENV - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 2 @@ -40,37 +40,38 @@ jobs: uses: r-lib/actions/setup-r@v2 with: r-version: '4.3.0' - + + - name: Serup renv + uses: r-lib/actions/setup-renv@v2 + - name: Populate untranslated pages run: | - rm .Rprofile # avoid starting renv Rscript scripts/missing_translations.R - name: Site data - Clean folders run: rm -r data/directory data/rblogs - name: Site data - DIRECTORY - Get - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: rladies/directory ssh-key: ${{ secrets.ssh_directoryy_repo }} path: tmpd/dir - - name: Site data - DIRECTORY - Move run: | cp -r tmpd/dir/data/json data/directory cp -r tmpd/dir/data/img/* assets/directory - name: Site data - Meetup - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: rladies/meetup_archive ssh-key: ${{ secrets.MEETUP_ARCHIVE_KEY}} path: tmpd/mtp - name: Site data - Get blogs list - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: rladies/awesome-rladies-blogs ssh-key: ${{ secrets.RLADIES_BLOGS_KEY}} diff --git a/.github/workflows/chapters-merge.yaml b/.github/workflows/chapters-merge.yaml index 891793b0b..1e7d99787 100644 --- a/.github/workflows/chapters-merge.yaml +++ b/.github/workflows/chapters-merge.yaml @@ -15,14 +15,14 @@ concurrency: jobs: merge: name: Merge chapters and meetup - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest env: RENV_PROFILE: "dev" RENV_CONFIG_SANDBOX_ENABLED: FALSE steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 2 @@ -40,7 +40,7 @@ jobs: uses: r-lib/actions/setup-renv@v2 - name: Site data - Meetup - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: rladies/meetup_archive ssh-key: ${{ secrets.MEETUP_ARCHIVE_KEY}} @@ -66,4 +66,4 @@ jobs: with: token: ${{ secrets.GLOBAL_GHA_PAT }} branch: main - \ No newline at end of file + diff --git a/.github/workflows/chapters-new.yaml b/.github/workflows/chapters-new.yaml index 73e08ad9a..63786498b 100644 --- a/.github/workflows/chapters-new.yaml +++ b/.github/workflows/chapters-new.yaml @@ -8,7 +8,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Print issue inputs env: diff --git a/.github/workflows/check-jsons.yaml b/.github/workflows/check-jsons.yaml index 77e0319d6..b11cde4d6 100644 --- a/.github/workflows/check-jsons.yaml +++ b/.github/workflows/check-jsons.yaml @@ -18,10 +18,10 @@ jobs: RENV_PROFILE: "json" RENV_CONFIG_SANDBOX_ENABLED: FALSE name: Check modified jsons - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 2 diff --git a/.gitignore b/.gitignore index 6e22c2d53..cef6a7090 100644 --- a/.gitignore +++ b/.gitignore @@ -56,12 +56,5 @@ tmp* ~/Library/Application Support/meetupr/meetupr-token.rds /var/folders/ws/1mjqfpsj3kv_b_z2091qkm600000gq/T//Rtmp4EPJ8U/fileecc479130cbd.rds -# default renv lock is here omitted -# we only use renv for development -# so make sure blog contributors dont add -# the lockfile when making their post -/renv.lock - .history .quarto - diff --git a/DESCRIPTION b/DESCRIPTION index 20cf7670b..35958d051 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,7 +10,7 @@ Authors@R: c( comment = c(ORCID = "0000-0002-5756-0223")) ) Encoding: UTF-8 -Imports: +Config/renv/profiles/default/dependencies: blogdown Config/renv/profiles/json/dependencies: jsonlite, @@ -18,8 +18,13 @@ Config/renv/profiles/json/dependencies: here, cli Config/renv/profiles/dev/dependencies: + blogdown, jsonlite, dplyr, here, tidyr, - cli + cli, + yaml +Config/renv/profiles/production/dependencies: + here, + yaml diff --git a/content/.gitignore b/content/.gitignore new file mode 100644 index 000000000..9feadd083 --- /dev/null +++ b/content/.gitignore @@ -0,0 +1,3 @@ +# ignore all renv related files and folders +**/renv.lock +**renv/ diff --git a/json/.Rprofile b/json/.Rprofile new file mode 100644 index 000000000..81b960f5c --- /dev/null +++ b/json/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/json/json.Rproj b/json/json.Rproj new file mode 100644 index 000000000..8e3c2ebc9 --- /dev/null +++ b/json/json.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/json/renv.lock b/json/renv.lock new file mode 100644 index 000000000..7e718152f --- /dev/null +++ b/json/renv.lock @@ -0,0 +1,23 @@ +{ + "R": { + "Version": "4.3.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "renv": { + "Package": "renv", + "Version": "1.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "41b847654f567341725473431dd0d5ab" + } + } +} diff --git a/json/renv/.gitignore b/json/renv/.gitignore new file mode 100644 index 000000000..0ec0cbba2 --- /dev/null +++ b/json/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/json/renv/activate.R b/json/renv/activate.R new file mode 100644 index 000000000..cb5401f93 --- /dev/null +++ b/json/renv/activate.R @@ -0,0 +1,1180 @@ + +local({ + + # the requested version of renv + version <- "1.0.3" + attr(version, "sha") <- NULL + + # the project directory + 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) + + # 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.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) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + 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$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + args$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 + + 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$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$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) + + 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_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) + } + + 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 <- 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, 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 + remote <- if (!is.null(description[["RemoteSha"]])) { + 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 = description[["RemoteSha"]] + ) + + 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" + ) + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + 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(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # 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 = getwd())) + } + + # 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 <- catch(renv_json_read_jsonlite(file, text)) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- catch(renv_json_read_default(file, text)) + 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 %||% 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) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/renv.lock b/renv.lock index 5b9f62ce5..9408f506b 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.2.0", + "Version": "4.3.0", "Repositories": [ { "Name": "ggseg", @@ -17,698 +17,15 @@ ] }, "Packages": { - "R6": { - "Package": 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"glue", - "lifecycle", - "rlang", - "vctrs", - "withr" - ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" - }, - "tinytex": { - "Package": "tinytex", - "Version": "0.42", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "xfun" - ], - "Hash": "7629c6c1540835d5248e6e7df265fa74" - }, - "utf8": { - "Package": "utf8", - "Version": "1.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "c9c462b759a5cc844ae25b5942654d13" - }, - "vctrs": { - "Package": "vctrs", - "Version": "0.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "rlang" - ], - "Hash": "970324f6572b4fd81db507b5d4062cb0" - }, - "withr": { - "Package": "withr", - "Version": "2.5.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "stats" - ], - "Hash": "c0e49a9760983e81e55cdd9be92e7182" - }, - "xfun": { - "Package": "xfun", - "Version": "0.36", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "stats", - "tools" - ], - "Hash": "f5baec54606751aa53ac9c0e05848ed6" - }, - "yaml": { - "Package": "yaml", - "Version": "2.3.5", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "458bb38374d73bf83b1bb85e353da200" + "Hash": "6523639dd021b32c3199a41cbe6db340" } } } diff --git a/renv/profile b/renv/profile index 38f8e886e..c44e75e79 100644 --- a/renv/profile +++ b/renv/profile @@ -1 +1 @@ -dev +production diff --git a/renv/profiles/dev/.renvignore b/renv/profiles/dev/.renvignore deleted file mode 100644 index ab14f0055..000000000 --- a/renv/profiles/dev/.renvignore +++ /dev/null @@ -1,2 +0,0 @@ -/content/ -/data/ diff --git a/renv/profiles/dev/renv.lock b/renv/profiles/dev/renv.lock index 35eabfeed..4c2b6603a 100644 --- a/renv/profiles/dev/renv.lock +++ b/renv/profiles/dev/renv.lock @@ -1,7 +1,15 @@ { "R": { - "Version": "4.3.0", + "Version": "4.3.2", "Repositories": [ + { + "Name": "ggseg", + "URL": "https://ggseg.r-universe.dev" + }, + { + "Name": "lcbc", + "URL": "https://lcbc-uio.r-universe.dev" + }, { "Name": "CRAN", "URL": "https://cloud.r-project.org" @@ -23,31 +31,18 @@ "Package": "Rcpp", "Version": "1.0.11", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "methods", "utils" ], "Hash": "ae6cbbe1492f4de79c45fce06f967ce8" }, - "V8": { - "Package": "V8", - "Version": "4.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Rcpp", - "curl", - "jsonlite", - "utils" - ], - "Hash": "85986a8a9f63af35ad24a022dfa48fdb" - }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R" ], @@ -125,7 +120,7 @@ "Package": "cli", "Version": "3.6.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "utils" @@ -139,21 +134,11 @@ "Repository": "CRAN", "Hash": "3f7d8664d7324406cd10cd650ad85e5f" }, - "curl": { - "Package": "curl", - "Version": "5.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "2118af9cb164c8d2dddc7b89eaf732d9" - }, "digest": { "Package": "digest", "Version": "0.6.33", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "utils" @@ -164,7 +149,7 @@ "Package": "dplyr", "Version": "1.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -187,7 +172,7 @@ "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "rlang" @@ -198,7 +183,7 @@ "Package": "evaluate", "Version": "0.21", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "methods" @@ -209,7 +194,7 @@ "Package": "fansi", "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", @@ -228,7 +213,7 @@ "Package": "fontawesome", "Version": "0.5.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "htmltools", @@ -240,7 +225,7 @@ "Package": "fs", "Version": "1.6.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods" @@ -283,7 +268,7 @@ "Package": "highr", "Version": "0.10", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "xfun" @@ -294,7 +279,7 @@ "Package": "htmltools", "Version": "0.5.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "base64enc", @@ -311,7 +296,7 @@ "Package": "httpuv", "Version": "1.6.11", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -326,7 +311,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "htmltools" ], @@ -336,27 +321,17 @@ "Package": "jsonlite", "Version": "1.8.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "methods" ], "Hash": "266a20443ca13c65688b2116d5220f76" }, - "jsonvalidate": { - "Package": "jsonvalidate", - "Version": "1.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "V8" - ], - "Hash": "cdc2843ef7f44f157198bb99aea7552d" - }, "knitr": { "Package": "knitr", "Version": "1.43", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "evaluate", @@ -383,7 +358,7 @@ "Package": "lifecycle", "Version": "1.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "cli", @@ -406,7 +381,7 @@ "Package": "memoise", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "cachem", "rlang" @@ -417,7 +392,7 @@ "Package": "mime", "Version": "0.12", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "tools" ], @@ -427,7 +402,7 @@ "Package": "pillar", "Version": "1.9.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "cli", "fansi", @@ -484,7 +459,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R" ], @@ -493,7 +468,12 @@ "renv": { "Package": "renv", "Version": "1.0.1", - "Source": "Repository" + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "6523639dd021b32c3199a41cbe6db340" }, "rlang": { "Package": "rlang", @@ -544,7 +524,7 @@ "Package": "sass", "Version": "0.4.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R6", "fs", @@ -572,7 +552,7 @@ "Package": "stringi", "Version": "1.7.12", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "stats", @@ -585,7 +565,7 @@ "Package": "stringr", "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "cli", @@ -602,7 +582,7 @@ "Package": "tibble", "Version": "3.2.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "fansi", @@ -621,7 +601,7 @@ "Package": "tidyr", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "cli", @@ -670,7 +650,7 @@ "Package": "utf8", "Version": "1.2.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], @@ -680,7 +660,7 @@ "Package": "vctrs", "Version": "0.6.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "cli", @@ -718,7 +698,7 @@ "Package": "yaml", "Version": "2.3.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0d0056cc5383fbc240ccd0cb584bf436" } } diff --git a/renv/profiles/dev/renv/settings.json b/renv/profiles/dev/renv/settings.json new file mode 100644 index 000000000..74c1d4bb8 --- /dev/null +++ b/renv/profiles/dev/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": "explicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/renv/profiles/json/.renvignore b/renv/profiles/json/.renvignore deleted file mode 100644 index 160cc4546..000000000 --- a/renv/profiles/json/.renvignore +++ /dev/null @@ -1,4 +0,0 @@ -/content/ -/data/ -/scripts/get_chapters.R -/scripts/missing_translations.R diff --git a/renv/profiles/json/renv.lock b/renv/profiles/json/renv.lock index 92432ecc8..0e756a650 100644 --- a/renv/profiles/json/renv.lock +++ b/renv/profiles/json/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.3.0", + "Version": "4.3.2", "Repositories": [ { "Name": "CRAN", @@ -11,18 +11,18 @@ "Packages": { "Rcpp": { "Package": "Rcpp", - "Version": "1.0.11", + "Version": "1.0.12", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "ae6cbbe1492f4de79c45fce06f967ce8" + "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" }, "V8": { "Package": "V8", - "Version": "4.3.2", + "Version": "4.4.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -31,28 +31,28 @@ "jsonlite", "utils" ], - "Hash": "85986a8a9f63af35ad24a022dfa48fdb" + "Hash": "435359b59b8a9b8f9235135da471ea3c" }, "cli": { "Package": "cli", - "Version": "3.6.1", + "Version": "3.6.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "89e6d8219950eac806ae0c489052048a" + "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" }, "curl": { "Package": "curl", - "Version": "5.0.1", + "Version": "5.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "2118af9cb164c8d2dddc7b89eaf732d9" + "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" }, "here": { "Package": "here", @@ -66,13 +66,13 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.7", + "Version": "1.8.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "266a20443ca13c65688b2116d5220f76" + "Hash": "e1b9c55281c5adc4dd113652d9e26768" }, "jsonvalidate": { "Package": "jsonvalidate", @@ -84,15 +84,25 @@ ], "Hash": "cdc2843ef7f44f157198bb99aea7552d" }, + "renv": { + "Package": "renv", + "Version": "1.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "41b847654f567341725473431dd0d5ab" + }, "rprojroot": { "Package": "rprojroot", - "Version": "2.0.3", + "Version": "2.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "1de7ab598047a87bba48434ba35d497d" + "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144" } } } diff --git a/renv/profiles/production/renv.lock b/renv/profiles/production/renv.lock new file mode 100644 index 000000000..1b5e06dc7 --- /dev/null +++ b/renv/profiles/production/renv.lock @@ -0,0 +1,50 @@ +{ + "R": { + "Version": "4.3.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "here": { + "Package": "here", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "rprojroot" + ], + "Hash": "24b224366f9c2e7534d2344d10d59211" + }, + "renv": { + "Package": "renv", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "6523639dd021b32c3199a41cbe6db340" + }, + "rprojroot": { + "Package": "rprojroot", + "Version": "2.0.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.8", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "29240487a071f535f5e5d5a323b7afbd" + } + } +} diff --git a/renv/profiles/production/renv/.gitignore b/renv/profiles/production/renv/.gitignore new file mode 100644 index 000000000..0ec0cbba2 --- /dev/null +++ b/renv/profiles/production/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/profiles/production/renv/settings.json b/renv/profiles/production/renv/settings.json new file mode 100644 index 000000000..74c1d4bb8 --- /dev/null +++ b/renv/profiles/production/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": "explicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/renv/settings.json b/renv/settings.json index 189febd96..fa6e46428 100644 --- a/renv/settings.json +++ b/renv/settings.json @@ -1,9 +1,14 @@ { + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], "package.dependency.fields": [ "Imports", "Depends", "LinkingTo" ], + "ppm.enabled": null, + "ppm.ignored.urls": [], "r.version": "4.3.0", "snapshot.type": "explicit", "use.cache": true, diff --git a/scripts/missing_translations.R b/scripts/missing_translations.R index 9b6dcf265..081954997 100644 --- a/scripts/missing_translations.R +++ b/scripts/missing_translations.R @@ -1,6 +1,7 @@ # Get all mds # Find all non-post content -content <- list.files("content","index", +library(here) +content <- list.files(here("content"),"index", recursive = TRUE, full.names = TRUE) content <- content[grepl("[.]md", content)] @@ -9,7 +10,7 @@ content <- content[grepl("[.]md", content)] dirs <- unique(dirname(content)) # Get the site languages -site_lang <- readLines("config/_default/languages.yaml") +site_lang <- readLines(here("config/_default/languages.yaml")) site_lang <- gsub(":", "", site_lang[grep("^[a-z]", site_lang)]) cat("Populating untranslated files:\n ") # Loop through dirs