From 096a7d5209f4a95b3aaf75ecfe7d91024c158cc8 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 14:55:53 +0000 Subject: [PATCH 01/43] renv --- .Rbuildignore | 2 ++ .Rprofile | 1 + DESCRIPTION | 8 +------- resources/rmarkdown/chunk07.png | Bin 70290 -> 70290 bytes 4 files changed, 4 insertions(+), 7 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 5e4a3338..0613275f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,4 @@ +^renv$ +^renv\.lock$ ^LICENSE\.md$ ^\.github$ diff --git a/.Rprofile b/.Rprofile index 0547dcc9..f2720dcd 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,3 +1,4 @@ +source("renv/activate.R") if (file.exists('~/.Rprofile')) sys.source('~/.Rprofile', envir = environment()) with_def <- (function() { diff --git a/DESCRIPTION b/DESCRIPTION index 679624bb..18a8ea58 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -55,7 +55,7 @@ Imports: ggplot2, cartography, import, - htmltools (>= 0.5.1), + htmltools, doremifasolData, readODS, kableExtra, @@ -65,7 +65,6 @@ Imports: sass, bslib, downlit, - utilitr, usethis, renv, remotes, @@ -103,9 +102,4 @@ Suggests: haven, rprojroot Remotes: - rstudio/htmltools@v0.5.1, - rstudio/sass, - yihui/xfun, - InseeFrLab/utilitr-template, - hadley/emo, InseeFrLab/doremifasolData@v0.2.0 diff --git a/resources/rmarkdown/chunk07.png b/resources/rmarkdown/chunk07.png index f152943b00fb156fd06c13f05b2f2a8f3109ad8c..6bffcc4a17383ddf4b6c35a495436bb58a6d6d65 100644 GIT binary patch delta 85 zcmbQVlx5OVmI-m3T!MV2qJc{UoEy`(rZd(HN*EgG8k&a~8e18gS{a&X8yHv_7-+ov X`Dyw;K}JcevXPq|{if>+F(v~57^)Yp delta 85 zcmbQVlx5OVmI-m3EK+Qm>XK?DZjI?%(;4dpB@9e-jZ8ue%&bg-$Wq(Dz{ Date: Thu, 17 Oct 2024 15:06:26 +0000 Subject: [PATCH 02/43] modify docker image --- Dockerfile | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index e501a492..30a8840e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,14 +2,11 @@ FROM inseefrlab/onyxia-rstudio:r4.3.2-2024.02.13 # R packages COPY ./DESCRIPTION /tmp/build_image/ -RUN Rscript -e "install.packages(c('xfun','knitr', 'insee', 'OECD', 'htmltools'))" -RUN Rscript -e "remotes::install_deps('/tmp/build_image', dependencies = TRUE, upgrade = FALSE)" -RUN Rscript -e "remotes::install_github('kevinushey/rex')" -RUN Rscript -e "remotes::install_github('inseefrlab/inseelocaldata')" +RUN Rscript -e "install.packages('renv')" RUN apt-get update \ && apt-get -qq install gnupg - + RUN sh -c 'echo "deb http://http.us.debian.org/debian stable main contrib non-free" >> /etc/apt/sources.list' \ && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138 \ && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9 \ From 1e655ed32d8af8e39b6997005e46f95b0bbfaced Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 15:07:07 +0000 Subject: [PATCH 03/43] restore --- .github/workflows/prod.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 49c32c5a..a0575e8e 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -6,7 +6,7 @@ on: branches: - main - master - - test + - renv jobs: docker: @@ -62,9 +62,7 @@ jobs: - name: Install dependencies run: | git config --global --add safe.directory /__w/utilitR/utilitR - Rscript -e "install.packages(c('remotes'))" - Rscript -e "remotes::install_github('rstudio/htmltools')" - Rscript -e "remotes::install_github('r-spatial/sf', dependencies = TRUE)" + Rscript -e "renv::restore()" env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book From 793ad34dc1ccca0af4bd8476153ba6d248fc2511 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 15:34:43 +0000 Subject: [PATCH 04/43] Add renv lock and co --- .github/workflows/prod.yaml | 1 - renv.lock | 2843 +++++++++++++++++++++++++++++++++++ renv/.gitignore | 7 + renv/activate.R | 1305 ++++++++++++++++ renv/settings.json | 19 + 5 files changed, 4174 insertions(+), 1 deletion(-) 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"Requirements": [ + "R", + "grDevices", + "graphics", + "lattice", + "stats", + "utils" + ], + "Hash": "5c715954112b45499fb1dadc6ee6ee3e" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 00000000..0ec0cbba --- /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 00000000..0eb51088 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1305 @@ + +local({ + + # the requested version of renv + version <- "1.0.11" + 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 + # 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 + + }) + + # 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;;ide:help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide: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) + + } + + 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))) { + 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 (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 <- 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 (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"]] + 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 <- 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_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), 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_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_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_read_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/settings.json b/renv/settings.json new file mode 100644 index 00000000..ffdbb320 --- /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 +} From e3e37abea5a1b2f11c9f8fc50289477edd738de8 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 15:41:05 +0000 Subject: [PATCH 05/43] restore --- .github/workflows/bookdown-test.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index 5aba1710..59457b48 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -8,7 +8,7 @@ on: - main - master -name: preview bookdown +name: Preview website jobs: build: @@ -24,7 +24,7 @@ jobs: - name: Install Dependencies if: ${{ github.repository == 'inseefrlab/utilitr' }} run: | - Rscript -e "install.packages(c('remotes', 'htmltools', 'sf'))" + Rscript -e "renv::restore()" env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book From 45fb2927ae1b257ac52fb023014d4625840c9606 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 15:43:55 +0000 Subject: [PATCH 06/43] upload artifact v4 --- .github/workflows/prod.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 1f85682a..7f93e617 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -72,7 +72,7 @@ jobs: git config --global user.name "Quarto GHA Workflow Runner" quarto render --to html quarto publish gh-pages --no-render --no-browser - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: name: _public path: _public/ From df4c47040a8f2cf1346e6134e4d45b5e22aea70b Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 15:45:25 +0000 Subject: [PATCH 07/43] rm cdoe --- index.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.qmd b/index.qmd index 8dcb9f15..13270199 100644 --- a/index.qmd +++ b/index.qmd @@ -5,7 +5,7 @@ ::::: {.headline .g-col-lg-9 .g-col-12 .g-col-md-12} :::::: h1 -`utilitR` +utilitR :::::: From e649db4b84af3241017585c75d8c7ea567c3fc7e Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 15:46:51 +0000 Subject: [PATCH 08/43] add yaml to test --- .github/workflows/bookdown-test.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index 59457b48..bb5a075f 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -25,6 +25,7 @@ jobs: if: ${{ github.repository == 'inseefrlab/utilitr' }} run: | Rscript -e "renv::restore()" + Rscript -e "install.packages('yaml')" env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book From 10f821eefa9277718a1052a4f69ce4c687858693 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 15:54:31 +0000 Subject: [PATCH 09/43] update lockfile --- renv.lock | 254 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 254 insertions(+) diff --git a/renv.lock b/renv.lock index 728b4147..5c85969a 100644 --- a/renv.lock +++ b/renv.lock @@ -148,6 +148,45 @@ ], "Hash": "0776bf7526869e0286b0463cb72fb211" }, + "R.methodsS3": { + "Package": "R.methodsS3", + "Version": "1.8.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "278c286fd6e9e75d0c2e8f731ea445c8" + }, + "R.oo": { + "Package": "R.oo", + "Version": "1.26.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "methods", + "utils" + ], + "Hash": "4fed809e53ddb5407b3da3d0f572e591" + }, + "R.utils": { + "Package": "R.utils", + "Version": "2.12.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "R.oo", + "methods", + "tools", + "utils" + ], + "Hash": "3dc2829b790254bfba21e60965787651" + }, "R6": { "Package": "R6", "Version": "2.5.1", @@ -343,6 +382,18 @@ ], "Hash": "d8b74e267a5774ded5c91786d6d777bb" }, + "boot": { + "Package": "boot", + "Version": "1.3-30", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "graphics", + "stats" + ], + "Hash": "96abeed416a286d4a0f52e550b612343" + }, "brio": { "Package": "brio", "Version": "1.1.5", @@ -353,6 +404,26 @@ ], "Hash": "c1ee497a6d999947c2c224ae46799b1a" }, + "broom": { + "Package": "broom", + "Version": "1.0.7", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "backports", + "dplyr", + "generics", + "glue", + "lifecycle", + "purrr", + "rlang", + "stringr", + "tibble", + "tidyr" + ], + "Hash": "8fcc818f3b9887aebaf206f141437cc9" + }, "bslib": { "Package": "bslib", "Version": "0.8.0", @@ -518,6 +589,20 @@ ], "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" }, + "cluster": { + "Package": "cluster", + "Version": "2.1.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Hash": "0aaa05204035dc43ea0004b9c76611dd" + }, "codetools": { "Package": "codetools", "Version": "0.2-20", @@ -1613,6 +1698,18 @@ ], "Hash": "f1fb7cc9fc60f3b039201174268aaad9" }, + "magick": { + "Package": "magick", + "Version": "2.8.5", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Rcpp", + "curl", + "magrittr" + ], + "Hash": "9bba16130de599cfe8e6a644911d7f32" + }, "magrittr": { "Package": "magrittr", "Version": "2.0.3", @@ -1695,6 +1792,24 @@ ], "Hash": "d19909f1b3fac42e7f3ac635321dbb15" }, + "modelr": { + "Package": "modelr", + "Version": "0.1.11", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "broom", + "magrittr", + "purrr", + "rlang", + "tibble", + "tidyr", + "tidyselect", + "vctrs" + ], + "Hash": "4f50122dc256b1b6996a4703fecea821" + }, "multcompView": { "Package": "multcompView", "Version": "0.1-10", @@ -1716,6 +1831,17 @@ ], "Hash": "4fd8900853b746af55b81fda99da7695" }, + "mvtnorm": { + "Package": "mvtnorm", + "Version": "1.3-1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "stats" + ], + "Hash": "77c61d51ce0f36e3c1a76e6b295aab31" + }, "nlme": { "Package": "nlme", "Version": "3.1-164", @@ -1737,6 +1863,18 @@ "Repository": "CRAN", "Hash": "27550641889a3abf3aec4d91186311ec" }, + "nnet": { + "Package": "nnet", + "Version": "7.3-19", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "2c797b46eea7fb58ede195bc0b1f1138" + }, "numDeriv": { "Package": "numDeriv", "Version": "2016.8-1.1", @@ -1846,6 +1984,17 @@ ], "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, + "plyr": { + "Package": "plyr", + "Version": "1.8.9", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp" + ], + "Hash": "6b8177fd19982f0020743fadbfdbd933" + }, "png": { "Package": "png", "Version": "0.1-8", @@ -2259,6 +2408,20 @@ ], "Hash": "eaf84737a6da68c1e843979963c09a6b" }, + "servr": { + "Package": "servr", + "Version": "0.32", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "httpuv", + "jsonlite", + "mime", + "xfun" + ], + "Hash": "63e4ea2379e79cf18813dd0d8146d27c" + }, "sf": { "Package": "sf", "Version": "1.0-18", @@ -2401,6 +2564,34 @@ ], "Hash": "960e2ae9e09656611e0b8214ad543207" }, + "survival": { + "Package": "survival", + "Version": "3.6-4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Matrix", + "R", + "graphics", + "methods", + "splines", + "stats", + "utils" + ], + "Hash": "e6e3071f471513e4b85f98ca041303c7" + }, + "svglite": { + "Package": "svglite", + "Version": "2.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11", + "systemfonts" + ], + "Hash": "124a41fdfa23e8691cb744c762f10516" + }, "sys": { "Package": "sys", "Version": "3.4.3", @@ -2408,6 +2599,18 @@ "Repository": "RSPM", "Hash": "de342ebfebdbf40477d0758d05426646" }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11", + "lifecycle" + ], + "Hash": "213b6b8ed5afbf934843e6c3b090d418" + }, "targets": { "Package": "targets", "Version": "1.8.0", @@ -2641,6 +2844,30 @@ ], "Hash": "62b65c52671e6665f803ff02954446e9" }, + "utilitr": { + "Package": "utilitr", + "Version": "0.1.0", + "Source": "GitHub", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteRepo": "utilitr-template", + "RemoteUsername": "InseeFrLab", + "RemoteSha": "b68d7a14c1c4e5adb9af0849ecca3baa3cde0bd9", + "Requirements": [ + "R.utils", + "bookdown", + "callr", + "fontawesome", + "htmltools", + "knitr", + "magick", + "pagedown", + "rmarkdown", + "xaringan", + "xfun" + ], + "Hash": "0471aef1195a0822e7495af618ed88bc" + }, "vctrs": { "Package": "vctrs", "Version": "0.6.5", @@ -2762,6 +2989,21 @@ ], "Hash": "37be35d733130f1de1ef51672cf7cdc0" }, + "xaringan": { + "Package": "xaringan", + "Version": "0.30", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "htmltools", + "knitr", + "rmarkdown", + "servr", + "xfun" + ], + "Hash": "40a1e30d3fb323f249a5e2fbec50c3b1" + }, "xfun": { "Package": "xfun", "Version": "0.48", @@ -2810,6 +3052,18 @@ ], "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" }, + "xts": { + "Package": "xts", + "Version": "0.14.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "methods", + "zoo" + ], + "Hash": "be0d8259b62c520dac5097ad7ba9baea" + }, "yaml": { "Package": "yaml", "Version": "2.3.10", From b7bc5137145400d45983fa9eb1c4df777ea439dd Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 17:28:58 +0000 Subject: [PATCH 10/43] upgrade R version --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 30a8840e..4aca703b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM inseefrlab/onyxia-rstudio:r4.3.2-2024.02.13 +FROM inseefrlab/onyxia-rstudio:r4.4.1-2024.10.14 # R packages COPY ./DESCRIPTION /tmp/build_image/ From 7231e99a115a1d26bd1cbd06ad0c2d4dfa89151f Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 17:59:34 +0000 Subject: [PATCH 11/43] use from documentation --- .github/workflows/prod.yaml | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 7f93e617..5bfe31da 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -52,16 +52,29 @@ jobs: needs: docker runs-on: ubuntu-latest container: inseefrlab/utilitr:latest + env: + RENV_PATHS_ROOT: ~/.cache/R/renv steps: - uses: actions/checkout@v4 with: fetch-depth: 0 ref: ${{ github.event.pull_request.head.ref }} repository: ${{github.event.pull_request.head.repo.full_name}} - - name: Install dependencies + - name: Configure safe repository run: | git config --global --add safe.directory /__w/utilitR/utilitR - Rscript -e "renv::restore()" + - name: Cache packages + uses: actions/cache@v1 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} + restore-keys: | + ${{ runner.os }}-renv- + - name: Restore packages + shell: Rscript {0} + run: | + if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv") + renv::restore() env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book From afbb95d5a3271274625af5500da11b67aa0e1c98 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 18:01:33 +0000 Subject: [PATCH 12/43] ici aussi --- .github/workflows/bookdown-test.yaml | 28 +++++++++++++++++++--------- 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index bb5a075f..004197e5 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -16,16 +16,26 @@ jobs: runs-on: ubuntu-latest container: inseefrlab/utilitr:latest steps: - - name: Checkout Repository - if: ${{ github.repository == 'inseefrlab/utilitr' }} - env: - GITHUB_PAT: ${{ secrets.PAT }} - uses: actions/checkout@master - - name: Install Dependencies - if: ${{ github.repository == 'inseefrlab/utilitr' }} + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + ref: ${{ github.event.pull_request.head.ref }} + repository: ${{github.event.pull_request.head.repo.full_name}} + - name: Configure safe repository + run: | + git config --global --add safe.directory /__w/utilitR/utilitR + - name: Cache packages + uses: actions/cache@v1 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} + restore-keys: | + ${{ runner.os }}-renv- + - name: Restore packages + shell: Rscript {0} run: | - Rscript -e "renv::restore()" - Rscript -e "install.packages('yaml')" + if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv") + renv::restore() env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book From aac9a57e845fa59f515a5b7596b4b0aa92f52921 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 18:07:13 +0000 Subject: [PATCH 13/43] use example doc --- .github/workflows/bookdown-test.yaml | 29 ++++++++++++++++++---------- .github/workflows/prod.yaml | 29 ++++++++++++++++++---------- 2 files changed, 38 insertions(+), 20 deletions(-) diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index 004197e5..b691d899 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -24,18 +24,27 @@ jobs: - name: Configure safe repository run: | git config --global --add safe.directory /__w/utilitR/utilitR - - name: Cache packages - uses: actions/cache@v1 - with: - path: ${{ env.RENV_PATHS_ROOT }} - key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} - restore-keys: | - ${{ runner.os }}-renv- - - name: Restore packages + - name: Set RENV_PATHS_ROOT + shell: bash + run: | + echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV + - name: Install and activate renv + run: | + install.packages("renv") + renv::activate() shell: Rscript {0} + - name: Get R and OS version + id: get-version run: | - if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv") - renv::restore() + cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "") + cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "") + shell: Rscript {0} + - name: Restore Renv package cache + uses: actions/cache@v4 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }} + restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}- env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 5bfe31da..ed45002b 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -63,18 +63,27 @@ jobs: - name: Configure safe repository run: | git config --global --add safe.directory /__w/utilitR/utilitR - - name: Cache packages - uses: actions/cache@v1 - with: - path: ${{ env.RENV_PATHS_ROOT }} - key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} - restore-keys: | - ${{ runner.os }}-renv- - - name: Restore packages + - name: Set RENV_PATHS_ROOT + shell: bash + run: | + echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV + - name: Install and activate renv + run: | + install.packages("renv") + renv::activate() shell: Rscript {0} + - name: Get R and OS version + id: get-version run: | - if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv") - renv::restore() + cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "") + cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "") + shell: Rscript {0} + - name: Restore Renv package cache + uses: actions/cache@v4 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }} + restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}- env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book From 8d06db2a084e4ce3637b4f47e2ba46707f3fb71b Mon Sep 17 00:00:00 2001 From: lgaliana Date: Thu, 17 Oct 2024 18:18:01 +0000 Subject: [PATCH 14/43] add yaml install --- .github/workflows/bookdown-test.yaml | 1 + .github/workflows/prod.yaml | 1 + 2 files changed, 2 insertions(+) diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index b691d899..3a7fd6cb 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -31,6 +31,7 @@ jobs: - name: Install and activate renv run: | install.packages("renv") + install.packages("yaml") renv::activate() shell: Rscript {0} - name: Get R and OS version diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index ed45002b..ee77f276 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -70,6 +70,7 @@ jobs: - name: Install and activate renv run: | install.packages("renv") + install.packages("yaml") renv::activate() shell: Rscript {0} - name: Get R and OS version From 315846e12ea9b3eae501ef4102de862569ea1b88 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Fri, 18 Oct 2024 07:11:22 +0000 Subject: [PATCH 15/43] install yaml then renv --- .github/workflows/bookdown-test.yaml | 2 +- .github/workflows/prod.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index 3a7fd6cb..62155396 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -30,8 +30,8 @@ jobs: echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV - name: Install and activate renv run: | - install.packages("renv") install.packages("yaml") + install.packages("renv") renv::activate() shell: Rscript {0} - name: Get R and OS version diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index ee77f276..e7537f94 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -69,8 +69,8 @@ jobs: echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV - name: Install and activate renv run: | - install.packages("renv") install.packages("yaml") + install.packages("renv") renv::activate() shell: Rscript {0} - name: Get R and OS version From e134a6eac9f98a99357189bbaa2ac135c3953897 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Fri, 18 Oct 2024 07:16:47 +0000 Subject: [PATCH 16/43] status --- .github/workflows/bookdown-test.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index 62155396..fd9df0e4 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -32,6 +32,7 @@ jobs: run: | install.packages("yaml") install.packages("renv") + renv::status() renv::activate() shell: Rscript {0} - name: Get R and OS version From 76aced5ee6b7340a155d18f5b76867b8ca63d47a Mon Sep 17 00:00:00 2001 From: lgaliana Date: Fri, 18 Oct 2024 07:29:14 +0000 Subject: [PATCH 17/43] renv yaml --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 4aca703b..8b82e01c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ FROM inseefrlab/onyxia-rstudio:r4.4.1-2024.10.14 # R packages COPY ./DESCRIPTION /tmp/build_image/ -RUN Rscript -e "install.packages('renv')" +RUN Rscript -e "install.packages(c('renv','yaml'))" RUN apt-get update \ && apt-get -qq install gnupg From 5321b74b40118d18f7457fb6eabdfe7bcd7e6149 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Fri, 18 Oct 2024 07:49:23 +0000 Subject: [PATCH 18/43] try using actions --- .github/workflows/prod.yaml | 121 +++++++++--------------------------- docker/dependencies.sh | 43 +++++++++++++ 2 files changed, 71 insertions(+), 93 deletions(-) create mode 100755 docker/dependencies.sh diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index e7537f94..b35c035f 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -1,102 +1,37 @@ -name: Production de la documentation - on: + workflow_dispatch: push: - branches: - - main - - master - - renv + branches: main + +name: Quarto Publish jobs: - docker: - if: "!contains(github.event.commits[0].message, '[skip ci]')" - runs-on: ubuntu-latest - steps: - - - name: Checkout - uses: actions/checkout@v2 - - - name: Set up QEMU - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/setup-qemu-action@v1 - - - name: Set up Docker Buildx - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/setup-buildx-action@v1 - - - name: Login to DockerHub - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - - name: Build and push - if: ${{ github.repository == 'inseefrlab/utilitr' }} - id: docker_build - uses: docker/build-push-action@v2 - env: - GITHUB_PAT: ${{ secrets.PAT }} - with: - push: true - context: . - tags: | - inseefrlab/utilitr:latest - inseefrlab/utilitr:0.9.1 - - - name: Image digest - run: echo ${{ steps.docker_build.outputs.digest }} - website: - name: Render website - if: "!contains(github.event.commits[0].message, '[skip ci]')" - needs: docker + build-deploy: runs-on: ubuntu-latest - container: inseefrlab/utilitr:latest - env: - RENV_PATHS_ROOT: ~/.cache/R/renv + permissions: + contents: write steps: - - uses: actions/checkout@v4 + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up Quarto + uses: quarto-dev/quarto-actions/setup@v2 + + - name: Install R + uses: r-lib/actions/setup-r@v2 + + - name: Install dependencies + run: sudo ./docker/dependencies.sh + + + - name: Install R Dependencies + uses: r-lib/actions/setup-renv@v2 with: - fetch-depth: 0 - ref: ${{ github.event.pull_request.head.ref }} - repository: ${{github.event.pull_request.head.repo.full_name}} - - name: Configure safe repository - run: | - git config --global --add safe.directory /__w/utilitR/utilitR - - name: Set RENV_PATHS_ROOT - shell: bash - run: | - echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV - - name: Install and activate renv - run: | - install.packages("yaml") - install.packages("renv") - renv::activate() - shell: Rscript {0} - - name: Get R and OS version - id: get-version - run: | - cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "") - cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "") - shell: Rscript {0} - - name: Restore Renv package cache - uses: actions/cache@v4 + cache-version: 1 + + - name: Render and Publish + uses: quarto-dev/quarto-actions/publish@v2 with: - path: ${{ env.RENV_PATHS_ROOT }} - key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }} - restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}- + target: gh-pages env: - GITHUB_PAT: ${{ secrets.PAT }} - - name: Render Book - run: | - ls - git remote -v - git config --global user.email quarto-github-actions-publish@example.com - git config --global user.name "Quarto GHA Workflow Runner" - quarto render --to html - quarto publish gh-pages --no-render --no-browser - - uses: actions/upload-artifact@v4 - with: - name: _public - path: _public/ - retention-days: 5 + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file diff --git a/docker/dependencies.sh b/docker/dependencies.sh new file mode 100755 index 00000000..cb204794 --- /dev/null +++ b/docker/dependencies.sh @@ -0,0 +1,43 @@ +#!/bin/bash + +# Update package lists +apt-get update && apt-get -qq install gnupg + +# Add Debian sources to apt and import necessary GPG keys +sh -c 'echo "deb http://http.us.debian.org/debian stable main contrib non-free" >> /etc/apt/sources.list' +apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138 +apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9 +apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 605C66F00D6C9793 + +# Update package lists and set debconf selections for mscorefonts installer +apt-get update +echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true" | debconf-set-selections + +# Install necessary packages without recommended dependencies +apt-get -qq install --no-install-recommends \ + ttf-mscorefonts-installer \ + fonts-liberation \ + fonts-freefont-ttf \ + libssl-dev + +apt-get -qq install --no-install-recommends \ + imagemagick \ + libmagick++-dev \ + ghostscript \ + libglpk40 + +apt-get -qq install --no-install-recommends \ + libgs-dev \ + librsvg2-dev \ + libwebp-dev \ + jq + +# Clean up apt cache +rm -rf /var/lib/apt/lists/* && rm -rf /src/*.deb + +# Upgrade packages +apt-get upgrade -y + +# Install mc (MinIO Client) +wget https://dl.min.io/client/mc/release/linux-amd64/mc -O /usr/local/bin/mc && \ + chmod +x /usr/local/bin/mc From 68a6071dbd9991f8aa489ef740601fa1eb812a0c Mon Sep 17 00:00:00 2001 From: lgaliana Date: Fri, 18 Oct 2024 08:21:45 +0000 Subject: [PATCH 19/43] change rbanch --- .github/workflows/prod.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index b35c035f..37c2bd02 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -1,7 +1,7 @@ on: workflow_dispatch: push: - branches: main + branches: renv name: Quarto Publish From 134e8c0be7a7356dd39928ba92730e66c2e36e4f Mon Sep 17 00:00:00 2001 From: lgaliana Date: Fri, 18 Oct 2024 08:40:38 +0000 Subject: [PATCH 20/43] r version --- .github/workflows/prod.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 37c2bd02..cbff3c28 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -19,7 +19,9 @@ jobs: - name: Install R uses: r-lib/actions/setup-r@v2 - + with: + r-version: '4.4.1' + - name: Install dependencies run: sudo ./docker/dependencies.sh From b7f34314cf972563fdc83f72fda60b9c2f5aec1f Mon Sep 17 00:00:00 2001 From: lgaliana Date: Wed, 6 Nov 2024 14:32:44 +0000 Subject: [PATCH 21/43] ajoute des data au lockfile --- renv.lock | 109 +++++++++++++++++++++++++++++++- resources/rmarkdown/chunk07.png | Bin 70290 -> 70290 bytes 2 files changed, 108 insertions(+), 1 deletion(-) diff --git a/renv.lock b/renv.lock index 5c85969a..1274a2e4 100644 --- a/renv.lock +++ b/renv.lock @@ -311,6 +311,34 @@ ], "Hash": "50c838a310445e954bc13f26f26a6ecf" }, + "aws.s3": { + "Package": "aws.s3", + "Version": "0.3.21", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "aws.signature", + "base64enc", + "curl", + "digest", + "httr", + "tools", + "utils", + "xml2" + ], + "Hash": "a0b873f71741bba67e3bc128d8f09fe3" + }, + "aws.signature": { + "Package": "aws.signature", + "Version": "0.6.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "base64enc", + "digest" + ], + "Hash": "0006bcef272aad12f78dd5a85fc7f4fc" + }, "backports": { "Package": "backports", "Version": "1.5.0", @@ -365,6 +393,18 @@ ], "Hash": "e84984bf5f12a18628d9a02322128dfd" }, + "blob": { + "Package": "blob", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "methods", + "rlang", + "vctrs" + ], + "Hash": "40415719b5a479b87949f3aa0aee737c" + }, "bookdown": { "Package": "bookdown", "Version": "0.41", @@ -742,6 +782,34 @@ ], "Hash": "2e00b378fc3be69c865120d9f313039a" }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "DBI", + "R", + "R6", + "blob", + "cli", + "dplyr", + "glue", + "lifecycle", + "magrittr", + "methods", + "pillar", + "purrr", + "rlang", + "tibble", + "tidyr", + "tidyselect", + "utils", + "vctrs", + "withr" + ], + "Hash": "39b2e002522bfd258039ee4e889e0fd1" + }, "dendextend": { "Package": "dendextend", "Version": "1.18.1", @@ -1038,6 +1106,19 @@ ], "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" }, + "foreign": { + "Package": "foreign", + "Version": "0.8-86", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods", + "stats", + "utils" + ], + "Hash": "550170303dbb19d07b2bcc288068e7dc" + }, "fs": { "Package": "fs", "Version": "1.6.4", @@ -2299,6 +2380,19 @@ ], "Hash": "062470668513dcda416927085ee9bdc7" }, + "rpart": { + "Package": "rpart", + "Version": "4.1.23", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats" + ], + "Hash": "b3d390424f41d04174cccf84d49676c2" + }, "rprojroot": { "Package": "rprojroot", "Version": "2.0.4", @@ -2517,6 +2611,19 @@ ], "Hash": "75940133cca2e339afce15a586f85b11" }, + "spatial": { + "Package": "spatial", + "Version": "7.3-17", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "graphics", + "stats", + "utils" + ], + "Hash": "1229a01b4ec059e9f2396724f2ec9010" + }, "stars": { "Package": "stars", "Version": "0.6-6", @@ -2866,7 +2973,7 @@ "xaringan", "xfun" ], - "Hash": "0471aef1195a0822e7495af618ed88bc" + "Hash": "cfb3ec218b90515512958168df22daa3" }, "vctrs": { "Package": "vctrs", diff --git a/resources/rmarkdown/chunk07.png b/resources/rmarkdown/chunk07.png index 6bffcc4a17383ddf4b6c35a495436bb58a6d6d65..e6c063d13daadf0f2917c8ac493b1180a5fcd973 100644 GIT binary patch delta 83 zcmbQVlx5OVmI-m3+-!Ut8k4(%sv6U`rZYAOiW}-0n1vV`S(#W`8Chr>7+4t?6xJlA VPyZ*#D1}XuLGjk@>H0#9$pGVR7Rdkr delta 83 zcmbQVlx5OVmI-m3T!MV2qJc{UoEy`(rZYAOiW}$}nuiz~TN#^L8JcJt7+4t?XuSLR WY5G4wMk#EPk((X;rt1qaCIbNPUKdON From a43eb533ed00f6145010b669e12c97af045f14cf Mon Sep 17 00:00:00 2001 From: lgaliana Date: Wed, 6 Nov 2024 14:50:34 +0000 Subject: [PATCH 22/43] remove activate --- .Rprofile | 1 - .github/workflows/prod.yaml | 6 +++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/.Rprofile b/.Rprofile index f2720dcd..0547dcc9 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,4 +1,3 @@ -source("renv/activate.R") if (file.exists('~/.Rprofile')) sys.source('~/.Rprofile', envir = environment()) with_def <- (function() { diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index cbff3c28..7e113281 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -23,9 +23,9 @@ jobs: r-version: '4.4.1' - name: Install dependencies - run: sudo ./docker/dependencies.sh - - + run: | + sudo ./docker/dependencies.sh + rm - name: Install R Dependencies uses: r-lib/actions/setup-renv@v2 with: From 3832d92a546bbfd3015a5679b96cc3e5e6af8787 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Wed, 6 Nov 2024 16:18:05 +0000 Subject: [PATCH 23/43] remove unfinished --- .github/workflows/prod.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 7e113281..67164e56 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -25,7 +25,6 @@ jobs: - name: Install dependencies run: | sudo ./docker/dependencies.sh - rm - name: Install R Dependencies uses: r-lib/actions/setup-renv@v2 with: From 9793ae2a8ac375221b8106ff7b02bd3162e68db9 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Wed, 6 Nov 2024 16:27:49 +0000 Subject: [PATCH 24/43] force install yaml --- .github/workflows/prod.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 67164e56..61b66a57 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -17,6 +17,10 @@ jobs: - name: Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 + - name: Install R dependency + run: | + Rscript -e "install.packages('yaml')" + - name: Install R uses: r-lib/actions/setup-r@v2 with: From 3427f1d38ae7d32963af1c4fc2bd28bd634bac8f Mon Sep 17 00:00:00 2001 From: lgaliana Date: Wed, 6 Nov 2024 16:42:57 +0000 Subject: [PATCH 25/43] rm DESCRIPTION --- DESCRIPTION | 105 ---------------------------------------------------- 1 file changed, 105 deletions(-) delete mode 100644 DESCRIPTION diff --git a/DESCRIPTION b/DESCRIPTION deleted file mode 100644 index 18a8ea58..00000000 --- a/DESCRIPTION +++ /dev/null @@ -1,105 +0,0 @@ -Package: documentationR -Type: Book -Title: Documentation R de l'Insee -Version: 0.8.0 -Description: Ce dépôt comprend les fichiers relatifs à la - documentation R de l'Insee. -Authors@R: c( - person("Lino" , "Galiana" , role = c("aut", "cre"), email = "lino.galiana@insee.fr"), - person("Olivier" , "Meslin" , role = c("aut", "cre"), email = "olivier.meslin@insee.fr"), - person("Gilles" , "Fidani" , role = "ctb", email = "gilles.fidani@insee.fr"), - person("Pierre" , "Lamarche" , role = "ctb", email = "pierre.lamarche@insee.fr"), - person("Gaëlle" , "Genin" , role = "ctb", email = "gaelle.genin@insee.fr"), - person("Romain" , "Lesur" , role = "ctb", email = "romain.lesur@insee.fr"), - person("Pierre-Yves" , "Berrard" , role = "ctb", email = "pierre-yves.berrard@insee.fr"), - person("Cédric" , "Tassart" , role = "ctb", email = "cedric.tassart@insee.fr"), - person("Pascal" , "Mercier" , role = "ctb", email = "pascal.mercier@insee.fr"), - person("Arthur" , "Cazaubiel" , role = "ctb", email = "arthur.cazaubiel@insee.fr"), - person("Arlindo" , "Dos Santos", role = "ctb", email = "arlindo.dos-santos@insee.fr"), - person("Alexis" , "Eidelman" , role = "ctb", email = "alexis.eidelman@travail.gouv.fr"), - person("Claire" , "Legroux" , role = "ctb", email = "claire.legroux@insee.fr"), - person("Lionel" , "Cacheux" , role = "ctb", email = "lionel.cacheux@insee.fr"), - person("Marie-Emmanuelle", "Faure" , role = "ctb", email = "marie-emmanuelle.faure@insee.fr"), - person("Mathias" , "André" , role = "ctb", email = "mathias.andre@insee.fr"), - person("Sylvain" , "Daubrée" , role = "ctb", email = "sylvain.daubree@insee.fr"), - person("Raphaële" , "Adjerad" , role = "ctb", email = "raphaele.adjerad@sante.gouv.fr"), - person("Jean-Daniel" , "Lomenède" , role = "ctb", email = "jean-daniel.lomenede@developpement-durable.gouv.fr"), - person("Géraldine" , "Rochambeau", role = "ctb", email = "geraldine.Rochambeau@justice.gouv.fr"), - person("Milena" , "Suarez Castillo", role = "ctb", email = "milena.suarez-castillo@insee.fr"), - person("Violaine" , "Poirot" , role = "ctb", email = "violaine.poirot@justice.gouv.fr"), - person("Frédérique" , "Cornuau" , role = "ctb", email = "frederique.cornuau@justice.gouv.fr"), - person("Clément" , "Rousset" , role = "ctb", email = "clement.rousset@insee.fr"), - person("Aurélien" , "D'Isanto" , role = "ctb", email = "aurelien.disanto@insee.fr"), - person("Sébastien" , "Li-Thiao-Té", role = "ctb", email = "sebastien.li-thiao-te@travail.gouv.fr"), - person(given = NULL, family = "Institut National de la Statistique et des Études Économiques", role = "cph") - ) -License: Licence Ouverte 2.0 -Encoding: UTF-8 -URL: https://github.com/InseeFrLab/utilitR -VignetteBuilder: knitr -Imports: - base, - utils, - xfun (>= 0.19), - rmarkdown, - bookdown, - pagedown (>= 0.13.11), - data.table, - readr, - openxlsx, - import, - FactoMineR, - factoextra, - corrplot, - tmap, - ggplot2, - cartography, - import, - htmltools, - doremifasolData, - readODS, - kableExtra, - fontawesome, - magick, - magrittr, - sass, - bslib, - downlit, - usethis, - renv, - remotes, - targets, - lintr, - parsedate, - lubridate, - zoo, - dygraphs, - yaml, - knitr, - desc, - dplyr, - MASS, - httr, - jsonlite, - arrow, - parallel, - tools, - stringr, - sf, - units, - rex, - duckdb, - DBI, - scales, - viridis, - readxl, - tibble, - tidyr, - doremifasol, - shiny -Suggests: - cranlogs, - haven, - rprojroot -Remotes: - InseeFrLab/doremifasolData@v0.2.0 From 6f7b7e4fcb1e216bca5e073ac8b89162f0bff776 Mon Sep 17 00:00:00 2001 From: Lino Galiana Date: Thu, 12 Dec 2024 15:03:45 +0100 Subject: [PATCH 26/43] Update .github/workflows/prod.yaml --- .github/workflows/prod.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 61b66a57..219ea6e6 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -14,7 +14,7 @@ jobs: - name: Check out repository uses: actions/checkout@v4 - - name: Set up Quarto + - name: Set up Quarto environement uses: quarto-dev/quarto-actions/setup@v2 - name: Install R dependency From f7b10212f9bcee66ea0c0a9cc55e7d753cfa9f9b Mon Sep 17 00:00:00 2001 From: Lino Galiana Date: Sat, 19 Apr 2025 11:47:29 +0200 Subject: [PATCH 27/43] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 1c9a82a7..4589ed76 100644 --- a/README.md +++ b/README.md @@ -35,6 +35,7 @@ Un environnement prêt à l'emploi est disponible pour les utilisateurs du `SSPC
+ ## :two: Objectifs de la documentation :book: ### Public cible From 1fa400d3662e7f6221c781c27d0b98c0b8b88f07 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Sat, 19 Apr 2025 10:20:10 +0000 Subject: [PATCH 28/43] logical order --- .github/workflows/prod.yaml | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 219ea6e6..147453d2 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -14,29 +14,26 @@ jobs: - name: Check out repository uses: actions/checkout@v4 - - name: Set up Quarto environement - uses: quarto-dev/quarto-actions/setup@v2 - - - name: Install R dependency - run: | - Rscript -e "install.packages('yaml')" - - name: Install R uses: r-lib/actions/setup-r@v2 with: r-version: '4.4.1' - + - name: Install dependencies run: | sudo ./docker/dependencies.sh + - name: Install R Dependencies uses: r-lib/actions/setup-renv@v2 with: cache-version: 1 + - name: Set up Quarto environment + uses: quarto-dev/quarto-actions/setup@v2 + - name: Render and Publish uses: quarto-dev/quarto-actions/publish@v2 with: target: gh-pages env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} From 7a365d662594d1d30009641122532bb8c63040dd Mon Sep 17 00:00:00 2001 From: lgaliana Date: Sat, 19 Apr 2025 11:36:50 +0000 Subject: [PATCH 29/43] upgraded envir --- .Rprofile | 1 + DocumentationR.Rproj | 1 + renv.lock | 8028 ++++++++++++++++++++++++++++++++++-------- 3 files changed, 6656 insertions(+), 1374 deletions(-) diff --git a/.Rprofile b/.Rprofile index 0547dcc9..f2720dcd 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,3 +1,4 @@ +source("renv/activate.R") if (file.exists('~/.Rprofile')) sys.source('~/.Rprofile', envir = environment()) with_def <- (function() { diff --git a/DocumentationR.Rproj b/DocumentationR.Rproj index 9eddaec0..6dbf42ab 100644 --- a/DocumentationR.Rproj +++ b/DocumentationR.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: e36da726-4a73-4cf5-bbff-99a6556f0a68 RestoreWorkspace: No SaveWorkspace: No diff --git a/renv.lock b/renv.lock index 1274a2e4..627b2a5b 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.4.1", + "Version": "4.4.2", "Repositories": [ { "Name": "CRAN", @@ -13,900 +13,2347 @@ "Package": "AsioHeaders", "Version": "1.22.1-2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "85bf3bd8fa58da21a22d84fd4f4ef0a8" + "Type": "Package", + "Title": "'Asio' C++ Header Files", + "Date": "2022-12-07", + "Author": "Dirk Eddelbuettel", + "Maintainer": "Dirk Eddelbuettel ", + "Description": "'Asio' is a cross-platform C++ library for network and low-level I/O programming that provides developers with a consistent asynchronous model using a modern C++ approach. It is also included in Boost but requires linking when used with Boost. Standalone it can be used header-only (provided a recent compiler). 'Asio' is written and maintained by Christopher M. Kohlhoff, and released under the 'Boost Software License', Version 1.0.", + "Copyright": "file inst/COPYRIGHTS", + "License": "BSL-1.0", + "URL": "https://github.com/eddelbuettel/asioheaders, https://dirk.eddelbuettel.com/code/asioheaders.html", + "BugReports": "https://github.com/eddelbuettel/asioheaders/issues", + "NeedsCompilation": "no", + "Repository": "RSPM", + "Encoding": "UTF-8" }, "DBI": { "Package": "DBI", "Version": "1.2.3", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "methods" + "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" ], - "Hash": "065ae649b05f1ff66bb0c793107508f5" + "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": "RSPM" }, "DT": { "Package": "DT", "Version": "0.33", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "crosstalk", - "htmltools", - "htmlwidgets", + "Type": "Package", + "Title": "A Wrapper of the JavaScript Library 'DataTables'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"Joe\", \"Cheng\", email = \"joe@posit.co\", role = c(\"aut\", \"cre\")), person(\"Xianying\", \"Tan\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Maximilian\", \"Girlich\", role = \"ctb\"), person(\"Greg\", \"Freedman Ellis\", role = \"ctb\"), person(\"Johannes\", \"Rauh\", role = \"ctb\"), person(\"SpryMedia Limited\", role = c(\"ctb\", \"cph\"), comment = \"DataTables in htmlwidgets/lib\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js in htmlwidgets/lib\"), person(\"Leon\", \"Gersen\", role = c(\"ctb\", \"cph\"), comment = \"noUiSlider in htmlwidgets/lib\"), person(\"Bartek\", \"Szopka\", role = c(\"ctb\", \"cph\"), comment = \"jquery.highlight.js in htmlwidgets/lib\"), person(\"Alex\", \"Pickering\", role = c(\"ctb\")), person(\"William\", \"Holmes\", role = c(\"ctb\")), person(\"Mikko\", \"Marttila\", role = c(\"ctb\")), person(\"Andres\", \"Quintero\", role = c(\"ctb\")), person(\"Stéphane\", \"Laurent\", role = c(\"ctb\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.", + "URL": "https://github.com/rstudio/DT", + "BugReports": "https://github.com/rstudio/DT/issues", + "License": "GPL-3 | file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "htmlwidgets (>= 1.3)", "httpuv", - "jquerylib", - "jsonlite", + "jsonlite (>= 0.9.16)", "magrittr", + "crosstalk", + "jquerylib", "promises" ], - "Hash": "64ff3427f559ce3f2597a4fe13255cb6" + "Suggests": [ + "knitr (>= 1.8)", + "rmarkdown", + "shiny (>= 1.6)", + "bslib", + "future", + "testit", + "tibble" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "7.3.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut], Joe Cheng [aut, cre], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), Alex Pickering [ctb], William Holmes [ctb], Mikko Marttila [ctb], Andres Quintero [ctb], Stéphane Laurent [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Joe Cheng ", + "Repository": "RSPM" }, "Deriv": { "Package": "Deriv", "Version": "4.1.6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Symbolic Differentiation", + "Date": "2024-09-12", + "Authors@R": "c(person(given=\"Andrew\", family=\"Clausen\", role=\"aut\"), person(given=\"Serguei\", family=\"Sokol\", role=c(\"aut\", \"cre\"), email=\"sokol@insa-toulouse.fr\", comment = c(ORCID = \"0000-0002-5674-3327\")), person(given=\"Andreas\", family=\"Rappold\", role=\"ctb\", email=\"arappold@gmx.at\"))", + "Description": "R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.", + "License": "GPL (>= 3)", + "Suggests": [ + "testthat (>= 0.11.0)" + ], + "BugReports": "https://github.com/sgsokol/Deriv/issues", + "RoxygenNote": "7.3.1", + "Imports": [ "methods" ], - "Hash": "cd52c065c9e687c60c56b51f10f7bcd3" + "NeedsCompilation": "no", + "Author": "Andrew Clausen [aut], Serguei Sokol [aut, cre] (), Andreas Rappold [ctb]", + "Maintainer": "Serguei Sokol ", + "Repository": "RSPM", + "Encoding": "UTF-8" }, "FactoMineR": { "Package": "FactoMineR", "Version": "2.11", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "DT", - "MASS", - "R", + "Title": "Multivariate Exploratory Data Analysis and Data Mining", + "Author": "Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet", + "Maintainer": "Francois Husson ", + "Depends": [ + "R (>= 4.0)" + ], + "Imports": [ "car", "cluster", + "DT", "ellipse", "emmeans", "flashClust", - "ggplot2", - "ggrepel", - "grDevices", "graphics", + "grDevices", "lattice", "leaps", + "MASS", "multcompView", "scatterplot3d", "stats", - "utils" + "utils", + "ggplot2", + "ggrepel" ], - "Hash": "54fc333adf872599b177a62d5759892a" + "Suggests": [ + "missMDA", + "knitr", + "Factoshiny", + "markdown" + ], + "Description": "Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. 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This package helps to design cartographic representations such as proportional symbols, choropleth, typology, flows or discontinuities maps. It also offers several features that improve the graphic presentation of maps, for instance, map palettes, layout elements (scale, north arrow, title...), labels or legends. 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It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.", + "License": "MIT + file LICENSE", + "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli", + "BugReports": "https://github.com/r-lib/cli/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ "utils" ], - "Hash": "b21916dd77a27642b447374a5d30ecf3" + "Suggests": [ + "callr", + "covr", + "crayon", + "digest", + "glue (>= 1.6.0)", + "grDevices", + "htmltools", + "htmlwidgets", + "knitr", + "methods", + "mockery", + "processx", + "ps (>= 1.3.4.9000)", + "rlang (>= 1.0.2.9003)", + "rmarkdown", + "rprojroot", + "rstudioapi", + "testthat", + "tibble", + "whoami", + "withr" + ], + "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" }, "clipr": { "Package": "clipr", "Version": "0.8.0", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ + "Type": "Package", + "Title": "Read and Write from the System Clipboard", + "Authors@R": "c( person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4387-3384\")), person(\"Louis\", \"Maddox\", role = \"ctb\"), person(\"Steve\", \"Simpson\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\") )", + "Description": "Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.", + "License": "GPL-3", + "URL": "https://github.com/mdlincoln/clipr, http://matthewlincoln.net/clipr/", + "BugReports": "https://github.com/mdlincoln/clipr/issues", + "Imports": [ "utils" ], - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "rstudioapi (>= 0.5)", + "testthat (>= 2.0.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.1.2", + "SystemRequirements": "xclip (https://github.com/astrand/xclip) or xsel (http://www.vergenet.net/~conrad/software/xsel/) for accessing the X11 clipboard, or wl-clipboard (https://github.com/bugaevc/wl-clipboard) for systems using Wayland.", + "NeedsCompilation": "no", + "Author": "Matthew Lincoln [aut, cre] (), Louis Maddox [ctb], Steve Simpson [ctb], Jennifer Bryan [ctb]", + "Maintainer": "Matthew Lincoln ", + "Repository": "RSPM" }, "cluster": { "Package": "cluster", "Version": "2.1.6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", + "Date": "2023-11-30", + "Priority": "recommended", + "Title": "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et al.", + "Description": "Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", + "Maintainer": "Martin Maechler ", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ "graphics", + "grDevices", "stats", "utils" ], - "Hash": "0aaa05204035dc43ea0004b9c76611dd" + "Suggests": [ + "MASS", + "Matrix" + ], + "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" }, "codetools": { "Package": "codetools", "Version": "0.2-20", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" ], - "Hash": "61e097f35917d342622f21cdc79c256e" + "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", - "Repository": "RSPM", - "Requirements": [ - "R", - "grDevices", + "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. 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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": "RSPM" }, "dbplyr": { "Package": "dbplyr", "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "DBI", - "R", - "R6", - "blob", - "cli", - "dplyr", - "glue", - "lifecycle", + "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", - "purrr", - "rlang", - "tibble", - "tidyr", - "tidyselect", + "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", - "withr" + "vctrs (>= 0.6.3)", + "withr (>= 2.5.0)" ], - "Hash": "39b2e002522bfd258039ee4e889e0fd1" + "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": "RSPM" }, "dendextend": { "Package": "dendextend", "Version": "1.18.1", "Source": "Repository", - 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You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "utils", + "stats", "datasets", + "magrittr (>= 1.0.1)", "ggplot2", - "magrittr", - "stats", - "utils", "viridis" ], - "Hash": "735689b7975ad5a4d72b571857d60a33" + "Suggests": [ + "knitr", + "rmarkdown", + "testthat", + "seriation", + "colorspace", + "ape", + "microbenchmark", + "gplots", + "heatmaply", + "dynamicTreeCut", + "pvclust", + "corrplot", + "DendSer", + "MASS", + "cluster", + "fpc", + "circlize (>= 0.2.5)", + "covr" + ], + "Enhances": [ + "ggdendro", + "dendroextras", + "Hmisc", + "data.table", + "rpart", + "WGCNA", + "moduleColor", + "distory", + "phangorn", + "zoo" + ], + "VignetteBuilder": "knitr", + "LazyData": "true", + "License": "GPL-2 | GPL-3", + "URL": "https://talgalili.github.io/dendextend/, https://github.com/talgalili/dendextend/, https://cran.r-project.org/package=dendextend, https://www.r-statistics.com/tag/dendextend/, https://doi.org/10.1093/bioinformatics/btv428", + "BugReports": "https://github.com/talgalili/dendextend/issues", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Yoav Benjamini [ths], Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Cath [ctb] (https://github.com/CathG), John Ma [ctb] (https://github.com/JohnMCMa), Krzysiek G [ctb] (https://github.com/storaged), Manuela Hummel [ctb] (https://github.com/hummelma), Chase Clark [ctb] (https://github.com/chasemc), Lucas Graybuck [ctb] (https://github.com/hypercompetent), jdetribol [ctb] (https://github.com/jdetribol), Ben Ho [ctb] (https://github.com/SplitInf), Samuel Perreault [ctb] (https://github.com/samperochkin), Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/), David Bradley [ctb] (https://github.com/DBradley27), Houyun Huang [ctb] (https://github.com/houyunhuang), Patrick Schupp [ctb] (https://github.com/pschupp), Alec Buetow [ctb] (https://github.com/alecbuetow)", + "Maintainer": "Tal Galili ", + "Repository": "RSPM" }, "desc": { "Package": "desc", "Version": "1.4.3", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", + "Title": "Manipulate DESCRIPTION Files", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", role = \"aut\"), person(\"Jim\", \"Hester\", , \"james.f.hester@gmail.com\", role = \"aut\"), person(\"Maëlle\", \"Salmon\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Gábor Csárdi ", + "Description": "Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.", + "License": "MIT + file LICENSE", + "URL": "https://desc.r-lib.org/, https://github.com/r-lib/desc", + "BugReports": "https://github.com/r-lib/desc/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ "cli", + "R6", "utils" ], - "Hash": "99b79fcbd6c4d1ce087f5c5c758b384f" + "Suggests": [ + "callr", + "covr", + "gh", + "spelling", + "testthat", + "whoami", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "Collate": "'assertions.R' 'authors-at-r.R' 'built.R' 'classes.R' 'collate.R' 'constants.R' 'deps.R' 'desc-package.R' 'description.R' 'encoding.R' 'find-package-root.R' 'latex.R' 'non-oo-api.R' 'package-archives.R' 'read.R' 'remotes.R' 'str.R' 'syntax_checks.R' 'urls.R' 'utils.R' 'validate.R' 'version.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Kirill Müller [aut], Jim Hester [aut], Maëlle Salmon [ctb] (), Posit Software, PBC [cph, fnd]", + "Repository": "RSPM" }, "dichromat": { "Package": "dichromat", "Version": "2.0-0.1", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", + "Date": "2013-01-23", + "Title": "Color Schemes for Dichromats", + "Authors@R": "c(person(given = \"Thomas\", family = \"Lumley\", role = c(\"aut\", \"cre\"), email = \"tlumley@u.washington.edu\"), person(given = \"Ken\", family = \"Knoblauch\", role = \"ctb\", email = \"ken.knoblauch@inserm.fr\"), person(given = \"Scott\", family = \"Waichler\", role = \"ctb\", email = \"scott.waichler@pnl.gov\"), person(given = \"Achim\", family = \"Zeileis\", role = \"ctb\", email = \"Achim.Zeileis@R-project.org\"))", + "Description": "Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness.", + "Depends": [ + "R (>= 2.10)", "stats" ], - "Hash": "16e66f2a483e124af5fc6582d26005f7" + "License": "GPL-2", + "LazyLoad": "Yes", + "Author": "Thomas Lumley [aut, cre], Ken Knoblauch [ctb], Scott Waichler [ctb], Achim Zeileis [ctb]", + "Maintainer": "Thomas Lumley ", + "Repository": "RSPM", + "NeedsCompilation": "no", + "Encoding": "UTF-8" }, "digest": { "Package": "digest", "Version": "0.6.37", "Source": "Repository", - 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The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", + "BugReports": "https://github.com/thomasp85/farver/issues", + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "RSPM" }, "fastmap": { "Package": "fastmap", "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" + "Title": "Fast Data Structures", + "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )", + "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. 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Labels repel away from each other and away from the data points.", + "Depends": [ + "R (>= 3.0.0)", + "ggplot2 (>= 2.2.0)" + ], + "Imports": [ "grid", - "rlang", - "scales", - "withr" + "Rcpp", + "rlang (>= 0.3.0)", + "scales (>= 0.5.0)", + "withr (>= 2.5.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "testthat", + "svglite", + "vdiffr", + "gridExtra", + "ggpp", + "patchwork", + "devtools", + "prettydoc", + "ggbeeswarm", + "dplyr", + "magrittr", + "readr", + "stringr" + ], + "VignetteBuilder": "knitr", + "License": "GPL-3 | file LICENSE", + "URL": "https://ggrepel.slowkow.com/, https://github.com/slowkow/ggrepel", + "BugReports": "https://github.com/slowkow/ggrepel/issues", + "RoxygenNote": "7.3.1", + "LinkingTo": [ + "Rcpp" ], - "Hash": "3d4156850acc1161f2f24bc61c9217c1" + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Kamil Slowikowski [aut, cre] (), Alicia Schep [ctb] (), Sean Hughes [ctb] (), Trung Kien Dang [ctb] (), Saulius Lukauskas [ctb], Jean-Olivier Irisson [ctb] (), Zhian N Kamvar [ctb] (), Thompson Ryan [ctb] (), Dervieux Christophe [ctb] (), Yutani Hiroaki [ctb], Pierre Gramme [ctb], Amir Masoud Abdol [ctb], Malcolm Barrett [ctb] (), Robrecht Cannoodt [ctb] (), Michał Krassowski [ctb] (), Michael Chirico [ctb] (), Pedro Aphalo [ctb] (), Francis Barton [ctb]", + "Maintainer": "Kamil Slowikowski ", + "Repository": "RSPM" }, "ggsci": { "Package": "ggsci", "Version": "3.2.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggplot2", + "Type": "Package", + "Title": "Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'", + "Authors@R": "c( person(\"Nan\", \"Xiao\", email = \"me@nanx.me\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0250-5673\")), person(\"Joshua\", \"Cook\", email = \"joshuacook0023@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Jégousse\", email = \"cat3@hi.is\", role = \"ctb\"), person(\"Hui\", \"Chen\", email = \"huichen@zju.edu.cn\", role = \"ctb\"), person(\"Miaozhu\", \"Li\", email = \"miaozhu.li@duke.edu\", role = \"ctb\") )", + "Maintainer": "Nan Xiao ", + "Description": "A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.", + "License": "GPL (>= 3)", + "URL": "https://nanx.me/ggsci/, https://github.com/nanxstats/ggsci", + "BugReports": "https://github.com/nanxstats/ggsci/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 2.0.0)", "grDevices", "scales" ], - "Hash": "0c3268cddf4d3a3ce4e7e6330f8e92c8" + "Suggests": [ + "gridExtra", + "knitr", + "ragg", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Nan Xiao [aut, cre] (), Joshua Cook [ctb], Clara Jégousse [ctb], Hui Chen [ctb], Miaozhu Li [ctb]", + "Repository": "RSPM" }, "ggsignif": { "Package": "ggsignif", "Version": "0.6.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "ggplot2" + "Type": "Package", + "Title": "Significance Brackets for 'ggplot2'", + "Authors@R": "c( person(given = \"Constantin\", family = \"Ahlmann-Eltze\", role = c(\"aut\", \"cre\", \"ctb\"), email = \"artjom31415@googlemail.com\", comment = c(ORCID = \"0000-0002-3762-068X\", Twitter = \"@const_ae\")), person(given = \"Indrajeet\", family = \"Patil\", role = c(\"aut\", \"ctb\"), email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\", Twitter = \"@patilindrajeets\")) )", + "Description": "Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.", + "License": "GPL-3 | file LICENSE", + "URL": "https://const-ae.github.io/ggsignif/, https://github.com/const-ae/ggsignif", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "Imports": [ + "ggplot2 (>= 3.3.5)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "testthat", + "vdiffr (>= 1.0.2)" ], - "Hash": "a57f0f5dbcfd0d77ad4ff33032f5dc79" + "RoxygenNote": "7.2.1", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "NeedsCompilation": "no", + "Author": "Constantin Ahlmann-Eltze [aut, cre, ctb] (, @const_ae), Indrajeet Patil [aut, ctb] (, @patilindrajeets)", + "Maintainer": "Constantin Ahlmann-Eltze ", + "Repository": "RSPM" }, "gh": { "Package": "gh", "Version": "1.4.1", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "cli", + "Title": "'GitHub' 'API'", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"cre\", \"ctb\")), person(\"Jennifer\", \"Bryan\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Minimal client to access the 'GitHub' 'API'.", + "License": "MIT + file LICENSE", + "URL": "https://gh.r-lib.org/, https://github.com/r-lib/gh#readme", + "BugReports": "https://github.com/r-lib/gh/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.0.1)", "gitcreds", "glue", "httr2", "ini", "jsonlite", "lifecycle", - "rlang" + "rlang (>= 1.0.0)" + ], + "Suggests": [ + "covr", + "knitr", + "mockery", + "rmarkdown", + "rprojroot", + "spelling", + "testthat (>= 3.0.0)", + "withr" ], - "Hash": "fbbbc48eba7a6626a08bb365e44b563b" + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.1.9000", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [cre, ctb], Jennifer Bryan [aut], Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" }, "gitcreds": { "Package": "gitcreds", "Version": "0.1.2", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" + "Title": "Query 'git' Credentials from 'R'", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "Query, set, delete credentials from the 'git' credential store. Manage 'GitHub' tokens and other 'git' credentials. 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The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. 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The syntax allows for importing multiple objects with a single command in an expressive way. The import package bridges some of the gap between using library (or require) and direct (single-object) imports. 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Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.", + "License": "MIT + file LICENSE", + "URL": "http://haozhu233.github.io/kableExtra/, https://github.com/haozhu233/kableExtra", + "BugReports": "https://github.com/haozhu233/kableExtra/issues", + "Depends": [ + "R (>= 3.1.0)" + ], + "Imports": [ + "knitr (>= 1.33)", "magrittr", - "rmarkdown", - "rstudioapi", + "stringr (>= 1.0)", + "xml2 (>= 1.1.1)", + "rmarkdown (>= 1.6.0)", "scales", + "viridisLite", "stats", - "stringr", - "svglite", + "grDevices", + "htmltools", + "rstudioapi", "tools", - "viridisLite", - "xml2" + "digest", + "graphics", + "svglite" ], - "Hash": "532d16304274c23c8563f94b79351c86" + "Suggests": [ + "testthat", + "magick", + "tinytex", + "formattable", + "sparkline", + "webshot2" + ], + "Config/testthat/edition": "3", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + 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The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", + "Collate": "'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R' 'plot.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. 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Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Yihui Xie ", + "Repository": "RSPM" }, "labeling": { "Package": "labeling", "Version": "0.4.3", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "graphics", - "stats" + "Type": "Package", + "Title": "Axis Labeling", + "Date": "2023-08-29", + "Author": "Justin Talbot,", + "Maintainer": "Nuno Sempere ", + "Description": "Functions which provide a range of axis labeling algorithms.", + "License": "MIT + file LICENSE | Unlimited", + "Collate": "'labeling.R'", + "NeedsCompilation": "no", + "Imports": [ + "stats", + "graphics" ], - "Hash": "b64ec208ac5bc1852b285f665d6368b3" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "later": { "Package": "later", "Version": "1.3.2", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "Rcpp", + "Type": "Package", + "Title": "Utilities for Scheduling Functions to Execute Later with Event Loops", + "Authors@R": "c( person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@posit.co\"), person(\"Joe\", \"Cheng\", role = c(\"aut\"), email = \"joe@posit.co\"), person(family = \"Posit Software, PBC\", role = \"cph\"), person(\"Marcus\", \"Geelnard\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\"), person(\"Evan\", \"Nemerson\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\") )", + "Description": "Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. 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Krivitsky [ctb, cph] (, shared copyright on simulate.formula), Emi Tanaka [ctb] (), Mikael Jagan [ctb] ()", + "Maintainer": "Ben Bolker ", + "Repository": "RSPM" }, "lubridate": { "Package": "lubridate", "Version": "1.9.3", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "generics", + "Type": "Package", + "Title": "Make Dealing with Dates a Little Easier", + "Authors@R": "c( person(\"Vitalie\", \"Spinu\", , \"spinuvit@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Garrett\", \"Grolemund\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Davis\", \"Vaughan\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Imanuel\", \"Costigan\", role = \"ctb\"), person(\"Jason\", \"Law\", role = \"ctb\"), person(\"Doug\", \"Mitarotonda\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Jonathan\", \"Boiser\", role = \"ctb\"), person(\"Chel Hee\", \"Lee\", role = \"ctb\") )", + "Maintainer": "Vitalie Spinu ", + "Description": "Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. 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The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. 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Warkentin [ctb], Mark Edmondson [ctb] (), Samantha Oliver [rev] (), Tristan Mahr [rev] (), Eli Lilly and Company [cph]", + "Maintainer": "William Michael Landau ", + "Repository": "RSPM" }, "terra": { "Package": "terra", "Version": "1.7-78", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "Rcpp", - "methods" + "Type": "Package", + "Title": "Spatial Data Analysis", + "Date": "2024-05-22", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "parallel", + "tinytest", + "ncdf4", + "sf (>= 0.9-8)", + "deldir", + "XML", + "leaflet (>= 2.2.1)", + "htmlwidgets" ], - "Hash": "8f020def0792119cb98bd8f696dab22d" + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "methods", + "Rcpp (>= 1.0-10)" + ], + "SystemRequirements": "C++17, GDAL (>= 2.2.3), GEOS (>= 3.4.0), PROJ (>= 4.9.3), sqlite3", + "Encoding": "UTF-8", + "Language": "en-US", + "Maintainer": "Robert J. 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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": "RSPM" }, "units": { "Package": "units", "Version": "0.8-5", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", + "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" ], - "Hash": "119d19da480e873f72241ff6962ffd83" + "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. 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The 'frameableWidget()' is used to add extra code to a 'htmlwidget' which allows is to be rendered correctly inside a responsive 'iframe'. The 'frameWidget()' is a 'htmlwidget' which displays content of another 'htmlwidget' inside a responsive 'iframe'. These functions allow for easier embedding of 'htmlwidgets' in content management systems such as 'wordpress', 'blogger' etc. They also allow for separation of widget content from main HTML content where CSS of the main HTML could interfere with the widget.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "LazyData": "true", + "Depends": [ + "R (>= 3.1.0)", + "htmlwidgets" + ], + "Imports": [ "htmltools", - "htmlwidgets", - "magrittr", "purrr", - "tools", - "utils" + "magrittr", + "utils", + "tools" + ], + "RoxygenNote": "6.0.1", + "URL": "https://github.com/bhaskarvk/widgetframe, https://bhaskarvk.github.io/widgetframe/", + "BugReports": "https://github.com/bhaskarvk/widgetframe/issues", + "Suggests": [ + "knitr", + "rmarkdown" ], - "Hash": "0ee89e6cb58182d39b30a5b506e04808" + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Bhaskar Karambelkar [aut, cre], Yihui Xie [ctb], NPR Visual Team [ctb, cph] (pym.js JavaScript library), Bjørn Klinggaard [ctb, cph] (bLazy.js JavaScript library)", + "Maintainer": "Bhaskar Karambelkar ", + "Repository": "RSPM" }, "withr": { "Package": "withr", "Version": "3.0.1", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "grDevices", - "graphics" + "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" ], - "Hash": "07909200e8bbe90426fbfeb73e1e27aa" + "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": "RSPM" }, "wk": { "Package": "wk", "Version": "0.9.4", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" + "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" ], - "Hash": "37be35d733130f1de1ef51672cf7cdc0" + "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": "RSPM" }, "xaringan": { "Package": "xaringan", "Version": "0.30", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", + "Type": "Package", + "Title": "Presentation Ninja", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), # contributors ordered alphabetically below person(\"Alessandro\", \"Gasparini\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8319-7624\")), person(\"Benjie\", \"Gillam\", role = \"ctb\"), person(\"Claus Thorn\", \"Ekstrøm\", role = \"ctb\"), person(\"Daniel\", \"Anderson\", role = \"ctb\"), person(\"Dawei\", \"Lang\", role = \"ctb\"), person(\"Deo\", \"Salil\", role = \"ctb\"), person(\"Emi\", \"Tanaka\", role = \"ctb\"), person(\"Garrick\", \"Aden-Buie\", role = \"ctb\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Iñaki\", \"Ucar\", role = \"ctb\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"John\", \"Little\", role = \"ctb\"), person(\"Joselyn\", \"Chávez\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4974-4591\")), person(\"Joseph\", \"Casillas\", role = \"ctb\"), person(\"JooYoung\", \"Seo\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4064-6012\")), person(\"Lucy\", \"D'Agostino McGowan\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7297-9359\")), person(\"Malcolm\", \"Barrett\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(c(\"Matthew\", \"Mark\"), \"Strasiotto\", role = \"ctb\", comment = c(github = \"mstr3336\")), person(\"Michael Wayne\", \"Kearney\", role = \"ctb\"), person(\"Nan-Hung\", \"Hsieh\", role = \"ctb\"), person(\"Ole Petter\", \"Bang\", role = \"ctb\", comment = \"CSS in rmarkdown/templates/xaringan/resources/default.css\"), person(\"Orlando\", \"Olaya Bucaro\", role = \"ctb\"), person(\"Patrick\", \"Schratz\", role = \"ctb\"), person(\"Paul\", \"Klemm\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5985-1737\")), person(\"Paul\", \"Lemmens\", role = \"ctb\"), person(\"Robert\", \"Fromont\", role = \"ctb\", email = \"robert.fromont@canterbury.ac.nz\", comment = c(ORCID = \"0000-0001-5271-5487\")), person(\"Sean\", \"Lopp\", role = \"ctb\"), person(\"Silvia\", \"Canelon\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1709-1394\")), person(\"Susan\", \"VanderPlas\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3803-0972\")), person(\"Tuo\", \"Wang\", role = \"ctb\"), person(\"Waldir\", \"Leoncio\", role = \"ctb\", email = \"w.l.netto@medisin.uio.no\"), person(\"Yongfu\", \"Liao\", role = \"ctb\"), person(\"Yue\", \"Jiang\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9798-5517\")), person(c(\"Zhian\", \"N.\"), \"Kamvar\", role = c(\"ctb\"), email = \"zkamvar@gmail.com\", comment = c(ORCID = \"0000-0003-1458-7108\")), person() )", + "Description": "Create HTML5 slides with R Markdown and the JavaScript library 'remark.js' ().", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ "htmltools", - "knitr", - "rmarkdown", - "servr", - "xfun" + "knitr (>= 1.30)", + "servr (>= 0.30)", + "xfun (>= 0.18)", + "rmarkdown (>= 2.8)" ], - "Hash": "40a1e30d3fb323f249a5e2fbec50c3b1" + "Suggests": [ + "rstudioapi", + "jsonlite", + "testit" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xaringan", + "BugReports": "https://github.com/yihui/xaringan/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Posit Software, PBC [cph, fnd], Alessandro Gasparini [ctb] (), Benjie Gillam [ctb], Claus Thorn Ekstrøm [ctb], Daniel Anderson [ctb], Dawei Lang [ctb], Deo Salil [ctb], Emi Tanaka [ctb], Garrick Aden-Buie [ctb] (), Iñaki Ucar [ctb] (), John Little [ctb], Joselyn Chávez [ctb] (), Joseph Casillas [ctb], JooYoung Seo [ctb] (), Lucy D'Agostino McGowan [ctb] (), Malcolm Barrett [ctb] (), Matthew Mark Strasiotto [ctb] (mstr3336), Michael Wayne Kearney [ctb], Nan-Hung Hsieh [ctb], Ole Petter Bang [ctb] (CSS in rmarkdown/templates/xaringan/resources/default.css), Orlando Olaya Bucaro [ctb], Patrick Schratz [ctb], Paul Klemm [ctb] (), Paul Lemmens [ctb], Robert Fromont [ctb] (), Sean Lopp [ctb], Silvia Canelon [ctb] (), Susan VanderPlas [ctb] (), Tuo Wang [ctb], Waldir Leoncio [ctb], Yongfu Liao [ctb], Yue Jiang [ctb] (), Zhian N. Kamvar [ctb] ()", + "Maintainer": "Yihui Xie ", + "Repository": "RSPM" }, "xfun": { "Package": "xfun", "Version": "0.48", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", + "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\")), 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" ], - "Hash": "89e455b87c84e227eb7f60a1b4e5fe1f" + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown", + "knitr (>= 1.47)", + "remotes", + "pak", + "rhub", + "renv", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs", + "rmarkdown" + ], + "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] (), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "RSPM" }, "xml2": { "Package": "xml2", "Version": "1.3.6", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", + "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" + "rlang (>= 1.1.0)" ], - "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" + "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": "RSPM" }, "xmlparsedata": { "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" + "Title": "Parse Data of 'R' Code as an 'XML' Tree", + "Author": "Gábor Csárdi", + "Maintainer": "Gábor Csárdi ", + "Description": "Convert the output of 'utils::getParseData()' to an 'XML' tree, that one can search via 'XPath', and easier to manipulate in general.", + "License": "MIT + file LICENSE", + "LazyData": "true", + "URL": "https://github.com/r-lib/xmlparsedata#readme", + "BugReports": "https://github.com/r-lib/xmlparsedata/issues", + "RoxygenNote": "6.0.1", + "Suggests": [ + "covr", + "testthat", + "xml2" ], - "Hash": "45e4bf3c46476896e821fc0a408fb4fc" + "Depends": [ + "R (>= 3.0.0)" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Repository": "RSPM" }, "xtable": { "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", + "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" ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" + "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": "RSPM", + "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]", + "Encoding": "UTF-8" }, "xts": { "Package": "xts", "Version": "0.14.1", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "methods", + "Type": "Package", + "Title": "eXtensible Time Series", + "Authors@R": "c( person(given=c(\"Jeffrey\",\"A.\"), family=\"Ryan\", role=c(\"aut\",\"cph\")), person(given=c(\"Joshua\",\"M.\"), family=\"Ulrich\", role=c(\"cre\",\"aut\"), email=\"josh.m.ulrich@gmail.com\"), person(given=\"Ross\", family=\"Bennett\", role=\"ctb\"), person(given=\"Corwin\", family=\"Joy\", role=\"ctb\") )", + "Depends": [ + "R (>= 3.6.0)", + "zoo (>= 1.7-12)" + ], + "Imports": [ + "methods" + ], + "LinkingTo": [ "zoo" ], - "Hash": "be0d8259b62c520dac5097ad7ba9baea" + "Suggests": [ + "timeSeries", + "timeDate", + "tseries", + "chron", + "tinytest" + ], + "LazyLoad": "yes", + "Description": "Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.", + "License": "GPL (>= 2)", + "URL": "https://joshuaulrich.github.io/xts/, https://github.com/joshuaulrich/xts", + "BugReports": "https://github.com/joshuaulrich/xts/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeffrey A. Ryan [aut, cph], Joshua M. Ulrich [cre, aut], Ross Bennett [ctb], Corwin Joy [ctb]", + "Maintainer": "Joshua M. Ulrich ", + "Repository": "RSPM" }, "yaml": { "Package": "yaml", "Version": "2.3.10", "Source": "Repository", - "Repository": "RSPM", - "Hash": "51dab85c6c98e50a18d7551e9d49f76c" + "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", + "Encoding": "UTF-8" }, "zip": { "Package": "zip", "Version": "2.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" + "Title": "Cross-Platform 'zip' Compression", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", + "BugReports": "https://github.com/r-lib/zip/issues", + "Suggests": [ + "covr", + "processx", + "R6", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" }, "zoo": { "Package": "zoo", "Version": "1.8-12", "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "grDevices", + "Date": "2023-04-11", + "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", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", "graphics", - "lattice", - "stats", - "utils" + "grDevices", + "lattice (>= 0.20-27)" ], - "Hash": "5c715954112b45499fb1dadc6ee6ee3e" + "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": "RSPM", + "Encoding": "UTF-8" } } } From 535f794a43e7aa0342aef4114413489d0fe8b4fc Mon Sep 17 00:00:00 2001 From: lgaliana Date: Sat, 19 Apr 2025 11:44:28 +0000 Subject: [PATCH 30/43] install yaml --- .github/workflows/prod.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 147453d2..02ded922 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -22,6 +22,7 @@ jobs: - name: Install dependencies run: | sudo ./docker/dependencies.sh + Rscript -e "install.packages('yaml')" - name: Install R Dependencies uses: r-lib/actions/setup-renv@v2 From 7a4a1fa54e9da8db71340a1560f732a7c25762b1 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Sat, 19 Apr 2025 11:57:39 +0000 Subject: [PATCH 31/43] restore --- .github/workflows/prod.yaml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 02ded922..e82ff4e3 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -23,11 +23,7 @@ jobs: run: | sudo ./docker/dependencies.sh Rscript -e "install.packages('yaml')" - - - name: Install R Dependencies - uses: r-lib/actions/setup-renv@v2 - with: - cache-version: 1 + Rscript -e 'renv::restore()' - name: Set up Quarto environment uses: quarto-dev/quarto-actions/setup@v2 From 4cc593451e572fbe70506a295c4b617bd0299e48 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Sat, 19 Apr 2025 12:06:20 +0000 Subject: [PATCH 32/43] force install yaml --- renv/activate.R | 1 + 1 file changed, 1 insertion(+) diff --git a/renv/activate.R b/renv/activate.R index 0eb51088..ddbc8a8c 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -1,3 +1,4 @@ +install.packages("yaml") local({ From e9fc1175a2d1559268ab1e12767162e2ed008799 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Sat, 19 Apr 2025 13:20:20 +0000 Subject: [PATCH 33/43] change location --- .Rprofile | 1 + renv/activate.R | 2 -- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.Rprofile b/.Rprofile index f2720dcd..3342e66c 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,3 +1,4 @@ +install.packages("yaml") source("renv/activate.R") if (file.exists('~/.Rprofile')) sys.source('~/.Rprofile', envir = environment()) diff --git a/renv/activate.R b/renv/activate.R index ddbc8a8c..2c9127fa 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -1,5 +1,3 @@ -install.packages("yaml") - local({ # the requested version of renv From bdf4427c1aa2353bc00859cfb326f4a4a02e4a94 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Sat, 19 Apr 2025 15:47:43 +0000 Subject: [PATCH 34/43] install renv --- .Rprofile | 1 - .github/workflows/prod.yaml | 6 +++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.Rprofile b/.Rprofile index 3342e66c..f2720dcd 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,4 +1,3 @@ -install.packages("yaml") source("renv/activate.R") if (file.exists('~/.Rprofile')) sys.source('~/.Rprofile', envir = environment()) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index e82ff4e3..4b76f7a0 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -23,7 +23,11 @@ jobs: run: | sudo ./docker/dependencies.sh Rscript -e "install.packages('yaml')" - Rscript -e 'renv::restore()' + + - name: Install renv packages + uses: r-lib/actions/setup-renv@v2 + with: + cache-version: 2 - name: Set up Quarto environment uses: quarto-dev/quarto-actions/setup@v2 From 10d5ec7e60f66cca1fd732fae266c3a7c61cf478 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Mon, 21 Apr 2025 13:00:47 +0000 Subject: [PATCH 35/43] remove renv --- .github/workflows/prod.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 147453d2..c5732850 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -22,6 +22,7 @@ jobs: - name: Install dependencies run: | sudo ./docker/dependencies.sh + rm .Rprofile - name: Install R Dependencies uses: r-lib/actions/setup-renv@v2 From b30d8cf3e3c601679fbac31865726077fbdb8a14 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Tue, 22 Apr 2025 08:00:03 +0000 Subject: [PATCH 36/43] rm renv --- .github/workflows/prod.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 4b76f7a0..fbb06e76 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -22,6 +22,7 @@ jobs: - name: Install dependencies run: | sudo ./docker/dependencies.sh + rm -rf renv/ Rscript -e "install.packages('yaml')" - name: Install renv packages From a58e0ad486f6e25b3928221bb342a9c982f11ea6 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Tue, 22 Apr 2025 09:17:48 +0000 Subject: [PATCH 37/43] install terra dependencies --- docker/dependencies.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docker/dependencies.sh b/docker/dependencies.sh index cb204794..50e8cde9 100755 --- a/docker/dependencies.sh +++ b/docker/dependencies.sh @@ -24,7 +24,8 @@ apt-get -qq install --no-install-recommends \ imagemagick \ libmagick++-dev \ ghostscript \ - libglpk40 + libglpk40 \ + libgdal-dev libgeos-dev apt-get -qq install --no-install-recommends \ libgs-dev \ From 4072d1f431fffea6a49ddcddd07ccd6e13450699 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Tue, 22 Apr 2025 12:27:22 +0000 Subject: [PATCH 38/43] libdunits --- docker/dependencies.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docker/dependencies.sh b/docker/dependencies.sh index 50e8cde9..97cf9720 100755 --- a/docker/dependencies.sh +++ b/docker/dependencies.sh @@ -25,7 +25,8 @@ apt-get -qq install --no-install-recommends \ libmagick++-dev \ ghostscript \ libglpk40 \ - libgdal-dev libgeos-dev + libgdal-dev libgeos-dev \ + libudunits2-dev apt-get -qq install --no-install-recommends \ libgs-dev \ From 5d911402d83c5136a0a8c9402232644ef981bae7 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Tue, 22 Apr 2025 12:36:12 +0000 Subject: [PATCH 39/43] rm keys --- docker/dependencies.sh | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/docker/dependencies.sh b/docker/dependencies.sh index 97cf9720..e3dbb6fc 100755 --- a/docker/dependencies.sh +++ b/docker/dependencies.sh @@ -3,16 +3,6 @@ # Update package lists apt-get update && apt-get -qq install gnupg -# Add Debian sources to apt and import necessary GPG keys -sh -c 'echo "deb http://http.us.debian.org/debian stable main contrib non-free" >> /etc/apt/sources.list' -apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138 -apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9 -apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 605C66F00D6C9793 - -# Update package lists and set debconf selections for mscorefonts installer -apt-get update -echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true" | debconf-set-selections - # Install necessary packages without recommended dependencies apt-get -qq install --no-install-recommends \ ttf-mscorefonts-installer \ From b3b8eefcf148f0098aaa37401a8621b8fb044cb0 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Tue, 22 Apr 2025 12:37:04 +0000 Subject: [PATCH 40/43] rm fonts --- docker/dependencies.sh | 3 --- 1 file changed, 3 deletions(-) diff --git a/docker/dependencies.sh b/docker/dependencies.sh index e3dbb6fc..6c70f511 100755 --- a/docker/dependencies.sh +++ b/docker/dependencies.sh @@ -5,9 +5,6 @@ apt-get update && apt-get -qq install gnupg # Install necessary packages without recommended dependencies apt-get -qq install --no-install-recommends \ - ttf-mscorefonts-installer \ - fonts-liberation \ - fonts-freefont-ttf \ libssl-dev apt-get -qq install --no-install-recommends \ From ea124ca47309e0b0ed05b94ec9d96813b7ff0b21 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Tue, 22 Apr 2025 14:36:01 +0000 Subject: [PATCH 41/43] update --- 01_R_Insee/presentation_utilitr.qmd | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/01_R_Insee/presentation_utilitr.qmd b/01_R_Insee/presentation_utilitr.qmd index 88b1b195..3a5938b3 100644 --- a/01_R_Insee/presentation_utilitr.qmd +++ b/01_R_Insee/presentation_utilitr.qmd @@ -36,12 +36,7 @@ avec `Github`. -```{r} -#| echo: false -#| output: false -#| warning: false -liste_contributeurs <- paste0(paste(format(Filter(function(x) !("cph" %in% x$role), desc::desc_get_authors()), include = c("given", "family")), collapse = ", "), ".") -``` +_to be completed_ Le projet `utilitR` est un projet collaboratif qui a bénéficié des contributions de : `{r} liste_contributeurs` From d80933265707c6d52573491fe85ad17ff9efc130 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Tue, 22 Apr 2025 15:59:34 +0000 Subject: [PATCH 42/43] eval false --- .../Fiche_utiliser_Rstudio_SSPCloud.qmd | 384 ------------------ 01_R_Insee/Fiche_utiliser_ressources.qmd | 21 +- .../Fiche_configurer_git.qmd | 4 + .../Fiche_git_utilisation.qmd | 4 + 03_Fiches_thematiques/Fiche_rmarkdown.qmd | 4 + .../Fiche_rmarkdown_param_report.qmd | 4 + 03_Fiches_thematiques/Fiche_rprojects.qmd | 4 + _quarto.yml | 1 - 8 files changed, 29 insertions(+), 397 deletions(-) delete mode 100644 01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd diff --git a/01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd b/01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd deleted file mode 100644 index 576d5721..00000000 --- a/01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd +++ /dev/null @@ -1,384 +0,0 @@ -# Utiliser `RStudio` sur l'environnement SSP Cloud {#sspcloud} - -::: {.callout-important} -## Tâche concernée et recommandation - -Vous pouvez utiliser `R` et RStudio sur le SSP Cloud pour mener des expérimentations qui seraient difficiles à réaliser dans AUS. En revanche, le SSP Cloud ne doit pas être utilisé pour réaliser des tâches de production statistique, ni pour traiter des données confidentielles. -::: - -::: {.callout-note} -Certains exemples de cette fiche utilisent les données disponibles dans le _package_ `doremifasolData` ; vous ne pourrez reproduire ces exemples que si ce _package_ est installé sur la machine sur laquelle vous travaillez. Si vous ne savez pas si ce _package_ est déjà installé, consultez la fiche [Comment utiliser la documentation `utilitR`](#presentation-utilitr). -::: - -## Présentation succincte du SSP Cloud - -**Le SSP Cloud est une plate-forme informatique hébergée à l'Insee et ouverte à tous les agents de la statistique publique.** Elle permet aux statisticiens d'utiliser un grand nombre de logiciels de _data science_ (`R`, `Python`, `PostgreSQL`, `Jupyter`, `Spark`, `Tensorflow`...) dans un environnement informatique ergonomique et performant. Il faut donc noter que le SSP Cloud n'est donc pas spécifiquement conçu pour utiliser `R`. - -**Le SSP Cloud est une plate-forme sur laquelle vous pouvez mener des expérimentations qui seraient difficiles à réaliser dans AUS**, soit parce qu'AUS ne propose pas le logiciel dont vous avez besoin, soit parce que votre traitement demande des ressources informatiques particulièrement importantes. - -En revanche, **le SSP Cloud n'est pas une infrastructure de production, et n'offre donc pas les mêmes garanties de service qu'AUS**. De plus, le traitement de données confidentielles sur le SSP Cloud n'est pas autorisé par défaut. - - -## Comment travailler avec un service RStudio sur le SSP Cloud - -### Créer un compte sur le SSP Cloud - -Il est nécessaire de disposer d'un compte personnel **SSP Cloud** pour en utiliser les services. Si vous n'avez pas de compte sur le **SSP Cloud**, vous pouvez vous en créer un en [cliquant sur ce lien (https://datalab.sspcloud.fr/home)](https://datalab.sspcloud.fr/home) puis suivre les indications. Deux points sont importants à noter : - -- vous devez utiliser votre adresse mail professionnelle (de l'Insee ou de votre SSM) ; -- **votre nom d'utilisateur ne doit contenir ni caractères accentués, ni caractère spécial, ni signe de ponctuation**. Ce point est essentiel, car votre compte ne fonctionnera pas si votre nom d'utilisateur comprend l'un de ces caractères. Pour les agents de l'Insee, le plus simple est de choisir votre IDEP puisqu'il respecte ces règles. Pour les agents des SSM ne disposant pas d'IDEP, vous pouvez adopter le format `prenomnom` en faisant attention aux règles précédentes. Par exemple, si vous vous appelez Jérôme-Gérard L'Hâltère, votre nom d'utilisateur pourra être `jeromegerardlhaltere`. - -::: {.callout-note} -La grande majorité des problèmes rencontrés à la création d'un compte SSP Cloud découle d'un `username` ne respectant pas ces règles. Dans ce cas, la seule solution consiste à demander aux administrateurs du SSP Cloud de supprimer votre compte, pour que vous puissiez en créer un nouveau. Vous pouvez contacter les administrateurs en écrivant un message sur le [salon Tchap `SSPCloud`](https://www.tchap.gouv.fr/#/room/#SSPCloudXDpAw6v:agent.finances.tchap.gouv.fr). -::: - -### Changer la langue du SSP Cloud - -Par défaut, l'interface du SSP Cloud est en anglais. Pour choisir le français, deux solutions sont offertes : - -- Cliquer en bas à droite de la fenêtre puis choisir le français dans les options proposées. - -![](../pics/SSPCloud/00_choisir_langue.png){fig-alt="Lancer un service RStudio"} - -- Cliquer sur `My account` dans le menu de gauche puis dans l'onglet `Interface preferences` vous pouvez changer la langue dans la fenêtre qui s'affiche. - -### Créer un service RStudio - -Voici comment procéder pour créer un service RStudio (avec l'interface en français) : - -- [Cliquer sur l'onglet **"Catalogue de services"**](https://datalab.sspcloud.fr/my-lab/catalogue) qui est accessible à gauche grâce au symbole - -![](../pics/SSPCloud/inline_pics/01_bouton_services.png){width="30px"} - -- La fenêtre suivante s'affiche (pour y accéder directement, -[suivre ce lien](https://datalab.sspcloud.fr/catalog/inseefrlab-helm-charts-datascience)). - - -![](../pics/SSPCloud/01_catalogue_services.png) - - -- RStudio est à la une. Cliquer sur le bouton `LANCER` ; -- La page suivante s'ouvre : - -![](../pics/SSPCloud/02_lancer_rstudio.png){fig-alt="Lancer un service RStudio"} - -- Dans la page qui s'affiche, vous pouvez définir les options de votre service RStudio (voir la section [Définir les options d'un service RStudio](#options-rstudio)). -Vous pouvez lancer le service en cliquant sur **Lancer**. - - -![](../pics/SSPCloud/02b_lancer_rstudio_options.png){fig-alt="Page de création d'un service RStudio"} - - - - -### Accéder à ses services - -Pour accéder à l'ensemble de ses services, il est nécessaire de cliquer sur le bouton -```{r bouton_mes_services, out.extra='style="display: inline-block; padding: 0; width: 30px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/03_bouton_mes_services.png", compression = FALSE) -``` -\ . La page qui s'ouvre permet alors de lister l'ensemble des services ouverts : - -```{r, echo = FALSE, fig.cap= "Liste des services ouverts", out.width = "100%"} -utilitr::include_image("../pics/SSPCloud/03_liste_services.png", ratio_compression = 1) -``` - -Pour accéder à l'un d'eux il faut cliquer sur le bouton - -![](../pics/SSPCloud/inline_pics/Se_connecter_service.png){width="60px"} - -Il est recommandé de ne pas garder actifs des services qui ne sont plus utiles. -Au coût environnemental d'avoir des ressources allouées inactives, s'ajoute -le fait que cela mobilise des ressources qui pourraient être utilisées -par d'autres. La procédure pour fermer des services est décrite plus bas. - - -### Se connecter à un service RStudio - -Une fois que votre service RStudio est créé, il faut vous connecter à ce service. -Pour ce faire, il faut vous identifier avec un nom d'utilisateur -et un mot de passe (différent de celui de votre compte SSP Cloud). -Pour récupérer ce mot de passe, il y a deux façons de faire. Vous pouvez cliquer sur `README` et copier le mot de passe, ou cliquer sur la clé -```{r key_button, out.extra='style="display: inline-block; padding: 0; width: 120px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/key.png", compression = FALSE) -``` -\ présente dans la page -*Mes services* -```{r, out.extra='style="display: inline-block; padding: 0; width: 30px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/03_bouton_mes_services.png", compression = FALSE) -``` -\ . Cette action permet de copier le mot de passe dans le presse-papier ce qui -facilite son utilisation. - -Pour accéder à un service, le bouton -```{r, out.extra='style="display: inline-block; padding: 0; width: 60px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/Se_connecter_service.png", compression = FALSE) -``` -\ permet d'ouvrir une page d'authentification. - -```{r 99_SSPCloud_4bis, echo = FALSE, out.width = "80%"} -utilitr::include_image("../pics/SSPCloud/99_SSPCloud_4bis.png", ratio_compression = 1) -``` - -Les identifiants sont : - -- `Username` : `rstudio` ; -- `Password` : le _password_ copié précédemment (il suffit de faire `Ctrl + V`). - -```{r 99_SSPCloud_5bis, echo = FALSE, out.width = "50%"} -utilitr::include_image("../pics/SSPCloud/99_SSPCloud_5bis.png", ratio_compression = 1) -``` - -L'interface habituelle de RStudio s'affiche alors dans la fenêtre. - -```{r 99_SSPCloud_6, echo = FALSE, out.width = "80%"} -utilitr::include_image("../pics/SSPCloud/99_SSPCloud_6.png", ratio_compression = 1) -``` - -## Définir les options d'un service RStudio {#options-rstudio} - -Lors de la création de votre service RStudio, vous pouvez définir les options du service en naviguant dans les différents onglets de l'interface du SSP Cloud (cadre rouge). - -```{r, echo = FALSE, out.width = "100%"} -utilitr::include_image("../pics/SSPCloud/99_SSPCloud_3bis.png", ratio_compression = 1) -``` - -Les principales options sont les suivantes : - -- L'**option `memory`** (dans l'onglet `Resources`) définit la quantité minimum garantie de mémoire vive (mesurée en Mo) que votre service RStudio peut utiliser. **Cette option est particulièrement importante** et vous devez choisir soigneusement sa valeur : si vos traitements requièrent plus de mémoire que la valeur de `mem`, la seule solution consiste à lancer un autre service RStudio avec une valeur de `mem` plus élevée. Il est conseillé d'utiliser 10000 comme valeur par défaut. -- L'**option `cpu`** (dans l'onglet `Resources`) définit le nombre minimal de processeurs alloués à votre service RStudio, c'est un minimum garanti. Il est conseillé d'utiliser 2 comme valeur par défaut si vos traitements nécessitent de la parallélisation et laisser l'option par défaut sinon. -- L'**option `Enable IP protection`** (dans l'onglet `Security`) est une option de sécurité informatique assez contraignante, qui est activée par défaut. Il est conseillé de la laisser activée. Toutefois, vous pouvez éventuellement la désactiver, notamment si vous savez que vous allez devoir accéder à l'environnement RStudio depuis des adresses IP différentes (exemple : au bureau puis en télétravail). -- L'**option `version`** (dans l'onglet `Service`) détermine l'environnement dans lequel RStudio va s'ouvrir. Il s'agit d'un environnement contenant une version donnée de `R` ainsi que des packages pré-installés. Par exemple, l'image `utilitR` disponible propose l'ensemble des dépendances (elles sont nombreuses...) nécessaires pour reproduire tous les exemples présents dans cette documentation. -- L'**option `PersonalInit`** (dans l'onglet `Init`) permet de référencer un script d'initialisation qui exécutera une série d'actions prédéfinies avant de lancer le service, par exemple copier localement des données, lancer un projet RStudio ou définir des paramètres d'affichage de l'interface. Un exemple d'un tel fichier Init utilisé pour des formations peut être trouvé [ici](https://github.com/InseeFrLab/formation-r-lissage-spatial/blob/f3258469513cabd2de328dc92165641f8f452bca/utils/init.sh). C'est l'URL du fichier sur github.com qui doit être référencé, **dans sa version *Raw*** (afficher le fichier dans Github et cliquer sur `Raw` en haut à droite pour obtenir cette URL). - -::: {.callout-note} -**Les options d'un service RStudio ne peuvent être définies qu'au moment de la création du service.** Si vous vous rendez compte qu'une option du service ne convient pas au traitement que vous voulez faire, vous devez supprimer votre service RStudio et en lancer un nouveau avec les bonnes options. Lorsqu'un ensemble d'options vous conviennent, il est possible de l'enregistrer pour les retrouver lors du prochain lancement d'un service. Pour cela, cliquez sur l'icône de marque-page en haut à droite du panneau de paramétrage. La liste des configurations ainsi définies comme favorites apparaîtront dans SSP Cloud dans la rubrique `Mes services`, dans la colonne `Enregistrés`. -::: - -### Utiliser Github et Gitlab sur le SSP Cloud - -Les services ouverts sur le SSPCloud ont une durée de vie limitée. -Pour conserver les codes afin de pouvoir les réutiliser ultérieurement ou les -rendre disponibles à d'autres personnes, il est nécessaire d'utiliser une -plateforme type Gitlab et Github. - -Dans le catalogue des services, une plateforme Gitlab est disponible. -Son adresse est (c'est un [`Service partagé`](https://datalab.sspcloud.fr/services)). Cependant, elle n'apporte pas un niveau de sécurité -supérieur aux plateformes ou -. Il est donc recommandé de privilégier l'une de -ces deux plateformes plutôt que le `Gitlab` mis à disposition sur le -SSPCloud. - -Le SSPCloud ne permet qu'une authentification HTTPS. L'authentification SSH -est donc désactivée -(voir la fiche [Configurer `Git` sur son poste de travail](#git-config) pour plus -de détails). Les fonctionnalités standards de RStudio pour favoriser l'usage -de Git sont disponibles (voir la fiche [Utiliser `Git` avec RStudio](#git) pour plus -de détails). - - -### Supprimer un service RStudio - -Les services RStudio peuvent être arrêtés à tout moment. Avant d'arrêter un service -RStudio, il est recommandé de s'assurer que les codes (via Gitlab ou autre Forge utilisant Git, voir ci-dessus) -et les données (via S3, voir ci-dessous) à conserver ont bien été -sauvegardés. - -```{r 04_exemple_service, echo = FALSE, fig.cap= "Accéder aux options d'un service", out.width = "35%"} -utilitr::include_image("../pics/SSPCloud/04_exemple_service.png", ratio_compression = 1) -``` - -Pour supprimer un service, il faut se servir de l'un des trois boutons qui permettent d'accéder aux options d'un service RStudio (cadre rouge) : - -* Le bouton de gauche permet d'obtenir des informations sur la configuration de votre service (notamment pour l'accès au système de stockage S3) ; -* Le bouton du milieu permet de tuer définitivement un service qui disparaîtra -du tableau des services ouverts ; -* Le dernier de droite d'accéder à *Graphana*, un outil qui permet de -suivre en temps réel l'usage mémoire et CPU d'un service RStudio. C'est utile pour bien comprendre ce que fait votre service RStudio. - -## Utiliser des données stockées sur le système de stockage S3 - -### Pourquoi utiliser S3 sur le SSP Cloud ? - -Le SSP Cloud propose des environnements (comme les services ` RStudio`, `Jupyter`, etc.) pour exécuter des programmes informatiques. Ces environnements sont **temporaires par définition** (quelques heures ou quelques jours), et ne peuvent donc pas servir à stocker des données ou des programmes informatiques. Cela a pour conséquence que les programmes informatiques et les données doivent être stockés dans d'autres espaces : - -* *stockage des codes* : il est nécessaire d'utiliser une plate-forme de développement pour stocker des programmes informatiques, telles que [Gitlab](www.gitlab.com) ou [Github](www.github.com). -* *stockage des données* : la plateforme SSP Cloud propose un système de stockage de données nommé S3. Depuis votre service RStudio, vous pourrez facilement accéder à des données stockées sur S3 grâce au _package_ `aws.s3`. - -::: {.callout-note} -Voici deux règles à respecter pour faire un bon usage de ces deux espaces de stockage : - -* Les plate-formes telles que Gitlab ou Github ne doivent **jamais** être utilisées pour stocker des données (uniquement des codes). -* Le système de stockage S3 ne doit **jamais** être utilisé pour stocker des données confidentielles. -::: - -### Qu'est-ce que le système de stockage S3 ? - -Le système S3 (*Simple Storage System*) est un système de stockage développé par Amazon et qui est maintenant devenu une référence pour le stockage en ligne. Il s'agit d'une architecture à la fois sécurisée (données cryptées, accès restreints) et performante. - -Le concept central du système S3 est le *bucket*. Un *bucket* est un espace (privé ou partagé) où on peut stocker une arborescence de fichiers. Pour accéder aux fichiers figurant dans un *bucket* privé, il faut fournir des jetons d'accès (l'équivalent d'un mot de passe) reconnus par le serveur de stockage. On peut alors lire et écrire dans le *bucket*. - -### Explorer son dépôt de fichiers - -Il est possible d'utiliser l'interface du `SSP Cloud` pour explorer les fichiers présents dans S3 ainsi qu'ajouter ou télécharger manuellement des fichiers. Le raccourci pour accéder aux fichiers disponibles se trouve dans la barre latérale *Mes fichiers* -```{r onyxia_files, out.extra='style="display: inline-block; padding: 0; width: 30px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/onyxia_files.png", compression = FALSE) -``` -\ . En cliquant sur cette icône, on ouvre un explorateur qui permet de visualiser les fichiers présents sur son *bucket* personnel : - -```{r onyxia_files2, echo = FALSE, out.width = "100%"} -utilitr::include_image("../pics/SSPCloud/minio/onyxia_files2.png", ratio_compression = 1) -``` - -Il est possible de naviguer dans l'arborescence depuis cette fenêtre afin, par exemple, de récupérer un chemin qu'on va utiliser avec `R`. La vignette verte sur la droite indique la commande à utiliser dans un terminal pour lister les fichiers du répertoire courant. Elle permet donc notamment de connaître le chemin d'accès à un fichier permettant d'y accéder à travers un service RStudio du SSP Cloud. - -Par défaut, le *bucket* utilisateur créé à l'inscription sur le SSP Cloud est vierge. Il est néanmoins utile de créer directement un dossier particulier, nommé "diffusion". Grâce à une politique de droits spécifique, ce dossier et son contenu sont accessibles (en lecture) à tous les utilisateurs du SSP Cloud. Il est donc à privilégier pour déposer des fichiers destinés à être diffusés, comme des données partagées ou des supports de formation. - -### Utiliser S3 avec un service RStudio - -**Lorsqu'on crée un service RStudio sur le SSP Cloud, des droits d'accès temporaires au système S3 sont automatiquement initialisés.** Ces droits permettent de communiquer avec le serveur de stockage, mais leur usage est complexe. Heureusement, il existe le _package_ `aws.s3` qui simplifie beaucoup les interactions entre le service RStudio et S3 en proposant des fonctions de lecture et d'écriture similaires à celles existantes pour lire ou écrire un fichier depuis un poste personnel. - -#### Vérifier les droits d'accès à un *bucket* - -**Pour lister l'ensemble des fichiers disponibles dans un _bucket_, il suffit de charger le _package_ `aws.s3` et d'exécuter la commande `get_bucket()`.** Cette commande donne quelques informations sur les fichiers stockés dans le _bucket_ : nom et emplacement, taille et date de dernière modification. Il n'est pas nécessaire de configurer les droits d'accès au système S3, car le service RStudio en dispose dès son lancement. - -Imaginons qu'on souhaite accéder au _bucket_ nommé `donnees-insee` qui contient des fichiers d'exemples ([lien](https://datalab.sspcloud.fr/my-files/donnees-insee)) et auquel tout utilisateur du SSP-Cloud a accès. Voici comment afficher la liste des objets contenus dans ce _bucket_ : - -```{r, eval = FALSE} -# Attention cet exemple renvoie un très grand nombre de résultats -# library(aws.s3) -aws.s3::get_bucket("donnees-insee", region = "") -``` - -::: {.callout-tip} -La commande `get_bucket()` peut renvoyer un grand nombre de résultats si le _bucket_ contient un grand nombre de fichiers. Le _bucket_ `donnees-insee` contient ainsi plus de 1000 fichiers. Il est donc conseillé d'utiliser l'option `prefix` pour restreindre le chemin des fichiers que l'on souhaite lister. Par exemple, le code suivant fournit la liste des fichiers situés dans le répertoire `diffusion/ESTEL/2015` du _bucket_ `donnees.insee` : - -```{r, eval = FALSE} -#library(aws.s3) -aws.s3::get_bucket("donnees-insee", region = "", prefix = "diffusion/ESTEL/2015") -``` -::: - -#### Renouveler des droits d'accès périmés - -**Les droits d'accès au S3 sont temporaires par définition et sont donc rapidement périmés.** Si vous utilisez un service RStudio pendant plusieurs jours, il est probable que `R` renverra l'erreur suivante : - -```{text} -$ Code : chr "InvalidAccessKeyId" -$ Message : chr "The Access Key Id you provided does not exist in our records." -$ BucketName : chr "donnees-insee" -$ Resource : chr "/donnees-insee/" -[... lignes coupées ...] -Error in parse_aws_s3_response(r, Sig, verbose = verbose) : - Forbidden (HTTP 403). -``` - -Voici la procédure à suivre pour renouveler les droits d'accès à S3. Cliquer sur `Mon compte` -```{r, out.extra='style="display: inline-block; padding: 0; width: 30px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/moncompte.png", compression = FALSE) -``` - -Cliquer sur l'onglet `Connexion au stockage`. -La première ligne vous indique jusqu'à quand les droits d'accès sont valides. Vérifier que les droits d'accès sont bien formatés pour `R` (cadre rouge), puis copier les droits d'accès (cadre bleu). - -```{r, echo = FALSE, out.width = "70%"} -utilitr::include_image("../pics/SSPCloud/jetons_onyxia.png", ratio_compression = 1) -``` - - - -Coller les droits d'accès dans un script `R` de votre service RStudio, puis exécuter les lignes de code sélectionnées dans la capture d'écran ci-dessous. Le bouton dans le cadre bleu ci-dessus permet de -copier les commandes qui conviennent dans le presse-papier. La partie la -plus importante est la suivante (en remplaçant `XXXXXXXXXXXXXXXXX` -par les valeurs en question): - -```{r, eval = FALSE} -Sys.setenv("AWS_ACCESS_KEY_ID" = "XXXXXXXXXXXXXXXXX", - "AWS_SECRET_ACCESS_KEY" = "XXXXXXXXXXXXXXXXX", - "AWS_DEFAULT_REGION" = "us-east-1", - "AWS_SESSION_TOKEN" = "XXXXXXXXXXXXXXXXX", - "AWS_S3_ENDPOINT"= "minio.lab.sspcloud.fr") -``` - -Ces variables d'environnement permettent au package `aws.s3` de -déterminer la localisation du système de fichier et l'identité -de la session `R` - - - - -#### Lire les fichiers d'un *bucket* - -**Une fois que l'on connaît l'emplacement d'un objet dans un _bucket_, on peut l'importer dans le service RStudio avec la fonction `s3read_using()`.** Cette fonction permet d'importer n'importe quel objet, mais nécessite que l'on précise la fonction à utiliser pour lire l'objet. Les arguments de `s3read_using()` sont les suivants : - -- `FUN` : la fonction à utiliser pour lire le fichier ; cet argument doit être écrit sous la forme `package::function` ; -- `object` : le chemin du fichier à importer ; -- `bucket` : le _bucket_ dans lequel se trouve l'objet ; -- `opts` : les options. - -Dans l'exemple qui suit, on souhaite importer les données du dispositif Filosofi 2017 agrégées par commune, qui sont stockées dans le chemin `/diffusion/FILOSOFI/2017/FILOSOFI_COM.csv` dans le *bucket* `donnees-insee`. On importe ces données avec la fonction `fread()` du _package_ `data.table`. Vous pouvez consulter la fiche [Importer des fichiers plats (`.csv`, `.tsv`, `.txt`)] pour une présentation détaillée de cette fonction. - -```{r, eval = FALSE} -df <- - aws.s3::s3read_using( - FUN = data.table::fread, - # Mettre les options de FUN ici - object = "/diffusion/FILOSOFI/2016/FILOSOFI_COM.csv", - bucket = "donnees-insee", - opts = list("region" = "") - ) -``` - -Il est possible d'utiliser toutes les options de la fonction d'importation, en les ajoutant immédiatement après l'argument `FUN`. Ainsi, dans l'exemple qui suit, les options `nrows` et `select` de la fonction `fread()` sont utilisées pour importer uniquement les 1000 premières lignes du fichier, et pour sélectionner trois colonnes. - -```{r, eval = FALSE} -df2 <- - aws.s3::s3read_using( - FUN = data.table::fread, - # Les options de fread sont ici - nrows = 1000L, - select = c("CODGEO", "LIBGEO", "TP6016"), - object = "/diffusion/FILOSOFI/2016/FILOSOFI_COM.csv", - bucket = "donnees-insee", - opts = list("region" = "") - ) -``` - - -#### Ecrire un fichier dans un *bucket* - -**La fonction `s3write_using()` permet d'exporter un objet depuis le service RStudio vers un _bucket_, mais nécessite que l'on précise la fonction à utiliser pour écrire l'objet.** Exporter vers un _bucket_ nécessite évidemment d'avoir les droits en écriture sur le _bucket_ concerné. Les arguments de `s3write_using()` sont les suivants : - -- `x` : l'objet à exporter ; -- `FUN` : la fonction à utiliser pour écrire le fichier ; cet argument doit être écrit sous la forme `package::function` ; -- `object` : le chemin du fichier à exporter ; -- `bucket` : le _bucket_ dans lequel l'objet sera exporté ; -- `opts` : les options. - -Comme pour la fonction `s3read_using`, il est possible d'utiliser toutes les options de la fonction d'exportation, en les ajoutant immédiatement après l'argument `FUN`. Dans l'exemple suivant, on charge dans le service RStudio la table du code officiel géographique 2019 disponible dans le _package_ `doremifasolData`, puis on l'exporte en format `csv` dans le fichier `data/cog_com_2019.csv` du _bucket_ `mon_bucket`. On utilise les options `sep` et `col.names` de la fonction `fwrite()` pour définir le séparateur et exporter les noms de colonnes. - -```{r, eval = FALSE} -# Attention, cet exemple n'est pas directement reproductible -# Il faut avoir les droits en écriture sur le bucket -library(doremifasolData) -cog_com_2019 <- doremifasolData::cog_com_2019 - -aws.s3::s3write_using( - cog_com_2019, - FUN = data.table::fwrite, - # Les options de fread sont ici - sep = " ;", - col.names = TRUE, - object = "data/cog_com_2019.csv", - bucket = "mon_bucket", - opts = list("region" = "") -) -``` - - -## Liens utiles - -- Le salon Tchap [SSPCloud](https://www.tchap.gouv.fr/#/room/#SSPCloudXDpAw6v:agent.finances.tchap.gouv.fr) ; -- Le salon Tchap d'assistance aux utilisateurs des **Logiciels Statistiques et Libre Service** [Insee - Outils Stats V2](https://www.tchap.gouv.fr/#/room/#InseeOutilsStatsv2wtxSdth:agent.finances.tchap.gouv.fr) ; -- Un [tutoriel sur le SSP Cloud](https://github.com/RLesur/sspcloud-demo). -- La [documentation en ligne du Datalab](https://docs.sspcloud.fr/) diff --git a/01_R_Insee/Fiche_utiliser_ressources.qmd b/01_R_Insee/Fiche_utiliser_ressources.qmd index c87aaa86..0a38d0e7 100644 --- a/01_R_Insee/Fiche_utiliser_ressources.qmd +++ b/01_R_Insee/Fiche_utiliser_ressources.qmd @@ -79,9 +79,9 @@ clavier suivant : Ctrl + ⇧ Shift + Echap. ::: Lorsque la fenêtre suivante s'affiche, il faut cliquer sur `Plus de détails`. -```{r entree_fiche_tskmngr, echo = FALSE, fig.cap = "Le gestionnaire des tâches Windows", out.width = "50%"} -utilitr::include_image("../pics/utiliser_ressources/TskMngr1small.png", compression = FALSE) -``` +![](/pics/utiliser_ressources/TskMngr1small.png) + + ### Utiliser le gestionnaire des tâches @@ -91,9 +91,7 @@ L'onglet qui vous sera le plus utile est l'onglet `Utilisateurs`. Il affiche la - les lignes du tableau indiquent le taux d'utilisation des processeurs et le taux d'occupation de la mémoire vive, _au niveau de chaque utilisateur_. Vous devez normalement retrouver votre IDEP dans la première colonne (les IDEP sont masqués sur les captures d'écran pour des raisons de sécurité). Le cadre bleu correspond par exemple à l'auteur de cette fiche. Vous pouvez constater qu'il utilise 7,5% des processeurs et qu'il occupe environ 10 Go de mémoire vive. - En cliquant sur la petite flèche grise (indiquée par la flèche noire), vous pouvez afficher la consommation de ressources de chacun des programmes que vous utilisez. -```{r, echo = FALSE, fig.cap= "L'onglet Utilisateurs du gestionnaire des tâches"} -utilitr::include_image("../pics/utiliser_ressources/TskMngr2bis.png", compression = FALSE) -``` +![](/pics/utiliser_ressources/TskMngr2bis.png) Voici trois références à garder en tête pour superviser votre session `R` : @@ -164,13 +162,12 @@ Il y a deux façons de nettoyer la mémoire vive: - Méthode n°1: exécuter `gc()`; - Méthode n°2: utiliser l'interface proposée par RStudio. Il faut cliquer sur la petite flèche rouge, puis sur `Free unused R Memory`. -```{r, echo = FALSE, fig.cap = "Libérer la mémoire inutilisée", out.width = "50%"} -utilitr::include_image("../pics/utiliser_ressources/gc_gui1.png", compression = FALSE) -``` -```{r, echo = FALSE, out.width = "50%"} -utilitr::include_image("../pics/utiliser_ressources/gc_gui2.png", compression = FALSE) -``` +![](/pics/utiliser_ressources/gc_gui1.png) + + +![](/pics/utiliser_ressources/gc_gui2.png) + ::: {.callout-note} Voici deux remarques sur la fonction `gc()` : diff --git a/03_Fiches_thematiques/Fiche_configurer_git.qmd b/03_Fiches_thematiques/Fiche_configurer_git.qmd index c21ca1ed..8cf47bb5 100644 --- a/03_Fiches_thematiques/Fiche_configurer_git.qmd +++ b/03_Fiches_thematiques/Fiche_configurer_git.qmd @@ -1,3 +1,7 @@ +--- +eval: false +--- + # Configurer `Git` sur son poste de travail {#git-config} ## Tâches concernées et recommandations diff --git a/03_Fiches_thematiques/Fiche_git_utilisation.qmd b/03_Fiches_thematiques/Fiche_git_utilisation.qmd index 0c682a37..0391eb13 100644 --- a/03_Fiches_thematiques/Fiche_git_utilisation.qmd +++ b/03_Fiches_thematiques/Fiche_git_utilisation.qmd @@ -1,3 +1,7 @@ +--- +eval: false +--- + # Utiliser `Git` avec RStudio {#git} ## Tâches concernées et recommandations diff --git a/03_Fiches_thematiques/Fiche_rmarkdown.qmd b/03_Fiches_thematiques/Fiche_rmarkdown.qmd index e2ab93c9..e4daa4c0 100644 --- a/03_Fiches_thematiques/Fiche_rmarkdown.qmd +++ b/03_Fiches_thematiques/Fiche_rmarkdown.qmd @@ -1,3 +1,7 @@ +--- +eval: false +--- + # Produire des documents avec `R Markdown` {#rmarkdown} diff --git a/03_Fiches_thematiques/Fiche_rmarkdown_param_report.qmd b/03_Fiches_thematiques/Fiche_rmarkdown_param_report.qmd index 89fd7745..3760efd7 100644 --- a/03_Fiches_thematiques/Fiche_rmarkdown_param_report.qmd +++ b/03_Fiches_thematiques/Fiche_rmarkdown_param_report.qmd @@ -169,6 +169,10 @@ params: Il faut ensuite remplacer dans les différents _chunks_ le code du département par `params$codeDpt`. Une fois ces 2 modifications (en-tête et _chunks_) effectués, il n'est plus besoin de changer le département qu'à un seul endroit. +--- +eval: false +--- + ### Utiliser un modèle de rapport paramétré Une fois que le modèle de rapport paramétré est défini, il est possible de l'utiliser pour publier facilement des rapports. La compilation du code source avec la commande `rmarkdown::render("rapportParametre.Rmd")` générera le document suivant : diff --git a/03_Fiches_thematiques/Fiche_rprojects.qmd b/03_Fiches_thematiques/Fiche_rprojects.qmd index 9530c399..b184c288 100644 --- a/03_Fiches_thematiques/Fiche_rprojects.qmd +++ b/03_Fiches_thematiques/Fiche_rprojects.qmd @@ -1,3 +1,7 @@ +--- +eval: false +--- + # Utiliser les projets `RStudio` {#rproject} ::: {.callout-important} diff --git a/_quarto.yml b/_quarto.yml index 9beef0ef..33fd4a71 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -106,7 +106,6 @@ book: - part: "Éléments de configuration" chapters: - 01_R_Insee/Fiche_utiliser_Rstudio_AUSv3.qmd - - 01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd - 03_Fiches_thematiques/Fiche_configurer_git.qmd - 01_R_Insee/Fiche-personnaliser-R.qmd - 01_R_Insee/Fiche_utiliser_ressources.qmd From 8d658ed6dde5f8c2c5bd12b5c46f8c2d3a35ccf6 Mon Sep 17 00:00:00 2001 From: lgaliana Date: Tue, 22 Apr 2025 17:01:24 +0000 Subject: [PATCH 43/43] with_def --- 01_R_Insee/Fiche_installer_packages.qmd | 2 +- .../Fiche_configurer_git.qmd | 6 +- .../Fiche_git_utilisation.qmd | 73 +++++++++---------- 3 files changed, 40 insertions(+), 41 deletions(-) diff --git a/01_R_Insee/Fiche_installer_packages.qmd b/01_R_Insee/Fiche_installer_packages.qmd index 04434162..fdf11dd9 100644 --- a/01_R_Insee/Fiche_installer_packages.qmd +++ b/01_R_Insee/Fiche_installer_packages.qmd @@ -122,7 +122,7 @@ contiendra les modifications les plus récentes. Installer depuis une forge permet ainsi de récupérer la version de développement d'un _package_ (seules les versions stables sont en général disponibles sur le CRAN). Pour installer un _package_ tel qu'il était à un moment donné, il est également possible de -faire suivre le nom du dépôt par une référence à un `r with_def("commit")`, à un _tag_ (une version) ou à une `r with_def("branche")`. Voici un exemple avec un _tag_ : `remotes::install_gitlab("py_b/funprog@v-0.3.0")`. Voici un exemple avec un commit : `remotes::install_github("InseeFrLab/doremifasolData@a9df2d3d0e372")`. +faire suivre le nom du dépôt par une référence à un `commit`, à un _tag_ (une version) ou à une ` branche`. Voici un exemple avec un _tag_ : `remotes::install_gitlab("py_b/funprog@v-0.3.0")`. Voici un exemple avec un commit : `remotes::install_github("InseeFrLab/doremifasolData@a9df2d3d0e372")`. ::: {.callout-note} Lorsque vous installez un _package_ depuis une forge logicielle, `R` crée automatiquement une archive temporaire (un fichier `.tar.gz`), puis installe le _package_ à partir de celle-ci. Si vous travaillez dans un environnement Windows, il est nécessaire que `Rtools` soit installé sur votre poste pour que `R` puisse construire l'archive. diff --git a/03_Fiches_thematiques/Fiche_configurer_git.qmd b/03_Fiches_thematiques/Fiche_configurer_git.qmd index 8cf47bb5..77d0f92e 100644 --- a/03_Fiches_thematiques/Fiche_configurer_git.qmd +++ b/03_Fiches_thematiques/Fiche_configurer_git.qmd @@ -25,7 +25,7 @@ un _login_ et un mot de passe. ## Les différentes forges utilisables -Une `r with_def("forge")` est un espace informatique en ligne qui accueille des dépôts distants. Un dépôt distant (_remote repository_ en anglais) est un dossier que vous pouvez utiliser pour stocker vos codes (et leur historique), et pour partager des codes avec vos collègues ou stocker vos codes personnels. +Une `forge` est un espace informatique en ligne qui accueille des dépôts distants. Un dépôt distant (_remote repository_ en anglais) est un dossier que vous pouvez utiliser pour stocker vos codes (et leur historique), et pour partager des codes avec vos collègues ou stocker vos codes personnels. Une forge prend généralement forme d'un site internet. Il existe deux forges principales : @@ -44,7 +44,7 @@ Une forge interne `GitLab` est accessible depuis AUS. Son adresse, ainsi que des ::: ::: {.callout-note} -Une instance `GitLab` est disponible sur le SSP Cloud [https://git.lab.sspcloud.fr/] avec laquelle peut interagir un service `RStudio` [lien vers fiche quand elle sera là], et vous pouvez l'utiliser si vous le souhaitez. Toutefois, le SSP Cloud est une plateforme accessible depuis Internet et a donc accès aux dépôts hébergés sur ou . Il est donc conseillé d'utiliser une de ces deux `r with_def("forges")` plutôt que . +Une instance `GitLab` est disponible sur le SSP Cloud [https://git.lab.sspcloud.fr/] avec laquelle peut interagir un service `RStudio` [lien vers fiche quand elle sera là], et vous pouvez l'utiliser si vous le souhaitez. Toutefois, le SSP Cloud est une plateforme accessible depuis Internet et a donc accès aux dépôts hébergés sur ou . Il est donc conseillé d'utiliser une de ces deux `forges` plutôt que . ::: @@ -136,7 +136,7 @@ utilitr::include_image("../pics/config_git/password_conf.png", compression = FAL ``` Une fois le mot de passe configuré, il ne reste plus -qu'à `r with_def("cloner")` le dépôt distant sur lequel on veut travailler, +qu'à `cloner` le dépôt distant sur lequel on veut travailler, par exemple depuis `RStudio`, suivant le protocole décrit dans la fiche [Utiliser Git avec RStudio](#git), en ayant pris soin de sélectionner l'URL correspondant au protocole `HTTPS`, comme ci-dessous : diff --git a/03_Fiches_thematiques/Fiche_git_utilisation.qmd b/03_Fiches_thematiques/Fiche_git_utilisation.qmd index 0391eb13..d80dff0a 100644 --- a/03_Fiches_thematiques/Fiche_git_utilisation.qmd +++ b/03_Fiches_thematiques/Fiche_git_utilisation.qmd @@ -20,18 +20,18 @@ Il est également souhaitable de lire au préalable la fiche [Configurer Git sur * Ne jamais utiliser `Git` pour sauvegarder les données ; * Utiliser l'interface graphique de `RStudio` pour les usages courants de `Git`, plutôt que la ligne de commande ; -Vous pouvez utiliser `Git` _via_ la ligne de commande si vous le souhaitez. En revanche, il est _très fortement déconseillé_ d'exécuter une commande qui comprendrait les termes `force` ou `r with_def('rebase')`. +Vous pouvez utiliser `Git` _via_ la ligne de commande si vous le souhaitez. En revanche, il est _très fortement déconseillé_ d'exécuter une commande qui comprendrait les termes `force` ou rebase. **Recommandations sur l'initialisation de `Git`** * Il est recommandé d'utiliser `Git` dès le lancement de votre projet, même s'il est possible de commencer à suivre un projet déjà existant avec `Git`. -* Il est recommandé de commencer par créer un dépôt distant sur une forge (`Gitlab`, `Github`...), puis de `r with_def("cloner")` ce dépôt pour travailler sur votre poste local. +* Il est recommandé de commencer par créer un dépôt distant sur une forge (`Gitlab`, `Github`...), puis de clôner ce dépôt pour travailler sur votre poste local. * Il est recommandé de renseigner immédiatement le fichier `.gitignore` afin d'exclure certains fichiers du suivi des modifications (notamment les fichiers de données). **Recommandations sur l'usage des branches** -* Utiliser RStudio pour créer une branche ou naviguer entre les `r with_def("branches")` ; -* Utiliser les interfaces `Github` ou `Gitlab` pour fusionner deux `r with_def("branches")`. +* Utiliser RStudio pour créer une branche ou naviguer entre les `branches` ; +* Utiliser les interfaces `Github` ou `Gitlab` pour fusionner deux `branches`. Sur ce point, vous pouvez consulter la formation [Travail collaboratif avec R](https://linogaliana.gitlab.io/collaboratif/git.html). ::: @@ -106,7 +106,7 @@ avec vos collègues ou stocker vos codes personnels. Deux points sont importants La marche à suivre pour créer un dépôt distant est -très similaire dans `Gitlab` et dans `Github`. Les seules différences entre les deux plateformes portent sur la dénomination (un dépôt s'appelle `r with_def('repository')` sur `Github` et `project` sur `Gitlab`) et sur l'endroit où il faut cliquer pour créer un dépôt : +très similaire dans `Gitlab` et dans `Github`. Les seules différences entre les deux plateformes portent sur la dénomination (un dépôt s'appelle `repository` sur `Github` et `project` sur `Gitlab`) et sur l'endroit où il faut cliquer pour créer un dépôt : * Sur `Gitlab`, il suffit de cliquer sur `New project` dans la partie supérieure de la fenêtre : @@ -147,7 +147,7 @@ Choisir la méthode d'authentification désirée, `SSH` ou `HTTPS` #### Etape 3 : Créer un projet RStudio en clonant le dépôt distant -**La troisième étape consiste à `r with_def("cloner")` le dépôt distant** (`git clone`) c'est-à-dire à créer un projet RStudio sur votre poste local qui est une copie du dépôt distant (voir fiche XXXX pour plus de détails sur les projets RStudio). Cliquer sur `File > New Project...`, puis choisissez la troisième option (_Version Control_) : +**La troisième étape consiste à `cloner` le dépôt distant** (`git clone`) c'est-à-dire à créer un projet RStudio sur votre poste local qui est une copie du dépôt distant (voir fiche XXXX pour plus de détails sur les projets RStudio). Cliquer sur `File > New Project...`, puis choisissez la troisième option (_Version Control_) : ```{r, echo = FALSE, out.width = '65%'} utilitr::include_image("../pics/git/create_project_1.png", compression = FALSE) @@ -194,7 +194,7 @@ usethis::use_git() Cette fonction réalise deux opérations : - elle crée automatiquement tous les fichiers de configuration nécessaires au bon fonctionnement de `Git` dans le projet sur lequel vous travaillez ; -- elle effectue un premier `r with_def("commit")` (voir [cette section](#etape-2-valider-la-sauvegarde-des-modifications)) pour valider la création de ces fichiers de configuration. +- elle effectue un premier `commit` (voir [cette section](#etape-2-valider-la-sauvegarde-des-modifications)) pour valider la création de ces fichiers de configuration. La fonction `usethis::use_git()` va finalement vous proposer de sauvegarder les fichiers qui figurent déjà dans votre projet (par exemple, les codes `R` et les fichiers `csv` présents dans votre projet). Si vous avez des fichiers qui ne doivent pas être sous contrôle de version (notamment des données), il est préférable de refuser cette possibilité (en choisissant le chiffre qui correspond à "Non" parmi la liste de choix), puis de procéder comme ceci : @@ -210,10 +210,10 @@ Cette étape est identique à celle qui est décrite dans la section [Créer le La troisième étape consiste à établir un lien entre votre projet local et un dépôt distant (`git add remote`). Dans le langage `Git`, -le dépôt distant s'appelle un `r with_def("remote")`. +le dépôt distant s'appelle un `remote`. Pour créer ce lien avec l'interface de `RStudio`, il faut se rendre dans la partie destinée à -la gestion des `r with_def("branches")` sur laquelle la partie [RStudio et les branches](#git-branches) revient plus en détails. +la gestion des `branches` sur laquelle la partie [RStudio et les branches](#git-branches) revient plus en détails. ```{r, echo = FALSE, out.width = '80%'} utilitr::include_image("../pics/git/add_remote2.png", compression = FALSE) @@ -302,13 +302,13 @@ utilitr::include_image("../pics/git/create_project_3.png", compression = FALSE) C'est grâce à cette interface que vous pourrez effectuer la plupart des opérations `Git` courantes, qui sont présentées ci-dessous. Les principales commandes de cette interface sont les suivantes : -- `r with_def("Commit")` : valider les modifications d'un ou plusieurs fichier(s) ; -- `r with_def("Pull")` : récupérer sur le dépôt distant les modifications apportées au projet par d'autres contributeurs ; -- `r with_def("Push")` : partager sur le dépôt distant les modifications que vous avez apportées au projet ; +- `Commit` : valider les modifications d'un ou plusieurs fichier(s) ; +- `Pull` : récupérer sur le dépôt distant les modifications apportées au projet par d'autres contributeurs ; +- `Push` : partager sur le dépôt distant les modifications que vous avez apportées au projet ; - `History` : consulter l'historique des modifications du projet ; - `More` : ajouter des fichiers à ignorer ou revenir en arrière ou utiliser le terminal ; -- `New Branch` : créer une nouvelle `r with_def("branche")` dans le dépôt `Git` ; -- le menu déroulant tout à droite permet de changer de `r with_def("branche")`. +- `New Branch` : créer une nouvelle `branche` dans le dépôt `Git` ; +- le menu déroulant tout à droite permet de changer de `branche`. ::: {.callout-note} Si l'onglet `Git` n'apparaît pas dans la fenêtre RStudio, c'est que votre projet RStudio n'est pas encore configuré pour utiliser `Git`. Reportez-vous à la section [Initialiser l'usage de `Git` dans un projet RStudio]. @@ -378,7 +378,7 @@ utilitr::include_image("../pics/git/statut_renamed.png", compression = FALSE) La seconde étape (`git commit`) consiste à valider les modifications choisies à l'étape précédente. Pour ce faire, il faut cliquer sur le -bouton `r with_def("commit")`, situé au-dessus de la liste des +bouton commit, situé au-dessus de la liste des fichiers modifiés. En cliquant sur ce bouton, une nouvelle fenêtre s'ouvre : ```{r, echo = FALSE, out.width= '100%'} @@ -387,10 +387,10 @@ utilitr::include_image("../pics/git/onglet_git4.png", compression = FALSE) Les modifications apportées à chaque fichier sont résumées ligne à ligne dans la partie inférieure (suppressions en rouge, ajouts en vert). -Pour valider ces modifications (`r with_def("commit")`), +Pour valider ces modifications (`commit`), il faut écrire un message qui décrit la nature des modifications sauvegardées (dans le cadre vert) puis cliquer sur le -bouton `r with_def("commit")` (ovale rouge). Une fenêtre s'ouvre alors +bouton `commit` (ovale rouge). Une fenêtre s'ouvre alors et confirme que la modification a été sauvegardée : ```{r, echo = FALSE, out.width= '80%'} @@ -405,9 +405,9 @@ Il est possible, depuis `RStudio`, de consulter la liste des modifications appor utilitr::include_image("../pics/git/onglet_git6.png", compression = FALSE) ``` -Cette action ouvre une fenêtre avec la liste des `with_def("commits")` réalisée sur la -`r with_def("branches")` (voir plus bas pour la notion de `r with_def("branches")`), avec -les modifications apportées par chaque `r with_def("commit")`. Cette interface +Cette action ouvre une fenêtre avec la liste des `commits` réalisée sur la +`branches` (voir plus bas pour la notion de `branches`), avec +les modifications apportées par chaque commit. Cette interface permet de balayer rapidement les modifications apportées aux fichiers, par exemple pour retrouver à quel moment une ligne de code a été modifiée. @@ -425,12 +425,12 @@ En revanche, si vous souhaitez revenir à un état plus ancien d'un fichier, il Après avoir effectué des opérations sur son dépôt local, on peut effectuer deux opérations pour interagir avec le dépôt distant. Les boutons dans `RStudio` illustrent bien les opérations en question : -* `r with_def("pull")` +* pull ```{r, out.width="3%", out.extra='style="display: inline-block; padding: 0;"', echo = FALSE} utilitr::include_image("../pics/git/pull.png", compression = FALSE) ``` : récupérer les modifications présentes sur le dépôt distant ; -* `r with_def("push")` +* push ```{r, out.width="3%", out.extra='style="display: inline-block; padding: 0;"', echo = FALSE} utilitr::include_image("../pics/git/push.png", compression = FALSE) ``` @@ -439,7 +439,7 @@ utilitr::include_image("../pics/git/push.png", compression = FALSE) Lorsque vous partagez les modifications que vous avez apportées au projet, vos modifications viennent s'ajouter à la dernière version commune disponible (celle qui figure dans le dépôt commun). C'est pourquoi il est nécessaire que votre dépôt local soit à jour de toutes les modifications partagées par les autres contributeurs avant de partager vos modifications. **Il faut donc toujours récupérer la dernière version du projet sur le dépôt distant (en cliquant sur `pull`) avant d'envoyer des modifications (en cliquant sur `push`).** ::: {.callout-note} -Les icônes de l'onglet `Git` sont placées dans l'ordre des actions à réaliser afin de publier un code sur un dépôt distant : (add), `r `with_def("commit")`, `r with_def("pull")`, `r `with_def("push")` +Les icônes de l'onglet `Git` sont placées dans l'ordre des actions à réaliser afin de publier un code sur un dépôt distant : (add), commit, pull, push ```{r, echo = FALSE, out.width= "75%"} utilitr::include_image("../pics/git/onglet_git7.png", compression = FALSE) @@ -450,20 +450,20 @@ Il peut arriver que d'autres contributeurs aient partagé sur le dépôt distant ## RStudio et les branches {#git-branches} -### La notion de `r with_def("branche")` +### La notion de `branche` Les **branches** sont l'une des fonctionnalités les plus puissantes -de la gestion de version. La création de `r with_def("branches")` dans un projet permet +de la gestion de version. La création de `branches` dans un projet permet de développer des codes sans modifier la version de référence des codes, et donc de faire cohabiter dans un projet plusieurs versions des mêmes codes sans risque de confusion. `Git` propose également des fonctions pour fusionner facilement des versions différentes des mêmes codes. Deux points sont particulièrement importants : -- Dans un projet collaboratif, il existe une `r with_def("branche")` particulière, appelée le plus souvent `main` ou `master`, qui joue le rôle de version de référence. C’est autour d’elle que se développent les `r with_def("branches")`. -- Les modifications faites sur les codes dans une `r with_def("branche")` n'altèrent pas la version de référence (celle de la `r with_def("branche")` `master`) tant qu'il n'y a pas de fusion -entre `r with_def("branches")` (`r with_def("merge")`). +- Dans un projet collaboratif, il existe une `branche` particulière, appelée le plus souvent `main` ou `master`, qui joue le rôle de version de référence. C’est autour d’elle que se développent les `branches`. +- Les modifications faites sur les codes dans une `branche` n'altèrent pas la version de référence (celle de la `branche` `master`) tant qu'il n'y a pas de fusion +entre `branches` (`merge`). -### Créer et utiliser des `r with_def("branches")` avec RStudio +### Créer et utiliser des `branches` avec RStudio La partie droite de l'interface `git` de RStudio permet de travailler avec -des `r with_def("branches")`. +des `branches`. ```{r, echo = FALSE, out.width = "100%"} utilitr::include_image("../pics/git/onglet_git8.png", compression = FALSE) @@ -471,10 +471,10 @@ utilitr::include_image("../pics/git/onglet_git8.png", compression = FALSE) Cette interface offre principalement deux fonctions : -- **Créer une nouvelle branche** (cadre orange) : si vous cliquez sur ce bouton, une boîte de dialogue s'ouvre, dans laquelle vous devrez définir le nom de la nouvelle `r with_def("branche")` L'instruction correspondante en ligne de commande est `git checkout -b ma-branche`, où `ma-branche` est le nom de la nouvelle `r with_def("branche")` Deux points sont à noter: - - La `r with_def("branche")` source, à partir de laquelle la nouvelle `r with_def("branche")` diverge, sera celle sur laquelle vous vous situez au moment de la création. - - Il est recommandé de se placer sur `master` avant chaque création de nouvelle `r with_def("branche")`. -- **Naviguer parmi les branches** (cadre bleu) : le menu déroulant affiche d'abord la liste des branches disponibles dans votre dépôt local (`LOCAL BRANCHES`) puis la liste des branches existantes sur le dépôt distant (`REMOTE: ORIGIN`). Pour afficher le contenu d'une `r with_def("branche")`, il suffit de cliquer sur le nom de cette `r with_def("branche")`. L'instruction correspondante en ligne de commande est `git checkout ma-branche`, où `ma-branche` est le nom de la `r with_def("branche")` dont vous souhaitez afficher le contenu. +- **Créer une nouvelle branche** (cadre orange) : si vous cliquez sur ce bouton, une boîte de dialogue s'ouvre, dans laquelle vous devrez définir le nom de la nouvelle `branche` L'instruction correspondante en ligne de commande est `git checkout -b ma-branche`, où `ma-branche` est le nom de la nouvelle `branche` Deux points sont à noter: + - La `branche` source, à partir de laquelle la nouvelle `branche` diverge, sera celle sur laquelle vous vous situez au moment de la création. + - Il est recommandé de se placer sur `master` avant chaque création de nouvelle `branche`. +- **Naviguer parmi les branches** (cadre bleu) : le menu déroulant affiche d'abord la liste des branches disponibles dans votre dépôt local (`LOCAL BRANCHES`) puis la liste des branches existantes sur le dépôt distant (`REMOTE: ORIGIN`). Pour afficher le contenu d'une `branche`, il suffit de cliquer sur le nom de cette `branche`. L'instruction correspondante en ligne de commande est `git checkout ma-branche`, où `ma-branche` est le nom de la `branche` dont vous souhaitez afficher le contenu. ::: {.callout-note} L'interface graphique de RStudio ne permet pas de réaliser toutes les opérations possibles sur les branches. En particulier, il n'est pas possible de fusionner des branches avec cette interface. Les interfaces des forges (telles que `Gitlab`, `Github`...) sont beaucoup plus adaptées pour mener ce type d'opération. Vous pouvez en apprendre davantage en consultant la [formation Travail collaboratif avec `R`](https://linogaliana.gitlab.io/collaboratif/). @@ -482,9 +482,9 @@ L'interface graphique de RStudio ne permet pas de réaliser toutes les opératio ## Utiliser le terminal {#terminal-git} -Utiliser `Git` avec la ligne de commande permet de faire davantage de choses qu'avec l'interface `RStudio`. Grâce à elle, on peut par exemple corriger une maladresse, ou fusionner des `r with_def("branches")` sans utiliser l'interface d'une forge. L'utilisation de la ligne de commande est toutefois moins facile pour les débutants. +Utiliser `Git` avec la ligne de commande permet de faire davantage de choses qu'avec l'interface `RStudio`. Grâce à elle, on peut par exemple corriger une maladresse, ou fusionner des `branches` sans utiliser l'interface d'une forge. L'utilisation de la ligne de commande est toutefois moins facile pour les débutants. -L'utilisation de la ligne de commande n'est pas plus risquée que l'interface RStudio, à condition de respecter une règle simple : il ne faut __jamais exécuter une commande qui comprend les termes `force` ou `r with_def('rebase')`__. En effet, ces options peuvent créer des conflits insolubles, voire rendre le projet inutilisable par vos collaborateurs. +L'utilisation de la ligne de commande n'est pas plus risquée que l'interface RStudio, à condition de respecter une règle simple : il ne faut __jamais exécuter une commande qui comprend les termes `force` ou `rebase`__. En effet, ces options peuvent créer des conflits insolubles, voire rendre le projet inutilisable par vos collaborateurs. Pour ouvrir un terminal `Git`, cliquer sur l'écrou dans l'onglet `Git`: @@ -503,7 +503,6 @@ Vous pouvez en apprendre davantage sur l'utilisation de la ligne de commande dan ## Pour en savoir plus {#RessourcesUsageGit} -* [Formation Travail collaboratif avec `R`](https://linogaliana.gitlab.io/collaboratif/git.html) * [Travailler avec Git via RStudio et versionner son code (thinkr.fr)](https://thinkr.fr/travailler-avec-git-via-rstudio-et-versionner-son-code) * [*Happy Git with R*](https://happygitwithr.com/) * [Une présentation vidéo d'une utilisation `Git` pour débutants faite à l'Insee](https://www.youtube.com/watch?v=lyzWU43DJ9I)