From 5067c28aeb76ae2cd0b8e37abc97066be3ba0bc0 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 1 Feb 2023 09:02:13 +0000 Subject: [PATCH 001/100] renv update from pharmaverse/admiralci --- renv.lock | 8 + renv/activate.R | 478 +++++++++++++++++++++++----------------------- renv/settings.dcf | 2 +- 3 files changed, 247 insertions(+), 241 deletions(-) diff --git a/renv.lock b/renv.lock index 3df24733..b6e48a22 100644 --- a/renv.lock +++ b/renv.lock @@ -130,6 +130,14 @@ "sys" ] }, + "assertthat": { + "Package": "assertthat", + "Version": "0.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "50c838a310445e954bc13f26f26a6ecf", + "Requirements": [] + }, "backports": { "Package": "backports", "Version": "1.2.1", diff --git a/renv/activate.R b/renv/activate.R index 019b5a66..e52e2dae 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -1,6 +1,4 @@ - local({ - # the requested version of renv version <- "0.16.0" @@ -58,100 +56,100 @@ local({ if ("renv" %in% loadedNamespaces()) unloadNamespace("renv") - # load bootstrap tools + # load bootstrap tools `%||%` <- function(x, y) { if (is.environment(x) || length(x)) x else y } - + bootstrap <- function(version, library) { - + # attempt to download renv tarball <- tryCatch(renv_bootstrap_download(version), error = identity) if (inherits(tarball, "error")) stop("failed to download renv ", version) - + # now attempt to install status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) if (inherits(status, "error")) stop("failed to install renv ", version) - + } - + renv_bootstrap_tests_running <- function() { getOption("renv.tests.running", default = FALSE) } - + renv_bootstrap_repos <- function() { - + # check for repos override repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) if (!is.na(repos)) return(repos) - + # check for lockfile repositories repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) if (!inherits(repos, "error") && length(repos)) return(repos) - + # if we're testing, re-use the test repositories if (renv_bootstrap_tests_running()) return(getOption("renv.tests.repos")) - + # retrieve current repos repos <- getOption("repos") - + # ensure @CRAN@ entries are resolved repos[repos == "@CRAN@"] <- getOption( "renv.repos.cran", "https://cloud.r-project.org" ) - + # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") extra <- getOption("renv.bootstrap.repos", default = default) repos <- c(repos, extra) - + # remove duplicates that might've snuck in dupes <- duplicated(repos) | duplicated(names(repos)) repos[!dupes] - + } - + renv_bootstrap_repos_lockfile <- function() { - + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") if (!file.exists(lockpath)) return(NULL) - + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) if (inherits(lockfile, "error")) { warning(lockfile) return(NULL) } - + repos <- lockfile$R$Repositories if (length(repos) == 0) return(NULL) - + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) names(vals) <- keys - + return(vals) - + } - + renv_bootstrap_download <- function(version) { - + # if the renv version number has 4 components, assume it must # be retrieved via github nv <- numeric_version(version) components <- unclass(nv)[[1]] - + # if this appears to be a development version of 'renv', we'll # try to restore from github dev <- length(components) == 4L - + # begin collecting different methods for finding renv methods <- c( renv_bootstrap_download_tarball, @@ -162,79 +160,79 @@ local({ renv_bootstrap_download_cran_archive ) ) - + for (method in methods) { path <- tryCatch(method(version), error = identity) if (is.character(path) && file.exists(path)) return(path) } - + stop("failed to download renv ", version) - + } - + renv_bootstrap_download_impl <- function(url, destfile) { - + mode <- "wb" - + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 fixup <- Sys.info()[["sysname"]] == "Windows" && substring(url, 1L, 5L) == "file:" - + if (fixup) mode <- "w+b" - + args <- list( url = url, destfile = destfile, mode = mode, quiet = TRUE ) - + if ("headers" %in% names(formals(utils::download.file))) args$headers <- renv_bootstrap_download_custom_headers(url) - + do.call(utils::download.file, args) - + } - + renv_bootstrap_download_custom_headers <- function(url) { - + headers <- getOption("renv.download.headers") if (is.null(headers)) return(character()) - + if (!is.function(headers)) stopf("'renv.download.headers' is not a function") - + headers <- headers(url) if (length(headers) == 0L) return(character()) - + if (is.list(headers)) headers <- unlist(headers, recursive = FALSE, use.names = TRUE) - + ok <- is.character(headers) && is.character(names(headers)) && all(nzchar(names(headers))) - + if (!ok) stop("invocation of 'renv.download.headers' did not return a named character vector") - + headers - + } - + renv_bootstrap_download_cran_latest <- function(version) { - + spec <- renv_bootstrap_download_cran_latest_find(version) type <- spec$type repos <- spec$repos - + message("* Downloading renv ", version, " ... ", appendLF = FALSE) - + baseurl <- utils::contrib.url(repos = repos, type = type) ext <- if (identical(type, "source")) ".tar.gz" @@ -244,39 +242,39 @@ local({ ".tgz" name <- sprintf("renv_%s%s", version, ext) url <- paste(baseurl, name, sep = "/") - + destfile <- file.path(tempdir(), name) status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (inherits(status, "condition")) { message("FAILED") return(FALSE) } - + # report success and return message("OK (downloaded ", type, ")") destfile - + } - + renv_bootstrap_download_cran_latest_find <- function(version) { - + # check whether binaries are supported on this system binary <- getOption("renv.bootstrap.binary", default = TRUE) && !identical(.Platform$pkgType, "source") && !identical(getOption("pkgType"), "source") && Sys.info()[["sysname"]] %in% c("Darwin", "Windows") - + types <- c(if (binary) "binary", "source") - + # iterate over types + repositories for (type in types) { for (repos in renv_bootstrap_repos()) { - + # retrieve package database db <- tryCatch( as.data.frame( @@ -285,98 +283,98 @@ local({ ), error = identity ) - + if (inherits(db, "error")) next - + # check for compatible entry entry <- db[db$Package %in% "renv" & db$Version %in% version, ] if (nrow(entry) == 0) next - + # found it; return spec to caller spec <- list(entry = entry, type = type, repos = repos) return(spec) - + } } - + # if we got here, we failed to find renv fmt <- "renv %s is not available from your declared package repositories" stop(sprintf(fmt, version)) - + } - + renv_bootstrap_download_cran_archive <- function(version) { - + name <- sprintf("renv_%s.tar.gz", version) repos <- renv_bootstrap_repos() urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - + message("* Downloading renv ", version, " ... ", appendLF = FALSE) - + for (url in urls) { - + status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (identical(status, 0L)) { message("OK") return(destfile) } - + } - + message("FAILED") return(FALSE) - + } - + renv_bootstrap_download_tarball <- function(version) { - + # if the user has provided the path to a tarball via # an environment variable, then use it tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) if (is.na(tarball)) return() - + # allow directories info <- file.info(tarball, extra_cols = FALSE) if (identical(info$isdir, TRUE)) { name <- sprintf("renv_%s.tar.gz", version) tarball <- file.path(tarball, name) } - + # bail if it doesn't exist if (!file.exists(tarball)) { - + # let the user know we weren't able to honour their request fmt <- "* RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." msg <- sprintf(fmt, tarball) warning(msg) - + # bail return() - + } - + fmt <- "* Bootstrapping with tarball at path '%s'." msg <- sprintf(fmt, tarball) message(msg) - + tarball - + } - + renv_bootstrap_download_github <- function(version) { - + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") if (!identical(enabled, "TRUE")) return(FALSE) - + # prepare download options pat <- Sys.getenv("GITHUB_PAT") if (nzchar(Sys.which("curl")) && nzchar(pat)) { @@ -392,48 +390,48 @@ local({ options(download.file.method = "wget", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) } - + message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) - + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) - + status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (!identical(status, 0L)) { message("FAILED") return(FALSE) } - + message("OK") return(destfile) - + } - + renv_bootstrap_install <- function(version, tarball, library) { - + # attempt to install it into project library message("* Installing renv ", version, " ... ", appendLF = FALSE) dir.create(library, showWarnings = FALSE, recursive = TRUE) - + # invoke using system2 so we can capture and report output bin <- R.home("bin") exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" r <- file.path(bin, exe) - + args <- c( "--vanilla", "CMD", "INSTALL", "--no-multiarch", "-l", shQuote(path.expand(library)), shQuote(path.expand(tarball)) ) - + output <- system2(r, args, stdout = TRUE, stderr = TRUE) message("Done!") - + # check for successful install status <- attr(output, "status") if (is.numeric(status) && !identical(status, 0L)) { @@ -442,101 +440,101 @@ local({ text <- c(header, lines, output) writeLines(text, con = stderr()) } - + status - + } - + renv_bootstrap_platform_prefix <- function() { - + # construct version prefix version <- paste(R.version$major, R.version$minor, sep = ".") prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") - + # include SVN revision for development versions of R # (to avoid sharing platform-specific artefacts with released versions of R) devel <- identical(R.version[["status"]], "Under development (unstable)") || identical(R.version[["nickname"]], "Unsuffered Consequences") - + if (devel) prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") - + # build list of path components components <- c(prefix, R.version$platform) - + # include prefix if provided by user prefix <- renv_bootstrap_platform_prefix_impl() if (!is.na(prefix) && nzchar(prefix)) components <- c(prefix, components) - + # build prefix paste(components, collapse = "/") - + } - + renv_bootstrap_platform_prefix_impl <- function() { - + # if an explicit prefix has been supplied, use it prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) if (!is.na(prefix)) return(prefix) - + # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) - + # empty string on failure "" - + } - + renv_bootstrap_platform_prefix_auto <- function() { - + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) if (inherits(prefix, "error") || prefix %in% "unknown") { - + msg <- paste( "failed to infer current operating system", "please file a bug report at https://github.com/rstudio/renv/issues", sep = "; " ) - + warning(msg) - + } - + prefix - + } - + renv_bootstrap_platform_os <- function() { - + sysinfo <- Sys.info() sysname <- sysinfo[["sysname"]] - + # handle Windows + macOS up front if (sysname == "Windows") return("windows") else if (sysname == "Darwin") return("macos") - + # check for os-release files for (file in c("/etc/os-release", "/usr/lib/os-release")) if (file.exists(file)) return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) - + # check for redhat-release files if (file.exists("/etc/redhat-release")) return(renv_bootstrap_platform_os_via_redhat_release()) - + "unknown" - + } - + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { - + # read /etc/os-release release <- utils::read.table( file = file, @@ -546,13 +544,13 @@ local({ 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")) { @@ -561,7 +559,7 @@ local({ break } } - + # read version version <- "unknown" for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { @@ -570,17 +568,17 @@ local({ 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" @@ -588,77 +586,77 @@ local({ "redhat" else "unknown" - + # try to find a version component (very hacky) version <- "unknown" - + parts <- strsplit(contents, "[[:space:]]")[[1L]] for (part in parts) { - + nv <- tryCatch(numeric_version(part), error = identity) if (inherits(nv, "error")) next - + version <- nv[1, 1] break - + } - + paste(c("linux", id, version), collapse = "-") - + } - + renv_bootstrap_library_root_name <- function(project) { - + # use project name as-is if requested asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") if (asis) return(basename(project)) - + # otherwise, disambiguate based on project's path id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) paste(basename(project), id, sep = "-") - + } - + renv_bootstrap_library_root <- function(project) { - + prefix <- renv_bootstrap_profile_prefix() - + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) if (!is.na(path)) return(paste(c(path, prefix), collapse = "/")) - + path <- renv_bootstrap_library_root_impl(project) if (!is.null(path)) { name <- renv_bootstrap_library_root_name(project) return(paste(c(path, prefix, name), collapse = "/")) } - + renv_bootstrap_paths_renv("library", project = project) - + } - + renv_bootstrap_library_root_impl <- function(project) { - + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) if (!is.na(root)) return(root) - + type <- renv_bootstrap_project_type(project) if (identical(type, "package")) { userdir <- renv_bootstrap_user_dir() return(file.path(userdir, "library")) } - + } - + renv_bootstrap_validate_version <- function(version) { - + loadedversion <- utils::packageDescription("renv", fields = "Version") if (version == loadedversion) return(TRUE) - + # assume four-component versions are from GitHub; three-component # versions are from CRAN components <- strsplit(loadedversion, "[.-]")[[1]] @@ -666,84 +664,84 @@ local({ paste("rstudio/renv", loadedversion, sep = "@") else paste("renv", loadedversion, sep = "@") - + fmt <- paste( "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", sep = "\n" ) - + msg <- sprintf(fmt, loadedversion, version, remote) warning(msg, call. = FALSE) - + FALSE - + } - + renv_bootstrap_hash_text <- function(text) { - + hashfile <- tempfile("renv-hash-") on.exit(unlink(hashfile), add = TRUE) - + writeLines(text, con = hashfile) tools::md5sum(hashfile) - + } - + renv_bootstrap_load <- function(project, libpath, version) { - + # try to load renv from the project library if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) return(FALSE) - + # warn if the version of renv loaded does not match renv_bootstrap_validate_version(version) - + # load the project renv::load(project) - + TRUE - + } - + renv_bootstrap_profile_load <- function(project) { - + # if RENV_PROFILE is already set, just use that profile <- Sys.getenv("RENV_PROFILE", unset = NA) if (!is.na(profile) && nzchar(profile)) return(profile) - + # check for a profile file (nothing to do if it doesn't exist) path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) if (!file.exists(path)) return(NULL) - + # read the profile, and set it if it exists contents <- readLines(path, warn = FALSE) if (length(contents) == 0L) return(NULL) - + # set RENV_PROFILE profile <- contents[[1L]] if (!profile %in% c("", "default")) Sys.setenv(RENV_PROFILE = profile) - + profile - + } - + renv_bootstrap_profile_prefix <- function() { profile <- renv_bootstrap_profile_get() if (!is.null(profile)) return(file.path("profiles", profile, "renv")) } - + renv_bootstrap_profile_get <- function() { profile <- Sys.getenv("RENV_PROFILE", unset = "") renv_bootstrap_profile_normalize(profile) } - + renv_bootstrap_profile_set <- function(profile) { profile <- renv_bootstrap_profile_normalize(profile) if (is.null(profile)) @@ -751,25 +749,25 @@ local({ 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 @@ -777,50 +775,50 @@ local({ 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) { @@ -828,7 +826,7 @@ local({ 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") @@ -836,57 +834,57 @@ local({ "~/Library/Caches/org.R-project.R/R/renv" else "~/.cache/R/renv" - + } - - + + renv_json_read <- function(file = NULL, text = NULL) { - + # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) renv_json_read_jsonlite(file, text) else renv_json_read_default(file, text) - + } - + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { text <- paste(text %||% read(file), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } - + renv_json_read_default <- function(file = NULL, text = NULL) { - + # find strings in the JSON text <- paste(text %||% read(file), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] - + # if any are found, replace them with placeholders replaced <- text strings <- character() replacements <- character() - + if (!identical(c(locs), -1L)) { - + # get the string values starts <- locs ends <- locs + attr(locs, "match.length") - 1L strings <- substring(text, starts, ends) - + # only keep those requiring escaping strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) - + # compute replacements replacements <- sprintf('"\032%i\032"', seq_along(strings)) - + # replace the strings mapply(function(string, replacement) { replaced <<- sub(string, replacement, replaced, fixed = TRUE) }, strings, replacements) - + } - + # transform the JSON into something the R parser understands transformed <- replaced transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) @@ -894,38 +892,38 @@ local({ transformed <- gsub("[]}]", ")", transformed, perl = TRUE) transformed <- gsub(":", "=", transformed, fixed = TRUE) text <- paste(transformed, collapse = "\n") - + # parse it json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] - + # construct map between source strings, replaced strings map <- as.character(parse(text = strings)) names(map) <- as.character(parse(text = replacements)) - + # convert to list map <- as.list(map) - + # remap strings in object remapped <- renv_json_remap(json, map) - + # evaluate eval(remapped, envir = baseenv()) - + } - + renv_json_remap <- function(json, map) { - + # fix names if (!is.null(names(json))) { lhs <- match(names(json), names(map), nomatch = 0L) rhs <- match(names(map), names(json), nomatch = 0L) names(json)[rhs] <- map[lhs] } - + # fix values if (is.character(json)) return(map[[json]] %||% json) - + # handle true, false, null if (is.name(json)) { text <- as.character(json) @@ -936,16 +934,16 @@ local({ else if (text == "null") return(NULL) } - + # recurse if (is.recursive(json)) { for (i in seq_along(json)) { json[i] <- list(renv_json_remap(json[[i]], map)) } } - + json - + } # load the renv profile, if any diff --git a/renv/settings.dcf b/renv/settings.dcf index 0c5119c7..5c06125d 100644 --- a/renv/settings.dcf +++ b/renv/settings.dcf @@ -1,6 +1,6 @@ ignored.packages: package.dependency.fields: Imports, Depends, LinkingTo r.version: -snapshot.type: implicit +snapshot.type: custom use.cache: TRUE vcs.ignore.library: TRUE From 74efe92fab74f7f6798c1008aa266d9d0409c028 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 1 Feb 2023 12:24:44 +0000 Subject: [PATCH 002/100] renv update from pharmaverse/admiralci --- renv/.gitignore | 1 + renv/settings.dcf | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/renv/.gitignore b/renv/.gitignore index 6ae4167d..2649d0a0 100644 --- a/renv/.gitignore +++ b/renv/.gitignore @@ -5,3 +5,4 @@ local/ lock/ python/ staging/ +profile diff --git a/renv/settings.dcf b/renv/settings.dcf index 5c06125d..0c5119c7 100644 --- a/renv/settings.dcf +++ b/renv/settings.dcf @@ -1,6 +1,6 @@ ignored.packages: package.dependency.fields: Imports, Depends, LinkingTo r.version: -snapshot.type: custom +snapshot.type: implicit use.cache: TRUE vcs.ignore.library: TRUE From 72c9a1a387e8777a9ff365a0928fb4a9b01c7dab Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 2 Feb 2023 10:32:58 +0000 Subject: [PATCH 003/100] renv update from pharmaverse/admiralci --- renv/profiles/4.1.0/renv.lock | 1480 +++++++++++++++++++++++++ renv/profiles/4.1.0/renv/.gitignore | 7 + renv/profiles/4.1.0/renv/settings.dcf | 10 + 3 files changed, 1497 insertions(+) create mode 100644 renv/profiles/4.1.0/renv.lock create mode 100644 renv/profiles/4.1.0/renv/.gitignore create mode 100644 renv/profiles/4.1.0/renv/settings.dcf diff --git a/renv/profiles/4.1.0/renv.lock b/renv/profiles/4.1.0/renv.lock new file mode 100644 index 00000000..6149ae61 --- /dev/null +++ b/renv/profiles/4.1.0/renv.lock @@ -0,0 +1,1480 @@ +{ + "R": { + "Version": "4.1.0", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + }, + { + "Name": "MRAN", + "URL": "https://cran.microsoft.com/snapshot/2022-03-10" + } + ] + }, + "Packages": { + "DT": { + "Package": "DT", + "Version": "0.27", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "3444e6ed78763f9f13aaa39f2481eb34", + "Requirements": [ + "crosstalk", + "htmltools", + 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"409328b8e1253c8d729a7836fe7f7a16", + "Requirements": [ + "cli", + "curl", + "xml2" + ] + }, + "usethis": { + "Package": "usethis", + "Version": "2.1.6", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "a67a22c201832b12c036cc059f1d137d", + "Requirements": [ + "cli", + "clipr", + "crayon", + "curl", + "desc", + "fs", + "gert", + "gh", + "glue", + "jsonlite", + "lifecycle", + "purrr", + "rappdirs", + "rlang", + "rprojroot", + "rstudioapi", + "whisker", + "withr", + "yaml" + ] + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "1fe17157424bb09c48a8b3b550c753bc", + "Requirements": [] + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.5.2", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "e4ffa94ceed5f124d429a5a5f0f5b378", + "Requirements": [ + "cli", + "glue", + "lifecycle", + "rlang" + ] + }, + "waldo": { + "Package": "waldo", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "035fba89d0c86e2113120f93301b98ad", + "Requirements": [ + "cli", + "diffobj", + "fansi", + "glue", + "rematch2", + "rlang", + "tibble" + ] + }, + "whisker": { + "Package": "whisker", + "Version": "0.4.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c6abfa47a46d281a7d5159d0a8891e88", + "Requirements": [] + }, + "withr": { + "Package": "withr", + "Version": "2.5.0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c0e49a9760983e81e55cdd9be92e7182", + "Requirements": [] + }, + "xfun": { + "Package": "xfun", + "Version": "0.37", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "a6860e1400a8fd1ddb6d9b4230cc34ab", + "Requirements": [] + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.3", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "40682ed6a969ea5abfd351eb67833adc", + "Requirements": [] + }, + "xmlparsedata": { + "Package": "xmlparsedata", + "Version": "1.0.5", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "45e4bf3c46476896e821fc0a408fb4fc", + "Requirements": [] + }, + "xopen": { + "Package": "xopen", + "Version": "1.0.0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "6c85f015dee9cc7710ddd20f86881f58", + "Requirements": [ + "processx" + ] + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", + "Requirements": [] + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.7", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "0d0056cc5383fbc240ccd0cb584bf436", + "Requirements": [] + }, + "zip": { + "Package": "zip", + "Version": "2.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88", + "Requirements": [] + } + } +} diff --git a/renv/profiles/4.0.5/renv/.gitignore b/renv/profiles/4.0.5/renv/.gitignore new file mode 100644 index 00000000..0ec0cbba --- /dev/null +++ b/renv/profiles/4.0.5/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/profiles/4.0.5/renv/settings.dcf b/renv/profiles/4.0.5/renv/settings.dcf new file mode 100644 index 00000000..c4ab61bd --- /dev/null +++ b/renv/profiles/4.0.5/renv/settings.dcf @@ -0,0 +1,10 @@ +bioconductor.version: +external.libraries: +ignored.packages: admiral, admiraldev, admiral.test, admiralci +package.dependency.fields: Imports, Depends, LinkingTo +r.version: +snapshot.type: custom +use.cache: TRUE +vcs.ignore.cellar: TRUE +vcs.ignore.library: TRUE +vcs.ignore.local: TRUE From a49e24cf5c59ff0b64e5327c70a9e16a1069df2f Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 2 Feb 2023 13:39:10 +0000 Subject: [PATCH 005/100] renv update from pharmaverse/admiralci --- renv.lock | 871 ++++++++++++++-------------------- renv/profiles/4.0.5/renv.lock | 15 +- renv/profiles/4.1.0/renv.lock | 15 +- 3 files changed, 364 insertions(+), 537 deletions(-) diff --git a/renv.lock b/renv.lock index b6e48a22..560d30ce 100644 --- a/renv.lock +++ b/renv.lock @@ -13,60 +13,27 @@ ] }, "Packages": { - "BH": { - "Package": "BH", - "Version": "1.75.0-0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "e4c04affc2cac20c8fec18385cd14691", - "Requirements": [] - }, "DT": { "Package": "DT", - "Version": "0.17", + "Version": "0.27", "Source": "Repository", - "Repository": "CRAN", - "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0", + "Repository": "RSPM", + "Hash": "3444e6ed78763f9f13aaa39f2481eb34", "Requirements": [ "crosstalk", "htmltools", "htmlwidgets", + "jquerylib", "jsonlite", "magrittr", "promises" ] }, - "KernSmooth": { - "Package": "KernSmooth", - "Version": "2.23-18", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9e703ad8bf0e99f3691f05da32dfe68b", - "Requirements": [] - }, - "MASS": { - "Package": "MASS", - "Version": "7.3-53.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "4ef21dd0348b9abb7f8bd1d77e4cd0c3", - "Requirements": [] - }, - "Matrix": { - "Package": "Matrix", - "Version": "1.3-2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "ff280503079ad8623d3c4b1519b24ea2", - "Requirements": [ - "lattice" - ] - }, "R.cache": { "Package": "R.cache", "Version": "0.16.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8", "Requirements": [ "R.methodsS3", @@ -77,28 +44,28 @@ }, "R.methodsS3": { "Package": "R.methodsS3", - "Version": "1.8.1", + "Version": "1.8.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4bf6453323755202d5909697b6f7c109", + "Repository": "RSPM", + "Hash": "278c286fd6e9e75d0c2e8f731ea445c8", "Requirements": [] }, "R.oo": { "Package": "R.oo", - "Version": "1.24.0", + "Version": "1.25.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "5709328352717e2f0a9c012be8a97554", + "Repository": "RSPM", + "Hash": "a0900a114f4f0194cf4aa8cd4a700681", "Requirements": [ "R.methodsS3" ] }, "R.utils": { "Package": "R.utils", - "Version": "2.12.0", + "Version": "2.12.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "d31333e10f14027e1cbbc6f266512806", + "Repository": "RSPM", + "Hash": "325f01db13da12c04d8f6e7be36ff514", "Requirements": [ "R.methodsS3", "R.oo" @@ -106,100 +73,86 @@ }, "R6": { "Package": "R6", - "Version": "2.5.0", + "Version": "2.5.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b203113193e70978a696b2809525649d", + "Repository": "RSPM", + "Hash": "470851b6d5d0ac559e9d01bb352b4021", "Requirements": [] }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.6", + "Version": "1.0.10", "Source": "Repository", - "Repository": "CRAN", - "Hash": "dbb5e436998a7eba5a9d682060533338", + "Repository": "RSPM", + "Hash": "e749cae40fa9ef469b6050959517453c", "Requirements": [] }, "askpass": { "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e8a22846fff485f0be3770c2da758713", "Requirements": [ "sys" ] }, - "assertthat": { - "Package": "assertthat", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "50c838a310445e954bc13f26f26a6ecf", - "Requirements": [] - }, "backports": { "Package": "backports", - "Version": "1.2.1", + "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "644043219fc24e190c2f620c1a380a69", + "Repository": "RSPM", + "Hash": "c39fbec8a30d23e721980b8afb31984c", "Requirements": [] }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, - "boot": { - "Package": "boot", - "Version": "1.3-27", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "d9778c960792721e8433daaf3db8f16a", - "Requirements": [] - }, "brew": { "Package": "brew", - "Version": "1.0-6", + "Version": "1.0-8", "Source": "Repository", - "Repository": "CRAN", - "Hash": "92a5f887f9ae3035ac7afde22ba73ee9", + "Repository": "RSPM", + "Hash": "d69a786e85775b126bddbee185ae6084", "Requirements": [] }, "brio": { "Package": "brio", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "976cf154dfb043c012d87cddd8bca363", "Requirements": [] }, "bslib": { "Package": "bslib", - "Version": "0.4.0", + "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "be5ee090716ce1671be6cd5d7c34d091", + "Repository": "RSPM", + "Hash": "a7fbf03946ad741129dc81098722fca1", "Requirements": [ + "base64enc", "cachem", "htmltools", "jquerylib", "jsonlite", "memoise", + "mime", "rlang", "sass" ] }, "cachem": { "Package": "cachem", - "Version": "1.0.4", + "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2703a46dcabfb902f10060b2bca9f708", + "Repository": "RSPM", + "Hash": "648c5b3d71e6a37e3043617489a0a0e9", "Requirements": [ "fastmap", "rlang" @@ -207,36 +160,15 @@ }, "callr": { "Package": "callr", - "Version": "3.7.2", + "Version": "3.7.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "358689cac9fe93b1bb3a19088d2dbed8", + "Hash": "9b2191ede20fa29828139b9900922e51", "Requirements": [ "R6", "processx" ] }, - "cellranger": { - "Package": "cellranger", - "Version": "1.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f61dbaec772ccd2e17705c1e872e9e7c", - "Requirements": [ - "rematch", - "tibble" - ] - }, - "class": { - "Package": "class", - "Version": "7.3-18", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "15ef288688a6919417ade6251deea2b3", - "Requirements": [ - "MASS" - ] - }, "cli": { "Package": "cli", "Version": "3.4.1", @@ -247,18 +179,10 @@ }, "clipr": { "Package": "clipr", - "Version": "0.7.1", + "Version": "0.8.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7", - "Requirements": [] - }, - "cluster": { - "Package": "cluster", - "Version": "2.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "5ea8f54741ff907e2c0b5efabc9de729", + "Repository": "RSPM", + "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", "Requirements": [] }, "codetools": { @@ -271,18 +195,18 @@ }, "commonmark": { "Package": "commonmark", - "Version": "1.7", + "Version": "1.8.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0f22be39ec1d141fd03683c06f3a6e67", + "Repository": "RSPM", + "Hash": "b6e3e947d1d7ebf3d2bdcea1bde63fe7", "Requirements": [] }, "covr": { "Package": "covr", - "Version": "3.5.1", + "Version": "3.6.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6d80a9fc3c0c8473153b54fa54719dfd", + "Repository": "RSPM", + "Hash": "a861cee34fbb4b107a73dd414ef56724", "Requirements": [ "crayon", "digest", @@ -297,24 +221,24 @@ "Package": "cpp11", "Version": "0.4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ed588261931ee3be2c700d22e94a29ab", "Requirements": [] }, "crayon": { "Package": "crayon", - "Version": "1.4.1", + "Version": "1.5.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "e75525c55c70e5f4f78c9960a4b402e9", + "Repository": "RSPM", + "Hash": "e8a1e41acf02548751f45c718d55aa6a", "Requirements": [] }, "credentials": { "Package": "credentials", - "Version": "1.3.0", + "Version": "1.3.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a96728288c75a814c900af9da84387be", + "Repository": "RSPM", + "Hash": "93762d0a34d78e6a025efdbfb5c6bb41", "Requirements": [ "askpass", "curl", @@ -325,10 +249,10 @@ }, "crosstalk": { "Package": "crosstalk", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2b06f9e415a62b6762e4b8098d2aecbc", + "Repository": "RSPM", + "Hash": "6aa54f69598c32177e920eb3402e8293", "Requirements": [ "R6", "htmltools", @@ -338,17 +262,17 @@ }, "curl": { "Package": "curl", - "Version": "4.3", + "Version": "5.0.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2b7d10581cc730804e9ed178c8374bd6", + "Repository": "RSPM", + "Hash": "e4f97056611e8e6b8b852d13b7400cf1", "Requirements": [] }, "cyclocomp": { "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "53cbed70a2f7472d48fb6aef08442f25", "Requirements": [ "callr", @@ -362,7 +286,7 @@ "Package": "desc", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", "Requirements": [ "R6", @@ -372,30 +296,30 @@ }, "devtools": { "Package": "devtools", - "Version": "2.3.2", + "Version": "2.4.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "415656f50722f5b6e6bcf80855ce11b9", + "Repository": "RSPM", + "Hash": "ea5bc8b4a6a01e4f12d98b58329930bb", "Requirements": [ - "DT", - "callr", "cli", - "covr", "desc", "ellipsis", - "httr", - "jsonlite", + "fs", + "lifecycle", "memoise", + "miniUI", "pkgbuild", + "pkgdown", "pkgload", + "profvis", "rcmdcheck", "remotes", "rlang", "roxygen2", - "rstudioapi", "rversions", "sessioninfo", "testthat", + "urlchecker", "usethis", "withr" ] @@ -404,7 +328,7 @@ "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9ddedef46959baad2080047a1b0117fe", "Requirements": [ "tibble" @@ -412,27 +336,27 @@ }, "diffobj": { "Package": "diffobj", - "Version": "0.3.4", + "Version": "0.3.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "feb5b7455eba422a2c110bb89852e6a3", + "Repository": "RSPM", + "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8", "Requirements": [ "crayon" ] }, "digest": { "Package": "digest", - "Version": "0.6.27", + "Version": "0.6.31", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a0cbe758a531d054b537d16dff4d58a1", + "Repository": "RSPM", + "Hash": "8b708f296afd9ae69f450f9640be8990", "Requirements": [] }, "downlit": { "Package": "downlit", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "79bf3f66590752ffbba20f8d2da94c7c", "Requirements": [ "brio", @@ -449,17 +373,18 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.5", + "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68", + "Repository": "RSPM", + "Hash": "d3c34618017e7ae252d46d79a1b9ec32", "Requirements": [ "R6", - "ellipsis", + "cli", "generics", "glue", "lifecycle", "magrittr", + "pillar", "rlang", "tibble", "tidyselect", @@ -470,7 +395,7 @@ "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", "Requirements": [ "rlang" @@ -478,58 +403,61 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.17", + "Version": "0.20", "Source": "Repository", - "Repository": "CRAN", - "Hash": "9171b012a55a1ef53f1442b1d798a3b4", + "Repository": "RSPM", + "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c", "Requirements": [] }, "fansi": { "Package": "fansi", - "Version": "0.4.2", + "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "fea074fb67fe4c25d47ad09087da847d", + "Repository": "RSPM", + "Hash": "1d9e7ad3c8312a192dea7d3db0274fde", "Requirements": [] }, "fastmap": { "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, - "foreign": { - "Package": "foreign", - "Version": "0.8-81", + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "74628ea7a3be5ee8a7b5bb0a8e84882e", - "Requirements": [] + "Repository": "RSPM", + "Hash": "e80750aec5717dedc019ad7ee40e4a7c", + "Requirements": [ + "htmltools", + "rlang" + ] }, "fs": { "Package": "fs", - "Version": "1.5.2", + "Version": "1.6.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "7c89603d81793f0d5486d91ab1fc6f1d", + "Repository": "RSPM", + "Hash": "0120e8c933bace1141e0b0d376b0c010", "Requirements": [] }, "generics": { "Package": "generics", - "Version": "0.1.0", + "Version": "0.1.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4d243a9c10b00589889fe32314ffd902", + "Repository": "RSPM", + "Hash": "15e9634c0fcd294799e9b2e929ed1b86", "Requirements": [] }, "gert": { "Package": "gert", - "Version": "1.9.1", + "Version": "1.9.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "9a091a6d2fb91e43afd4337e2dcef2e7", + "Repository": "RSPM", + "Hash": "9122b3958e749badb5c939f498038b57", "Requirements": [ "askpass", "credentials", @@ -543,7 +471,7 @@ "Package": "gh", "Version": "1.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b6a12054ee13dce0f6696c019c10e539", "Requirements": [ "cli", @@ -555,42 +483,44 @@ }, "git2r": { "Package": "git2r", - "Version": "0.28.0", + "Version": "0.31.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "f64fd34026f6025de71a4354800e6d79", + "Repository": "RSPM", + "Hash": "acb972e0be37f83b9c762d962d75a188", "Requirements": [] }, "gitcreds": { "Package": "gitcreds", - "Version": "0.1.1", + "Version": "0.1.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "f3aefccc1cc50de6338146b62f115de8", + "Repository": "RSPM", + "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe", "Requirements": [] }, "glue": { "Package": "glue", "Version": "1.6.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", "Requirements": [] }, "highr": { "Package": "highr", - "Version": "0.8", + "Version": "0.10", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4dc5bb88961e347a0f4d8aad597cbfac", - "Requirements": [] + "Repository": "RSPM", + "Hash": "06230136b2d2b9ba5805e1963fa6e890", + "Requirements": [ + "xfun" + ] }, "hms": { "Package": "hms", - "Version": "1.0.0", + "Version": "1.1.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "bf552cdd96f5969873afdac7311c7d0d", + "Repository": "RSPM", + "Hash": "41100392191e1244b887878b533eea91", "Requirements": [ "ellipsis", "lifecycle", @@ -601,37 +531,39 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.3", + "Version": "0.5.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6496090a9e00f8354b811d1a2d47b566", + "Repository": "RSPM", + "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7", "Requirements": [ "base64enc", "digest", + "ellipsis", "fastmap", "rlang" ] }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.5.3", + "Version": "1.6.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6fdaa86d0700f8b3e92ee3c445a5a10d", + "Repository": "RSPM", + "Hash": "b677ee5954471eaa974c0d099a343a1a", "Requirements": [ "htmltools", "jsonlite", + "knitr", + "rmarkdown", "yaml" ] }, "httpuv": { "Package": "httpuv", - "Version": "1.5.5", + "Version": "1.6.8", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b9d5d39be2150cf86538b8488334b8f8", + "Repository": "RSPM", + "Hash": "08e611aee165b27f8ff18770285fb535", "Requirements": [ - "BH", "R6", "Rcpp", "later", @@ -640,10 +572,10 @@ }, "httr": { "Package": "httr", - "Version": "1.4.2", + "Version": "1.4.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a525aba14184fec243f9eaec62fbed43", + "Repository": "RSPM", + "Hash": "57557fac46471f0dbbf44705cc6a5c8c", "Requirements": [ "R6", "curl", @@ -654,10 +586,10 @@ }, "hunspell": { "Package": "hunspell", - "Version": "3.0.1", + "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "3987784c19192ad0f2261c456d936df1", + "Repository": "RSPM", + "Hash": "656219b6f3f605499d7cdbe208656639", "Requirements": [ "Rcpp", "digest" @@ -667,7 +599,7 @@ "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, @@ -675,7 +607,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5aab57a3bd297eee1c1d862735972182", "Requirements": [ "htmltools" @@ -683,51 +615,41 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.7.2", + "Version": "1.8.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "98138e0994d41508c7a6b84a0600cfcb", + "Repository": "RSPM", + "Hash": "a4269a09a9b865579b2635c77e572374", "Requirements": [] }, "knitr": { "Package": "knitr", - "Version": "1.40", + "Version": "1.42", "Source": "Repository", - "Repository": "CRAN", - "Hash": "caea8b0f899a0b1738444b9bc47067e7", + "Repository": "RSPM", + "Hash": "8329a9bcc82943c8069104d4be3ee22d", "Requirements": [ "evaluate", "highr", - "stringr", "xfun", "yaml" ] }, "later": { "Package": "later", - "Version": "1.1.0.1", + "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "d0a62b247165aabf397fded504660d8a", + "Repository": "RSPM", + "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e", "Requirements": [ - "BH", "Rcpp", "rlang" ] }, - "lattice": { - "Package": "lattice", - "Version": "0.20-41", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "fbd9285028b0263d76d18c95ae51a53d", - "Requirements": [] - }, "lazyeval": { "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d908914ae53b04d4c0c0fd72ecc35370", "Requirements": [] }, @@ -735,7 +657,7 @@ "Package": "lifecycle", "Version": "1.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "001cecbeac1cff9301bdc3775ee46a86", "Requirements": [ "cli", @@ -745,145 +667,93 @@ }, "lintr": { "Package": "lintr", - "Version": "2.0.1", + "Version": "3.0.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "023cecbdc0a32f86ad3cb1734c018d2e", + "Hash": "b21ebd652d940f099915221f3328ab7b", "Requirements": [ + "backports", "codetools", "crayon", "cyclocomp", "digest", - "httr", + "glue", "jsonlite", "knitr", "rex", - "rstudioapi", - "testthat", "xml2", "xmlparsedata" ] }, "lubridate": { "Package": "lubridate", - "Version": "1.7.10", + "Version": "1.9.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "1ebfdc8a3cfe8fe19184f5481972b092", + "Repository": "RSPM", + "Hash": "88ad585eb49669b7f2db3f5ef3c8307d", "Requirements": [ - "Rcpp", - "generics" + "generics", + "timechange" ] }, "magrittr": { "Package": "magrittr", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7ce2733a9826b3aeb1775d56fd305472", "Requirements": [] }, - "markdown": { - "Package": "markdown", - "Version": "1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "61e4a10781dd00d7d81dd06ca9b94e95", - "Requirements": [ - "mime", - "xfun" - ] - }, "memoise": { "Package": "memoise", - "Version": "2.0.0", + "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a0bc51650201a56d00a4798523cc91b3", + "Repository": "RSPM", + "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c", "Requirements": [ "cachem", "rlang" ] }, - "mgcv": { - "Package": "mgcv", - "Version": "1.8-34", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "bd4a6c4b600f58651d60d381b0e9a397", - "Requirements": [ - "Matrix", - "nlme" - ] - }, "mime": { "Package": "mime", - "Version": "0.10", + "Version": "0.12", "Source": "Repository", - "Repository": "CRAN", - "Hash": "26fa77e707223e1ce042b2b5d09993dc", + "Repository": "RSPM", + "Hash": "18e9c28c1d3ca1560ce30658b22ce104", "Requirements": [] }, "miniUI": { "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fec5f52652d60615fdb3957b3d74324a", "Requirements": [ "htmltools", "shiny" ] }, - "mockery": { - "Package": "mockery", - "Version": "0.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "313fa6504824ba5aab9308412135fb5f", - "Requirements": [ - "testthat" - ] - }, - "nlme": { - "Package": "nlme", - "Version": "3.1-152", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "35de1ce639f20b5e10f7f46260730c65", - "Requirements": [ - "lattice" - ] - }, - "nnet": { - "Package": "nnet", - "Version": "7.3-15", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b67ac021b3fb3a4b69d0d3c2bc049e9f", - "Requirements": [] - }, "openssl": { "Package": "openssl", - "Version": "2.0.4", + "Version": "2.0.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "e86c5ffeb8474a9e03d75f5d2919683e", + "Repository": "RSPM", + "Hash": "b04c27110bf367b4daa93f34f3d58e75", "Requirements": [ "askpass" ] }, "pillar": { "Package": "pillar", - "Version": "1.5.1", + "Version": "1.8.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "24622aa4a0d3de3463c34513edca99b2", + "Repository": "RSPM", + "Hash": "f2316df30902c81729ae9de95ad5a608", "Requirements": [ "cli", - "crayon", - "ellipsis", "fansi", + "glue", "lifecycle", "rlang", "utf8", @@ -892,10 +762,10 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.2.0", + "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "725fcc30222d4d11ec68efb8ff11a9af", + "Repository": "RSPM", + "Hash": "d6c3008d79653a0f267703288230105e", "Requirements": [ "R6", "callr", @@ -903,6 +773,7 @@ "crayon", "desc", "prettyunits", + "processx", "rprojroot", "withr" ] @@ -911,16 +782,16 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "01f28d4278f15c76cddbea05899c5d6f", "Requirements": [] }, "pkgdown": { "Package": "pkgdown", - "Version": "2.0.6", + "Version": "2.0.7", "Source": "Repository", "Repository": "CRAN", - "Hash": "f958d0b2a5dabc5ffd414f062b1ffbe7", + "Hash": "16fa15449c930bf3a7761d3c68f8abf9", "Requirements": [ "bslib", "callr", @@ -946,18 +817,18 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.2.0", + "Version": "1.3.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "cb57de933545960a86f03513e4bd2911", + "Repository": "RSPM", + "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2", "Requirements": [ "cli", "crayon", "desc", - "pkgbuild", + "fs", + "glue", "rlang", "rprojroot", - "rstudioapi", "withr" ] }, @@ -965,7 +836,7 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a555924add98c99d2f411e37e7d25e9f", "Requirements": [] }, @@ -973,39 +844,37 @@ "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", "Requirements": [] }, "processx": { "Package": "processx", - "Version": "3.8.0", + "Version": "3.6.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "a33ee2d9bf07564efb888ad98410da84", + "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6", "Requirements": [ "R6", "ps" ] }, - "progress": { - "Package": "progress", - "Version": "1.2.2", + "profvis": { + "Package": "profvis", + "Version": "0.3.7", "Source": "Repository", - "Repository": "CRAN", - "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061", + "Repository": "RSPM", + "Hash": "e9d21e79848e02e524bea6f5bd53e7e4", "Requirements": [ - "R6", - "crayon", - "hms", - "prettyunits" + "htmlwidgets", + "stringr" ] }, "promises": { "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4ab2c43adb4d4699cf3690acd378d75d", "Requirements": [ "R6", @@ -1017,29 +886,32 @@ }, "ps": { "Package": "ps", - "Version": "1.6.0", + "Version": "1.7.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "32620e2001c1dce1af49c49dccbb9420", + "Repository": "RSPM", + "Hash": "68dd03d98a5efd1eb3012436de45ba83", "Requirements": [] }, "purrr": { "Package": "purrr", - "Version": "0.3.4", + "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "97def703420c8ab10d8f0e6c72101e02", + "Repository": "RSPM", + "Hash": "d71c815267c640f17ddbf7f16144b4bb", "Requirements": [ + "cli", + "lifecycle", "magrittr", - "rlang" + "rlang", + "vctrs" ] }, "ragg": { "Package": "ragg", - "Version": "1.2.4", + "Version": "1.2.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0db17bd5a1d4abfec76487b6f5dd957b", + "Repository": "RSPM", + "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9", "Requirements": [ "systemfonts", "textshaping" @@ -1049,21 +921,21 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, "rcmdcheck": { "Package": "rcmdcheck", - "Version": "1.3.3", + "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ed95895886dab6d2a584da45503555da", + "Repository": "RSPM", + "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4", "Requirements": [ "R6", "callr", "cli", - "crayon", + "curl", "desc", "digest", "pkgbuild", @@ -1074,32 +946,11 @@ "xopen" ] }, - "readxl": { - "Package": "readxl", - "Version": "1.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "63537c483c2dbec8d9e3183b3735254a", - "Requirements": [ - "Rcpp", - "cellranger", - "progress", - "tibble" - ] - }, - "rematch": { - "Package": "rematch", - "Version": "1.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "c66b930d20bb6d858cd18e1cebcfae5c", - "Requirements": [] - }, "rematch2": { "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ "tibble" @@ -1107,26 +958,18 @@ }, "remotes": { "Package": "remotes", - "Version": "2.2.0", + "Version": "2.4.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "430a0908aee75b1fcba0e62857cab0ce", - "Requirements": [] - }, - "renv": { - "Package": "renv", - "Version": "0.16.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "c9e8442ab69bc21c9697ecf856c1e6c7", + "Repository": "RSPM", + "Hash": "227045be9aee47e6dda9bb38ac870d67", "Requirements": [] }, "rex": { "Package": "rex", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "093584b944440c5cd07a696b3c8e0e4c", + "Repository": "RSPM", + "Hash": "ae34cd56890607370665bee5bd17812f", "Requirements": [ "lazyeval" ] @@ -1135,16 +978,16 @@ "Package": "rlang", "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", "Requirements": [] }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.17", + "Version": "2.20", "Source": "Repository", - "Repository": "CRAN", - "Hash": "e97c8be593e010f93520e8215c0f9189", + "Repository": "RSPM", + "Hash": "716fde5382293cc94a71f68c85b78d19", "Requirements": [ "bslib", "evaluate", @@ -1182,36 +1025,28 @@ "xml2" ] }, - "rpart": { - "Package": "rpart", - "Version": "4.1-15", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "9787c1fcb680e655d062e7611cadf78e", - "Requirements": [] - }, "rprojroot": { "Package": "rprojroot", - "Version": "2.0.2", + "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "249d8cd1e74a8f6a26194a91b47f21d1", + "Repository": "RSPM", + "Hash": "1de7ab598047a87bba48434ba35d497d", "Requirements": [] }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.13", + "Version": "0.14", "Source": "Repository", - "Repository": "CRAN", - "Hash": "06c85365a03fdaf699966cc1d3cf53ea", + "Repository": "RSPM", + "Hash": "690bd2acc42a9166ce34845884459320", "Requirements": [] }, "rversions": { "Package": "rversions", - "Version": "2.0.2", + "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0ec41191f744d0f5afad8c6f35cc36e4", + "Repository": "RSPM", + "Hash": "a9881dfed103e83f9de151dc17002cd1", "Requirements": [ "curl", "xml2" @@ -1219,10 +1054,10 @@ }, "sass": { "Package": "sass", - "Version": "0.4.2", + "Version": "0.4.5", "Source": "Repository", - "Repository": "CRAN", - "Hash": "1b191143d7d3444d504277843f3a95fe", + "Repository": "RSPM", + "Hash": "2bb4371a4c80115518261866eab6ab11", "Requirements": [ "R6", "fs", @@ -1233,30 +1068,29 @@ }, "sessioninfo": { "Package": "sessioninfo", - "Version": "1.1.1", + "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "308013098befe37484df72c39cf90d6e", + "Repository": "RSPM", + "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", "Requirements": [ - "cli", - "withr" + "cli" ] }, "shiny": { "Package": "shiny", - "Version": "1.6.0", + "Version": "1.7.4", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6e3b6ae7fe02b5859e4bb277f218b8ae", + "Repository": "RSPM", + "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5", "Requirements": [ "R6", "bslib", "cachem", "commonmark", "crayon", - "digest", "ellipsis", "fastmap", + "fontawesome", "glue", "htmltools", "httpuv", @@ -1275,23 +1109,15 @@ "Package": "sourcetools", "Version": "0.1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "947e4e02a79effa5d512473e10f41797", "Requirements": [] }, - "spatial": { - "Package": "spatial", - "Version": "7.3-13", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8d0918547149f72e78ae942ccd1fdbc7", - "Requirements": [] - }, "spelling": { "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", @@ -1302,15 +1128,15 @@ }, "staged.dependencies": { "Package": "staged.dependencies", - "Version": "0.2.7", + "Version": "0.2.8", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteRepo": "staged.dependencies", "RemoteUsername": "openpharma", - "RemoteRef": "HEAD", - "RemoteSha": "669f45a95d8772899551ad51fc3b38a3b5a1056a", - "Hash": "348648f944ce5dbcbdc2b120c9ba3a3c", + "RemoteRepo": "staged.dependencies", + "RemoteRef": "main", + "RemoteSha": "ce7c112ba3d75cf48e4dd6310b3140ab0ec3b486", + "Hash": "89f2e1d1009601f58f64b7092abcc0d7", "Requirements": [ "desc", "devtools", @@ -1331,30 +1157,34 @@ }, "stringi": { "Package": "stringi", - "Version": "1.5.3", + "Version": "1.7.12", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a063ebea753c92910a4cca7b18bc1f05", + "Repository": "RSPM", + "Hash": "ca8bd84263c77310739d2cf64d84d7c9", "Requirements": [] }, "stringr": { "Package": "stringr", - "Version": "1.4.0", + "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0759e6b6c0957edb1311028a49a35e76", + "Repository": "RSPM", + "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8", "Requirements": [ + "cli", "glue", + "lifecycle", "magrittr", - "stringi" + "rlang", + "stringi", + "vctrs" ] }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c855e70eb69b3dd8883660b7110e0c44", + "Repository": "RSPM", + "Hash": "1c038945a5e14cce208f5214c1dd167c", "Requirements": [ "R.cache", "cli", @@ -1366,29 +1196,19 @@ "withr" ] }, - "survival": { - "Package": "survival", - "Version": "3.2-10", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "6b7453cd9bb32b12577c78d54eeea56a", - "Requirements": [ - "Matrix" - ] - }, "sys": { "Package": "sys", - "Version": "3.4", + "Version": "3.4.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "b227d13e29222b4574486cfcbde077fa", + "Repository": "RSPM", + "Hash": "34c16f1ef796057bfa06d3f4ff818a5d", "Requirements": [] }, "systemfonts": { "Package": "systemfonts", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "90b28393209827327de889f49935140a", "Requirements": [ "cpp11" @@ -1396,16 +1216,15 @@ }, "testthat": { "Package": "testthat", - "Version": "3.0.2", + "Version": "3.1.6", "Source": "Repository", - "Repository": "CRAN", - "Hash": "495e0434d9305716b6a87031570ce109", + "Repository": "RSPM", + "Hash": "7910146255835c66e9eb272fb215248d", "Requirements": [ "R6", "brio", "callr", "cli", - "crayon", "desc", "digest", "ellipsis", @@ -1426,7 +1245,7 @@ "Package": "textshaping", "Version": "0.3.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1ab6223d3670fac7143202cb6a2d43d5", "Requirements": [ "cpp11", @@ -1435,12 +1254,11 @@ }, "tibble": { "Package": "tibble", - "Version": "3.1.0", + "Version": "3.1.8", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4d894a114dbd4ecafeda5074e7c538e6", + "Repository": "RSPM", + "Hash": "56b6934ef0f8c68225949a8672fe1a8f", "Requirements": [ - "ellipsis", "fansi", "lifecycle", "magrittr", @@ -1452,19 +1270,20 @@ }, "tidyr": { "Package": "tidyr", - "Version": "1.1.3", + "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "450d7dfaedde58e28586b854eeece4fa", + "Repository": "RSPM", + "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf", "Requirements": [ + "cli", "cpp11", "dplyr", - "ellipsis", "glue", "lifecycle", "magrittr", "purrr", "rlang", + "stringr", "tibble", "tidyselect", "vctrs" @@ -1472,33 +1291,56 @@ }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.0", + "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "6ea435c354e8448819627cf686f66e0a", + "Repository": "RSPM", + "Hash": "79540e5fcd9e0435af547d885f184fd5", "Requirements": [ - "ellipsis", + "cli", "glue", - "purrr", + "lifecycle", "rlang", - "vctrs" + "vctrs", + "withr" + ] + }, + "timechange": { + "Package": "timechange", + "Version": "0.2.0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "8548b44f79a35ba1791308b61e6012d7", + "Requirements": [ + "cpp11" ] }, "tinytex": { "Package": "tinytex", - "Version": "0.42", + "Version": "0.43", "Source": "Repository", - "Repository": "CRAN", - "Hash": "7629c6c1540835d5248e6e7df265fa74", + "Repository": "RSPM", + "Hash": "facc02f3d63ed7dd765513c004c394ce", "Requirements": [ "xfun" ] }, + "urlchecker": { + "Package": "urlchecker", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "409328b8e1253c8d729a7836fe7f7a16", + "Requirements": [ + "cli", + "curl", + "xml2" + ] + }, "usethis": { "Package": "usethis", "Version": "2.1.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a67a22c201832b12c036cc059f1d137d", "Requirements": [ "cli", @@ -1524,18 +1366,18 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.1", + "Version": "1.2.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7", + "Repository": "RSPM", + "Hash": "1fe17157424bb09c48a8b3b550c753bc", "Requirements": [] }, "vctrs": { "Package": "vctrs", - "Version": "0.5.0", + "Version": "0.5.2", "Source": "Repository", - "Repository": "CRAN", - "Hash": "001fd6a5ebfff8316baf9fb2b5516dc9", + "Repository": "RSPM", + "Hash": "e4ffa94ceed5f124d429a5a5f0f5b378", "Requirements": [ "cli", "glue", @@ -1543,25 +1385,12 @@ "rlang" ] }, - "visNetwork": { - "Package": "visNetwork", - "Version": "2.0.9", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "12545f2acf49d1d346d075580122d89c", - "Requirements": [ - "htmltools", - "htmlwidgets", - "jsonlite", - "magrittr" - ] - }, "waldo": { "Package": "waldo", - "Version": "0.2.5", + "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "20c45f1d511a3f730b7b469f4d11e104", + "Repository": "RSPM", + "Hash": "035fba89d0c86e2113120f93301b98ad", "Requirements": [ "cli", "diffobj", @@ -1574,33 +1403,33 @@ }, "whisker": { "Package": "whisker", - "Version": "0.4", + "Version": "0.4.1", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ca970b96d894e90397ed20637a0c1bbe", + "Repository": "RSPM", + "Hash": "c6abfa47a46d281a7d5159d0a8891e88", "Requirements": [] }, "withr": { "Package": "withr", "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c0e49a9760983e81e55cdd9be92e7182", "Requirements": [] }, "xfun": { "Package": "xfun", - "Version": "0.34", + "Version": "0.37", "Source": "Repository", - "Repository": "CRAN", - "Hash": "9eba2411b0b1f879797141bd24df7407", + "Repository": "RSPM", + "Hash": "a6860e1400a8fd1ddb6d9b4230cc34ab", "Requirements": [] }, "xml2": { "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "40682ed6a969ea5abfd351eb67833adc", "Requirements": [] }, @@ -1608,7 +1437,7 @@ "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "45e4bf3c46476896e821fc0a408fb4fc", "Requirements": [] }, @@ -1616,7 +1445,7 @@ "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" @@ -1626,23 +1455,23 @@ "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, "yaml": { "Package": "yaml", - "Version": "2.2.1", + "Version": "2.3.7", "Source": "Repository", - "Repository": "CRAN", - "Hash": "2826c5d9efb0a88f657c7a679c7106db", + "Repository": "RSPM", + "Hash": "0d0056cc5383fbc240ccd0cb584bf436", "Requirements": [] }, "zip": { "Package": "zip", "Version": "2.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88", "Requirements": [] } diff --git a/renv/profiles/4.0.5/renv.lock b/renv/profiles/4.0.5/renv.lock index c26a61d9..560d30ce 100644 --- a/renv/profiles/4.0.5/renv.lock +++ b/renv/profiles/4.0.5/renv.lock @@ -171,13 +171,11 @@ }, "cli": { "Package": "cli", - "Version": "3.3.0", + "Version": "3.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "23abf173c2b783dcc43379ab9bba00ee", - "Requirements": [ - "glue" - ] + "Hash": "0d297d01734d2bcea40197bd4971a764", + "Requirements": [] }, "clipr": { "Package": "clipr", @@ -1005,10 +1003,10 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.3", + "Version": "7.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7b153c746193b143c14baa072bae4e27", + "Repository": "CRAN", + "Hash": "da1f278262e563c835345872f2fef537", "Requirements": [ "R6", "brew", @@ -1016,6 +1014,7 @@ "commonmark", "cpp11", "desc", + "digest", "knitr", "pkgload", "purrr", diff --git a/renv/profiles/4.1.0/renv.lock b/renv/profiles/4.1.0/renv.lock index 6149ae61..3412e646 100644 --- a/renv/profiles/4.1.0/renv.lock +++ b/renv/profiles/4.1.0/renv.lock @@ -171,13 +171,11 @@ }, "cli": { "Package": "cli", - "Version": "3.3.0", + "Version": "3.4.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "23abf173c2b783dcc43379ab9bba00ee", - "Requirements": [ - "glue" - ] + "Hash": "0d297d01734d2bcea40197bd4971a764", + "Requirements": [] }, "clipr": { "Package": "clipr", @@ -1005,10 +1003,10 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.3", + "Version": "7.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7b153c746193b143c14baa072bae4e27", + "Repository": "CRAN", + "Hash": "da1f278262e563c835345872f2fef537", "Requirements": [ "R6", "brew", @@ -1016,6 +1014,7 @@ "commonmark", "cpp11", "desc", + "digest", "knitr", "pkgload", "purrr", From 6ae3f612c1e4b79bfc9b7cd105a98bee7c7485f6 Mon Sep 17 00:00:00 2001 From: galachad Date: Mon, 6 Feb 2023 02:45:50 +0000 Subject: [PATCH 006/100] renv update from pharmaverse/admiralci --- renv.lock | 8 ++++---- renv/profiles/4.0.5/renv.lock | 8 ++++---- renv/profiles/4.1.0/renv.lock | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/renv.lock b/renv.lock index 560d30ce..6625a978 100644 --- a/renv.lock +++ b/renv.lock @@ -1107,10 +1107,10 @@ }, "sourcetools": { "Package": "sourcetools", - "Version": "0.1.7", + "Version": "0.1.7-1", "Source": "Repository", "Repository": "RSPM", - "Hash": "947e4e02a79effa5d512473e10f41797", + "Hash": "5f5a7629f956619d519205ec475fe647", "Requirements": [] }, "spelling": { @@ -1316,10 +1316,10 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.43", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", - "Hash": "facc02f3d63ed7dd765513c004c394ce", + "Hash": "c0f007e2eeed7722ce13d42b84a22e07", "Requirements": [ "xfun" ] diff --git a/renv/profiles/4.0.5/renv.lock b/renv/profiles/4.0.5/renv.lock index 560d30ce..6625a978 100644 --- a/renv/profiles/4.0.5/renv.lock +++ b/renv/profiles/4.0.5/renv.lock @@ -1107,10 +1107,10 @@ }, "sourcetools": { "Package": "sourcetools", - "Version": "0.1.7", + "Version": "0.1.7-1", "Source": "Repository", "Repository": "RSPM", - "Hash": "947e4e02a79effa5d512473e10f41797", + "Hash": "5f5a7629f956619d519205ec475fe647", "Requirements": [] }, "spelling": { @@ -1316,10 +1316,10 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.43", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", - "Hash": "facc02f3d63ed7dd765513c004c394ce", + "Hash": "c0f007e2eeed7722ce13d42b84a22e07", "Requirements": [ "xfun" ] diff --git a/renv/profiles/4.1.0/renv.lock b/renv/profiles/4.1.0/renv.lock index 3412e646..9dc35f6c 100644 --- a/renv/profiles/4.1.0/renv.lock +++ b/renv/profiles/4.1.0/renv.lock @@ -1107,10 +1107,10 @@ }, "sourcetools": { "Package": "sourcetools", - "Version": "0.1.7", + "Version": "0.1.7-1", "Source": "Repository", "Repository": "RSPM", - "Hash": "947e4e02a79effa5d512473e10f41797", + "Hash": "5f5a7629f956619d519205ec475fe647", "Requirements": [] }, "spelling": { @@ -1316,10 +1316,10 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.43", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", - "Hash": "facc02f3d63ed7dd765513c004c394ce", + "Hash": "c0f007e2eeed7722ce13d42b84a22e07", "Requirements": [ "xfun" ] From a611f233b90f8b64740be9b173b4b0c229d21a8e Mon Sep 17 00:00:00 2001 From: galachad Date: Mon, 6 Feb 2023 06:06:03 +0000 Subject: [PATCH 007/100] renv update from pharmaverse/admiralci --- renv.lock | 25 ++++++++++++------------- renv/profiles/4.0.5/renv.lock | 25 ++++++++++++------------- renv/profiles/4.1.0/renv.lock | 25 ++++++++++++------------- 3 files changed, 36 insertions(+), 39 deletions(-) diff --git a/renv.lock b/renv.lock index 6625a978..a77db8d4 100644 --- a/renv.lock +++ b/renv.lock @@ -162,7 +162,7 @@ "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9b2191ede20fa29828139b9900922e51", "Requirements": [ "R6", @@ -171,10 +171,10 @@ }, "cli": { "Package": "cli", - "Version": "3.4.1", + "Version": "3.6.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0d297d01734d2bcea40197bd4971a764", + "Repository": "RSPM", + "Hash": "3177a5a16c243adc199ba33117bd9657", "Requirements": [] }, "clipr": { @@ -669,7 +669,7 @@ "Package": "lintr", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b21ebd652d940f099915221f3328ab7b", "Requirements": [ "backports", @@ -790,7 +790,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "16fa15449c930bf3a7761d3c68f8abf9", "Requirements": [ "bslib", @@ -850,10 +850,10 @@ }, "processx": { "Package": "processx", - "Version": "3.6.1", + "Version": "3.8.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6", + "Repository": "RSPM", + "Hash": "a33ee2d9bf07564efb888ad98410da84", "Requirements": [ "R6", "ps" @@ -1003,10 +1003,10 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "da1f278262e563c835345872f2fef537", + "Repository": "RSPM", + "Hash": "7b153c746193b143c14baa072bae4e27", "Requirements": [ "R6", "brew", @@ -1014,7 +1014,6 @@ "commonmark", "cpp11", "desc", - "digest", "knitr", "pkgload", "purrr", diff --git a/renv/profiles/4.0.5/renv.lock b/renv/profiles/4.0.5/renv.lock index 6625a978..a77db8d4 100644 --- a/renv/profiles/4.0.5/renv.lock +++ b/renv/profiles/4.0.5/renv.lock @@ -162,7 +162,7 @@ "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9b2191ede20fa29828139b9900922e51", "Requirements": [ "R6", @@ -171,10 +171,10 @@ }, "cli": { "Package": "cli", - "Version": "3.4.1", + "Version": "3.6.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0d297d01734d2bcea40197bd4971a764", + "Repository": "RSPM", + "Hash": "3177a5a16c243adc199ba33117bd9657", "Requirements": [] }, "clipr": { @@ -669,7 +669,7 @@ "Package": "lintr", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b21ebd652d940f099915221f3328ab7b", "Requirements": [ "backports", @@ -790,7 +790,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "16fa15449c930bf3a7761d3c68f8abf9", "Requirements": [ "bslib", @@ -850,10 +850,10 @@ }, "processx": { "Package": "processx", - "Version": "3.6.1", + "Version": "3.8.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6", + "Repository": "RSPM", + "Hash": "a33ee2d9bf07564efb888ad98410da84", "Requirements": [ "R6", "ps" @@ -1003,10 +1003,10 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "da1f278262e563c835345872f2fef537", + "Repository": "RSPM", + "Hash": "7b153c746193b143c14baa072bae4e27", "Requirements": [ "R6", "brew", @@ -1014,7 +1014,6 @@ "commonmark", "cpp11", "desc", - "digest", "knitr", "pkgload", "purrr", diff --git a/renv/profiles/4.1.0/renv.lock b/renv/profiles/4.1.0/renv.lock index 9dc35f6c..19f661be 100644 --- a/renv/profiles/4.1.0/renv.lock +++ b/renv/profiles/4.1.0/renv.lock @@ -162,7 +162,7 @@ "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9b2191ede20fa29828139b9900922e51", "Requirements": [ "R6", @@ -171,10 +171,10 @@ }, "cli": { "Package": "cli", - "Version": "3.4.1", + "Version": "3.6.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0d297d01734d2bcea40197bd4971a764", + "Repository": "RSPM", + "Hash": "3177a5a16c243adc199ba33117bd9657", "Requirements": [] }, "clipr": { @@ -669,7 +669,7 @@ "Package": "lintr", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b21ebd652d940f099915221f3328ab7b", "Requirements": [ "backports", @@ -790,7 +790,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "16fa15449c930bf3a7761d3c68f8abf9", "Requirements": [ "bslib", @@ -850,10 +850,10 @@ }, "processx": { "Package": "processx", - "Version": "3.6.1", + "Version": "3.8.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6", + "Repository": "RSPM", + "Hash": "a33ee2d9bf07564efb888ad98410da84", "Requirements": [ "R6", "ps" @@ -1003,10 +1003,10 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "da1f278262e563c835345872f2fef537", + "Repository": "RSPM", + "Hash": "7b153c746193b143c14baa072bae4e27", "Requirements": [ "R6", "brew", @@ -1014,7 +1014,6 @@ "commonmark", "cpp11", "desc", - "digest", "knitr", "pkgload", "purrr", From a83cdf83d851f012e6ead7316980db6f0140cca8 Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 14 Feb 2023 13:03:46 +0000 Subject: [PATCH 008/100] renv update from pharmaverse/admiralci --- renv.lock | 767 +++++---- renv/profiles/4.0/renv.lock | 1439 +++++++++++++++++ renv/profiles/{4.0.5 => 4.0}/renv/.gitignore | 0 .../profiles/{4.0.5 => 4.0}/renv/settings.dcf | 0 renv/profiles/{4.1.0 => 4.1}/renv.lock | 624 ++++--- renv/profiles/{4.1.0 => 4.1}/renv/.gitignore | 0 .../profiles/{4.1.0 => 4.1}/renv/settings.dcf | 0 renv/profiles/{4.0.5 => 4.2}/renv.lock | 447 +++-- renv/profiles/4.2/renv/.gitignore | 7 + renv/profiles/4.2/renv/settings.dcf | 10 + 10 files changed, 2321 insertions(+), 973 deletions(-) create mode 100644 renv/profiles/4.0/renv.lock rename renv/profiles/{4.0.5 => 4.0}/renv/.gitignore (100%) rename renv/profiles/{4.0.5 => 4.0}/renv/settings.dcf (100%) rename renv/profiles/{4.1.0 => 4.1}/renv.lock (71%) rename renv/profiles/{4.1.0 => 4.1}/renv/.gitignore (100%) rename renv/profiles/{4.1.0 => 4.1}/renv/settings.dcf (100%) rename renv/profiles/{4.0.5 => 4.2}/renv.lock (79%) create mode 100644 renv/profiles/4.2/renv/.gitignore create mode 100644 renv/profiles/4.2/renv/settings.dcf diff --git a/renv.lock b/renv.lock index a77db8d4..f51a6fd8 100644 --- a/renv.lock +++ b/renv.lock @@ -13,17 +13,24 @@ ] }, "Packages": { + "BH": { + "Package": "BH", + "Version": "1.75.0-0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e4c04affc2cac20c8fec18385cd14691", + "Requirements": [] + }, "DT": { "Package": "DT", - "Version": "0.27", + "Version": "0.17", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3444e6ed78763f9f13aaa39f2481eb34", + "Repository": "CRAN", + "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0", "Requirements": [ "crosstalk", "htmltools", "htmlwidgets", - "jquerylib", "jsonlite", "magrittr", "promises" @@ -31,10 +38,10 @@ }, "R.cache": { "Package": "R.cache", - "Version": "0.16.0", + "Version": "0.14.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8", + "Repository": "CRAN", + "Hash": "1ca02d43e1a4d49e616bd23bb39b17e6", "Requirements": [ "R.methodsS3", "R.oo", @@ -44,28 +51,28 @@ }, "R.methodsS3": { "Package": "R.methodsS3", - "Version": "1.8.2", + "Version": "1.8.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "278c286fd6e9e75d0c2e8f731ea445c8", + "Repository": "CRAN", + "Hash": "4bf6453323755202d5909697b6f7c109", "Requirements": [] }, "R.oo": { "Package": "R.oo", - "Version": "1.25.0", + "Version": "1.24.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a0900a114f4f0194cf4aa8cd4a700681", + "Repository": "CRAN", + "Hash": "5709328352717e2f0a9c012be8a97554", "Requirements": [ "R.methodsS3" ] }, "R.utils": { "Package": "R.utils", - "Version": "2.12.2", + "Version": "2.10.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "325f01db13da12c04d8f6e7be36ff514", + "Repository": "CRAN", + "Hash": "a9e316277ff12a43997266f2f6567780", "Requirements": [ "R.methodsS3", "R.oo" @@ -73,25 +80,25 @@ }, "R6": { "Package": "R6", - "Version": "2.5.1", + "Version": "2.5.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "470851b6d5d0ac559e9d01bb352b4021", + "Repository": "CRAN", + "Hash": "b203113193e70978a696b2809525649d", "Requirements": [] }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.10", + "Version": "1.0.6", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e749cae40fa9ef469b6050959517453c", + "Repository": "CRAN", + "Hash": "dbb5e436998a7eba5a9d682060533338", "Requirements": [] }, "askpass": { "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "e8a22846fff485f0be3770c2da758713", "Requirements": [ "sys" @@ -99,60 +106,58 @@ }, "backports": { "Package": "backports", - "Version": "1.4.1", + "Version": "1.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c39fbec8a30d23e721980b8afb31984c", + "Repository": "CRAN", + "Hash": "644043219fc24e190c2f620c1a380a69", "Requirements": [] }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, "brew": { "Package": "brew", - "Version": "1.0-8", + "Version": "1.0-6", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d69a786e85775b126bddbee185ae6084", + "Repository": "CRAN", + "Hash": "92a5f887f9ae3035ac7afde22ba73ee9", "Requirements": [] }, "brio": { "Package": "brio", - "Version": "1.1.3", + "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "976cf154dfb043c012d87cddd8bca363", + "Repository": "CRAN", + "Hash": "36758510e65a457efeefa50e1e7f0576", "Requirements": [] }, "bslib": { "Package": "bslib", - "Version": "0.4.2", + "Version": "0.2.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a7fbf03946ad741129dc81098722fca1", + "Repository": "CRAN", + "Hash": "4830a372b241d78ed6f53731ee3023ac", "Requirements": [ - "base64enc", - "cachem", + "digest", "htmltools", "jquerylib", "jsonlite", - "memoise", - "mime", + "magrittr", "rlang", "sass" ] }, "cachem": { "Package": "cachem", - "Version": "1.0.6", + "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "648c5b3d71e6a37e3043617489a0a0e9", + "Repository": "CRAN", + "Hash": "2703a46dcabfb902f10060b2bca9f708", "Requirements": [ "fastmap", "rlang" @@ -162,7 +167,7 @@ "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "9b2191ede20fa29828139b9900922e51", "Requirements": [ "R6", @@ -171,18 +176,18 @@ }, "cli": { "Package": "cli", - "Version": "3.6.0", + "Version": "3.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3177a5a16c243adc199ba33117bd9657", + "Repository": "CRAN", + "Hash": "0d297d01734d2bcea40197bd4971a764", "Requirements": [] }, "clipr": { "Package": "clipr", - "Version": "0.8.0", + "Version": "0.7.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", + "Repository": "CRAN", + "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7", "Requirements": [] }, "codetools": { @@ -195,18 +200,18 @@ }, "commonmark": { "Package": "commonmark", - "Version": "1.8.1", + "Version": "1.7", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b6e3e947d1d7ebf3d2bdcea1bde63fe7", + "Repository": "CRAN", + "Hash": "0f22be39ec1d141fd03683c06f3a6e67", "Requirements": [] }, "covr": { "Package": "covr", - "Version": "3.6.1", + "Version": "3.5.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a861cee34fbb4b107a73dd414ef56724", + "Repository": "CRAN", + "Hash": "6d80a9fc3c0c8473153b54fa54719dfd", "Requirements": [ "crayon", "digest", @@ -219,26 +224,26 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.4.3", + "Version": "0.2.7", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ed588261931ee3be2c700d22e94a29ab", + "Repository": "CRAN", + "Hash": "730eebcc741a5c36761f7d4d0f5e37b8", "Requirements": [] }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e8a1e41acf02548751f45c718d55aa6a", + "Repository": "CRAN", + "Hash": "e75525c55c70e5f4f78c9960a4b402e9", "Requirements": [] }, "credentials": { "Package": "credentials", - "Version": "1.3.2", + "Version": "1.3.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "93762d0a34d78e6a025efdbfb5c6bb41", + "Repository": "CRAN", + "Hash": "a96728288c75a814c900af9da84387be", "Requirements": [ "askpass", "curl", @@ -249,10 +254,10 @@ }, "crosstalk": { "Package": "crosstalk", - "Version": "1.2.0", + "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "6aa54f69598c32177e920eb3402e8293", + "Repository": "CRAN", + "Hash": "2b06f9e415a62b6762e4b8098d2aecbc", "Requirements": [ "R6", "htmltools", @@ -262,17 +267,17 @@ }, "curl": { "Package": "curl", - "Version": "5.0.0", + "Version": "4.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e4f97056611e8e6b8b852d13b7400cf1", + "Repository": "CRAN", + "Hash": "2b7d10581cc730804e9ed178c8374bd6", "Requirements": [] }, "cyclocomp": { "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "53cbed70a2f7472d48fb6aef08442f25", "Requirements": [ "callr", @@ -284,42 +289,42 @@ }, "desc": { "Package": "desc", - "Version": "1.4.2", + "Version": "1.3.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", + "Repository": "CRAN", + "Hash": "b6963166f7f10b970af1006c462ce6cd", "Requirements": [ "R6", - "cli", + "crayon", "rprojroot" ] }, "devtools": { "Package": "devtools", - "Version": "2.4.5", + "Version": "2.3.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ea5bc8b4a6a01e4f12d98b58329930bb", + "Repository": "CRAN", + "Hash": "415656f50722f5b6e6bcf80855ce11b9", "Requirements": [ + "DT", + "callr", "cli", + "covr", "desc", "ellipsis", - "fs", - "lifecycle", + "httr", + "jsonlite", "memoise", - "miniUI", "pkgbuild", - "pkgdown", "pkgload", - "profvis", "rcmdcheck", "remotes", "rlang", "roxygen2", + "rstudioapi", "rversions", "sessioninfo", "testthat", - "urlchecker", "usethis", "withr" ] @@ -328,7 +333,7 @@ "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "9ddedef46959baad2080047a1b0117fe", "Requirements": [ "tibble" @@ -336,55 +341,51 @@ }, "diffobj": { "Package": "diffobj", - "Version": "0.3.5", + "Version": "0.3.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8", + "Repository": "CRAN", + "Hash": "feb5b7455eba422a2c110bb89852e6a3", "Requirements": [ "crayon" ] }, "digest": { "Package": "digest", - "Version": "0.6.31", + "Version": "0.6.27", "Source": "Repository", - "Repository": "RSPM", - "Hash": "8b708f296afd9ae69f450f9640be8990", + "Repository": "CRAN", + "Hash": "a0cbe758a531d054b537d16dff4d58a1", "Requirements": [] }, "downlit": { "Package": "downlit", - "Version": "0.4.2", + "Version": "0.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "79bf3f66590752ffbba20f8d2da94c7c", + "Repository": "CRAN", + "Hash": "f24f1e44320a978c03050b8403a83793", "Requirements": [ "brio", - "desc", "digest", "evaluate", "fansi", - "memoise", "rlang", "vctrs", - "withr", "yaml" ] }, "dplyr": { "Package": "dplyr", - "Version": "1.1.0", + "Version": "1.0.5", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d3c34618017e7ae252d46d79a1b9ec32", + "Repository": "CRAN", + "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68", "Requirements": [ "R6", - "cli", + "ellipsis", "generics", "glue", "lifecycle", "magrittr", - "pillar", "rlang", "tibble", "tidyselect", @@ -393,71 +394,60 @@ }, "ellipsis": { "Package": "ellipsis", - "Version": "0.3.2", + "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", + "Repository": "CRAN", + "Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a", "Requirements": [ "rlang" ] }, "evaluate": { "Package": "evaluate", - "Version": "0.20", + "Version": "0.14", "Source": "Repository", - "Repository": "RSPM", - "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c", + "Repository": "CRAN", + "Hash": "ec8ca05cffcc70569eaaad8469d2a3a7", "Requirements": [] }, "fansi": { "Package": "fansi", - "Version": "1.0.4", + "Version": "0.4.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1d9e7ad3c8312a192dea7d3db0274fde", + "Repository": "CRAN", + "Hash": "fea074fb67fe4c25d47ad09087da847d", "Requirements": [] }, "fastmap": { "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, - "fontawesome": { - "Package": "fontawesome", - "Version": "0.5.0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "e80750aec5717dedc019ad7ee40e4a7c", - "Requirements": [ - "htmltools", - "rlang" - ] - }, "fs": { "Package": "fs", - "Version": "1.6.0", + "Version": "1.5.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "0120e8c933bace1141e0b0d376b0c010", + "Repository": "CRAN", + "Hash": "44594a07a42e5f91fac9f93fda6d0109", "Requirements": [] }, "generics": { "Package": "generics", - "Version": "0.1.3", + "Version": "0.1.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "15e9634c0fcd294799e9b2e929ed1b86", + "Repository": "CRAN", + "Hash": "4d243a9c10b00589889fe32314ffd902", "Requirements": [] }, "gert": { "Package": "gert", - "Version": "1.9.2", + "Version": "1.3.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "9122b3958e749badb5c939f498038b57", + "Repository": "CRAN", + "Hash": "56f398846cd40937be6b435a66bd3f37", "Requirements": [ "askpass", "credentials", @@ -469,10 +459,10 @@ }, "gh": { "Package": "gh", - "Version": "1.3.1", + "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b6a12054ee13dce0f6696c019c10e539", + "Repository": "CRAN", + "Hash": "05129b4387282404780d2f8593636388", "Requirements": [ "cli", "gitcreds", @@ -483,44 +473,42 @@ }, "git2r": { "Package": "git2r", - "Version": "0.31.0", + "Version": "0.28.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "acb972e0be37f83b9c762d962d75a188", + "Repository": "CRAN", + "Hash": "f64fd34026f6025de71a4354800e6d79", "Requirements": [] }, "gitcreds": { "Package": "gitcreds", - "Version": "0.1.2", + "Version": "0.1.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe", + "Repository": "CRAN", + "Hash": "f3aefccc1cc50de6338146b62f115de8", "Requirements": [] }, "glue": { "Package": "glue", - "Version": "1.6.2", + "Version": "1.4.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", + "Repository": "CRAN", + "Hash": "6efd734b14c6471cfe443345f3e35e29", "Requirements": [] }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.8", "Source": "Repository", - "Repository": "RSPM", - "Hash": "06230136b2d2b9ba5805e1963fa6e890", - "Requirements": [ - "xfun" - ] + "Repository": "CRAN", + "Hash": "4dc5bb88961e347a0f4d8aad597cbfac", + "Requirements": [] }, "hms": { "Package": "hms", - "Version": "1.1.2", + "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "41100392191e1244b887878b533eea91", + "Repository": "CRAN", + "Hash": "bf552cdd96f5969873afdac7311c7d0d", "Requirements": [ "ellipsis", "lifecycle", @@ -531,39 +519,36 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.4", + "Version": "0.5.1.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7", + "Repository": "CRAN", + "Hash": "af2c2531e55df5cf230c4b5444fc973c", "Requirements": [ "base64enc", "digest", - "ellipsis", - "fastmap", "rlang" ] }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.6.1", + "Version": "1.5.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b677ee5954471eaa974c0d099a343a1a", + "Repository": "CRAN", + "Hash": "6fdaa86d0700f8b3e92ee3c445a5a10d", "Requirements": [ "htmltools", "jsonlite", - "knitr", - "rmarkdown", "yaml" ] }, "httpuv": { "Package": "httpuv", - "Version": "1.6.8", + "Version": "1.5.5", "Source": "Repository", - "Repository": "RSPM", - "Hash": "08e611aee165b27f8ff18770285fb535", + "Repository": "CRAN", + "Hash": "b9d5d39be2150cf86538b8488334b8f8", "Requirements": [ + "BH", "R6", "Rcpp", "later", @@ -572,10 +557,10 @@ }, "httr": { "Package": "httr", - "Version": "1.4.4", + "Version": "1.4.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "57557fac46471f0dbbf44705cc6a5c8c", + "Repository": "CRAN", + "Hash": "a525aba14184fec243f9eaec62fbed43", "Requirements": [ "R6", "curl", @@ -586,10 +571,10 @@ }, "hunspell": { "Package": "hunspell", - "Version": "3.0.2", + "Version": "3.0.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "656219b6f3f605499d7cdbe208656639", + "Repository": "CRAN", + "Hash": "3987784c19192ad0f2261c456d936df1", "Requirements": [ "Rcpp", "digest" @@ -599,48 +584,51 @@ "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, "jquerylib": { "Package": "jquerylib", - "Version": "0.1.4", + "Version": "0.1.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "5aab57a3bd297eee1c1d862735972182", + "Repository": "CRAN", + "Hash": "5ff50b36f7f0832f8421745af333e73c", "Requirements": [ "htmltools" ] }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.4", + "Version": "1.7.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a4269a09a9b865579b2635c77e572374", + "Repository": "CRAN", + "Hash": "98138e0994d41508c7a6b84a0600cfcb", "Requirements": [] }, "knitr": { "Package": "knitr", - "Version": "1.42", + "Version": "1.31", "Source": "Repository", - "Repository": "RSPM", - "Hash": "8329a9bcc82943c8069104d4be3ee22d", + "Repository": "CRAN", + "Hash": "c3994c036d19fc22c5e2a209c8298bfb", "Requirements": [ "evaluate", "highr", + "markdown", + "stringr", "xfun", "yaml" ] }, "later": { "Package": "later", - "Version": "1.3.0", + "Version": "1.1.0.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e", + "Repository": "CRAN", + "Hash": "d0a62b247165aabf397fded504660d8a", "Requirements": [ + "BH", "Rcpp", "rlang" ] @@ -649,18 +637,17 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "d908914ae53b04d4c0c0fd72ecc35370", "Requirements": [] }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "001cecbeac1cff9301bdc3775ee46a86", + "Repository": "CRAN", + "Hash": "3471fb65971f1a7b2d4ae7848cf2db8d", "Requirements": [ - "cli", "glue", "rlang" ] @@ -669,7 +656,7 @@ "Package": "lintr", "Version": "3.0.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b21ebd652d940f099915221f3328ab7b", "Requirements": [ "backports", @@ -687,29 +674,40 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.9.1", + "Version": "1.7.10", "Source": "Repository", - "Repository": "RSPM", - "Hash": "88ad585eb49669b7f2db3f5ef3c8307d", + "Repository": "CRAN", + "Hash": "1ebfdc8a3cfe8fe19184f5481972b092", "Requirements": [ - "generics", - "timechange" + "Rcpp", + "generics" ] }, "magrittr": { "Package": "magrittr", - "Version": "2.0.3", + "Version": "2.0.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7ce2733a9826b3aeb1775d56fd305472", + "Repository": "CRAN", + "Hash": "41287f1ac7d28a92f0a286ed507928d3", "Requirements": [] }, + "markdown": { + "Package": "markdown", + "Version": "1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "61e4a10781dd00d7d81dd06ca9b94e95", + "Requirements": [ + "mime", + "xfun" + ] + }, "memoise": { "Package": "memoise", - "Version": "2.0.1", + "Version": "2.0.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c", + "Repository": "CRAN", + "Hash": "a0bc51650201a56d00a4798523cc91b3", "Requirements": [ "cachem", "rlang" @@ -717,17 +715,17 @@ }, "mime": { "Package": "mime", - "Version": "0.12", + "Version": "0.10", "Source": "Repository", - "Repository": "RSPM", - "Hash": "18e9c28c1d3ca1560ce30658b22ce104", + "Repository": "CRAN", + "Hash": "26fa77e707223e1ce042b2b5d09993dc", "Requirements": [] }, "miniUI": { "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "fec5f52652d60615fdb3957b3d74324a", "Requirements": [ "htmltools", @@ -736,24 +734,25 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.5", + "Version": "1.4.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b04c27110bf367b4daa93f34f3d58e75", + "Repository": "CRAN", + "Hash": "a399e4773075fc2375b71f45fca186c4", "Requirements": [ "askpass" ] }, "pillar": { "Package": "pillar", - "Version": "1.8.1", + "Version": "1.5.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "f2316df30902c81729ae9de95ad5a608", + "Repository": "CRAN", + "Hash": "24622aa4a0d3de3463c34513edca99b2", "Requirements": [ "cli", + "crayon", + "ellipsis", "fansi", - "glue", "lifecycle", "rlang", "utf8", @@ -762,10 +761,10 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.4.0", + "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d6c3008d79653a0f267703288230105e", + "Repository": "CRAN", + "Hash": "725fcc30222d4d11ec68efb8ff11a9af", "Requirements": [ "R6", "callr", @@ -773,7 +772,6 @@ "crayon", "desc", "prettyunits", - "processx", "rprojroot", "withr" ] @@ -782,7 +780,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "01f28d4278f15c76cddbea05899c5d6f", "Requirements": [] }, @@ -790,7 +788,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "16fa15449c930bf3a7761d3c68f8abf9", "Requirements": [ "bslib", @@ -817,18 +815,18 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.2", + "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2", + "Repository": "CRAN", + "Hash": "cb57de933545960a86f03513e4bd2911", "Requirements": [ "cli", "crayon", "desc", - "fs", - "glue", + "pkgbuild", "rlang", "rprojroot", + "rstudioapi", "withr" ] }, @@ -836,7 +834,7 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a555924add98c99d2f411e37e7d25e9f", "Requirements": [] }, @@ -844,37 +842,26 @@ "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", "Requirements": [] }, "processx": { "Package": "processx", - "Version": "3.8.0", + "Version": "3.6.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a33ee2d9bf07564efb888ad98410da84", + "Repository": "CRAN", + "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6", "Requirements": [ "R6", "ps" ] }, - "profvis": { - "Package": "profvis", - "Version": "0.3.7", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "e9d21e79848e02e524bea6f5bd53e7e4", - "Requirements": [ - "htmlwidgets", - "stringr" - ] - }, "promises": { "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4ab2c43adb4d4699cf3690acd378d75d", "Requirements": [ "R6", @@ -886,32 +873,29 @@ }, "ps": { "Package": "ps", - "Version": "1.7.2", + "Version": "1.6.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "68dd03d98a5efd1eb3012436de45ba83", + "Repository": "CRAN", + "Hash": "32620e2001c1dce1af49c49dccbb9420", "Requirements": [] }, "purrr": { "Package": "purrr", - "Version": "1.0.1", + "Version": "0.3.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d71c815267c640f17ddbf7f16144b4bb", + "Repository": "CRAN", + "Hash": "97def703420c8ab10d8f0e6c72101e02", "Requirements": [ - "cli", - "lifecycle", "magrittr", - "rlang", - "vctrs" + "rlang" ] }, "ragg": { "Package": "ragg", - "Version": "1.2.5", + "Version": "1.1.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9", + "Repository": "CRAN", + "Hash": "3f0ac98597bebdc31b747def3eb9b6ca", "Requirements": [ "systemfonts", "textshaping" @@ -921,21 +905,21 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, "rcmdcheck": { "Package": "rcmdcheck", - "Version": "1.4.0", + "Version": "1.3.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4", + "Repository": "CRAN", + "Hash": "ed95895886dab6d2a584da45503555da", "Requirements": [ "R6", "callr", "cli", - "curl", + "crayon", "desc", "digest", "pkgbuild", @@ -950,7 +934,7 @@ "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ "tibble" @@ -958,18 +942,18 @@ }, "remotes": { "Package": "remotes", - "Version": "2.4.2", + "Version": "2.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "227045be9aee47e6dda9bb38ac870d67", + "Repository": "CRAN", + "Hash": "430a0908aee75b1fcba0e62857cab0ce", "Requirements": [] }, "rex": { "Package": "rex", - "Version": "1.2.1", + "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ae34cd56890607370665bee5bd17812f", + "Repository": "CRAN", + "Hash": "093584b944440c5cd07a696b3c8e0e4c", "Requirements": [ "lazyeval" ] @@ -978,21 +962,19 @@ "Package": "rlang", "Version": "1.0.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", "Requirements": [] }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.20", + "Version": "2.7", "Source": "Repository", - "Repository": "RSPM", - "Hash": "716fde5382293cc94a71f68c85b78d19", + "Repository": "CRAN", + "Hash": "edbf4cb1aefae783fd8d3a008ae51943", "Requirements": [ - "bslib", "evaluate", "htmltools", - "jquerylib", "jsonlite", "knitr", "stringr", @@ -1003,10 +985,10 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.3", + "Version": "7.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7b153c746193b143c14baa072bae4e27", + "Repository": "CRAN", + "Hash": "da1f278262e563c835345872f2fef537", "Requirements": [ "R6", "brew", @@ -1014,6 +996,7 @@ "commonmark", "cpp11", "desc", + "digest", "knitr", "pkgload", "purrr", @@ -1026,26 +1009,26 @@ }, "rprojroot": { "Package": "rprojroot", - "Version": "2.0.3", + "Version": "2.0.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1de7ab598047a87bba48434ba35d497d", + "Repository": "CRAN", + "Hash": "249d8cd1e74a8f6a26194a91b47f21d1", "Requirements": [] }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.14", + "Version": "0.13", "Source": "Repository", - "Repository": "RSPM", - "Hash": "690bd2acc42a9166ce34845884459320", + "Repository": "CRAN", + "Hash": "06c85365a03fdaf699966cc1d3cf53ea", "Requirements": [] }, "rversions": { "Package": "rversions", - "Version": "2.1.2", + "Version": "2.0.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a9881dfed103e83f9de151dc17002cd1", + "Repository": "CRAN", + "Hash": "0ec41191f744d0f5afad8c6f35cc36e4", "Requirements": [ "curl", "xml2" @@ -1053,12 +1036,13 @@ }, "sass": { "Package": "sass", - "Version": "0.4.5", + "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "2bb4371a4c80115518261866eab6ab11", + "Repository": "CRAN", + "Hash": "3ef1adfe46b7b144b970d74ce33ab0d6", "Requirements": [ "R6", + "digest", "fs", "htmltools", "rappdirs", @@ -1067,29 +1051,30 @@ }, "sessioninfo": { "Package": "sessioninfo", - "Version": "1.2.2", + "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", + "Repository": "CRAN", + "Hash": "308013098befe37484df72c39cf90d6e", "Requirements": [ - "cli" + "cli", + "withr" ] }, "shiny": { "Package": "shiny", - "Version": "1.7.4", + "Version": "1.6.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5", + "Repository": "CRAN", + "Hash": "6e3b6ae7fe02b5859e4bb277f218b8ae", "Requirements": [ "R6", "bslib", "cachem", "commonmark", "crayon", + "digest", "ellipsis", "fastmap", - "fontawesome", "glue", "htmltools", "httpuv", @@ -1106,17 +1091,17 @@ }, "sourcetools": { "Package": "sourcetools", - "Version": "0.1.7-1", + "Version": "0.1.7", "Source": "Repository", - "Repository": "RSPM", - "Hash": "5f5a7629f956619d519205ec475fe647", + "Repository": "CRAN", + "Hash": "947e4e02a79effa5d512473e10f41797", "Requirements": [] }, "spelling": { "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", @@ -1156,74 +1141,74 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.12", + "Version": "1.5.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ca8bd84263c77310739d2cf64d84d7c9", + "Repository": "CRAN", + "Hash": "a063ebea753c92910a4cca7b18bc1f05", "Requirements": [] }, "stringr": { "Package": "stringr", - "Version": "1.5.0", + "Version": "1.4.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8", + "Repository": "CRAN", + "Hash": "0759e6b6c0957edb1311028a49a35e76", "Requirements": [ - "cli", "glue", - "lifecycle", "magrittr", - "rlang", - "stringi", - "vctrs" + "stringi" ] }, "styler": { "Package": "styler", - "Version": "1.9.0", + "Version": "1.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1c038945a5e14cce208f5214c1dd167c", + "Repository": "CRAN", + "Hash": "2ec6308547ffe73208cef3ef3766fc33", "Requirements": [ "R.cache", + "backports", "cli", "magrittr", "purrr", + "rematch2", "rlang", "rprojroot", - "vctrs", - "withr" + "tibble", + "withr", + "xfun" ] }, "sys": { "Package": "sys", - "Version": "3.4.1", + "Version": "3.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "34c16f1ef796057bfa06d3f4ff818a5d", + "Repository": "CRAN", + "Hash": "b227d13e29222b4574486cfcbde077fa", "Requirements": [] }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.4", + "Version": "1.0.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "90b28393209827327de889f49935140a", + "Repository": "CRAN", + "Hash": "6e899d7c097698d50ec87b1d8e65f246", "Requirements": [ "cpp11" ] }, "testthat": { "Package": "testthat", - "Version": "3.1.6", + "Version": "3.0.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7910146255835c66e9eb272fb215248d", + "Repository": "CRAN", + "Hash": "495e0434d9305716b6a87031570ce109", "Requirements": [ "R6", "brio", "callr", "cli", + "crayon", "desc", "digest", "ellipsis", @@ -1242,10 +1227,10 @@ }, "textshaping": { "Package": "textshaping", - "Version": "0.3.6", + "Version": "0.3.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1ab6223d3670fac7143202cb6a2d43d5", + "Repository": "CRAN", + "Hash": "fff317575e7191e2d077292309bed575", "Requirements": [ "cpp11", "systemfonts" @@ -1253,11 +1238,12 @@ }, "tibble": { "Package": "tibble", - "Version": "3.1.8", + "Version": "3.1.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "56b6934ef0f8c68225949a8672fe1a8f", + "Repository": "CRAN", + "Hash": "4d894a114dbd4ecafeda5074e7c538e6", "Requirements": [ + "ellipsis", "fansi", "lifecycle", "magrittr", @@ -1269,20 +1255,19 @@ }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.1.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf", + "Repository": "CRAN", + "Hash": "450d7dfaedde58e28586b854eeece4fa", "Requirements": [ - "cli", "cpp11", "dplyr", + "ellipsis", "glue", "lifecycle", "magrittr", "purrr", "rlang", - "stringr", "tibble", "tidyselect", "vctrs" @@ -1290,57 +1275,34 @@ }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "79540e5fcd9e0435af547d885f184fd5", + "Repository": "CRAN", + "Hash": "6ea435c354e8448819627cf686f66e0a", "Requirements": [ - "cli", + "ellipsis", "glue", - "lifecycle", + "purrr", "rlang", - "vctrs", - "withr" - ] - }, - "timechange": { - "Package": "timechange", - "Version": "0.2.0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "8548b44f79a35ba1791308b61e6012d7", - "Requirements": [ - "cpp11" + "vctrs" ] }, "tinytex": { "Package": "tinytex", - "Version": "0.44", + "Version": "0.31", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c0f007e2eeed7722ce13d42b84a22e07", + "Repository": "CRAN", + "Hash": "25b572f764f3c19fef9aac33b5724f3d", "Requirements": [ "xfun" ] }, - "urlchecker": { - "Package": "urlchecker", - "Version": "1.0.1", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "409328b8e1253c8d729a7836fe7f7a16", - "Requirements": [ - "cli", - "curl", - "xml2" - ] - }, "usethis": { "Package": "usethis", - "Version": "2.1.6", + "Version": "2.0.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": 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"Repository": "CRAN", + "Hash": "d4d71a75dd3ea9eb5fa28cc21f9585e2", "Requirements": [] }, "xmlparsedata": { "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "45e4bf3c46476896e821fc0a408fb4fc", "Requirements": [] }, @@ -1444,7 +1405,7 @@ "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" @@ -1454,24 +1415,24 @@ "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, "yaml": { "Package": "yaml", - "Version": "2.3.7", + "Version": "2.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436", + "Repository": "CRAN", + "Hash": "2826c5d9efb0a88f657c7a679c7106db", "Requirements": [] }, "zip": { "Package": "zip", - 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"Repository": "CRAN", + "Hash": "6c85f015dee9cc7710ddd20f86881f58", + "Requirements": [ + "processx" + ] + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", + "Requirements": [] + }, + "yaml": { + "Package": "yaml", + "Version": "2.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "2826c5d9efb0a88f657c7a679c7106db", + "Requirements": [] + }, + "zip": { + "Package": "zip", + "Version": "2.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "3bc8405c637d988801ec5ea88372d0c2", + "Requirements": [] + } + } +} diff --git a/renv/profiles/4.0.5/renv/.gitignore b/renv/profiles/4.0/renv/.gitignore similarity index 100% rename from renv/profiles/4.0.5/renv/.gitignore rename to renv/profiles/4.0/renv/.gitignore diff --git a/renv/profiles/4.0.5/renv/settings.dcf b/renv/profiles/4.0/renv/settings.dcf similarity index 100% rename from renv/profiles/4.0.5/renv/settings.dcf rename to renv/profiles/4.0/renv/settings.dcf diff --git a/renv/profiles/4.1.0/renv.lock b/renv/profiles/4.1/renv.lock similarity index 71% rename from renv/profiles/4.1.0/renv.lock rename to renv/profiles/4.1/renv.lock index 19f661be..818d838b 100644 --- a/renv/profiles/4.1.0/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.1.0", + "Version": "4.1.3", "Repositories": [ { "Name": "CRAN", @@ -15,10 +15,10 @@ "Packages": { "DT": { "Package": "DT", - "Version": "0.27", + "Version": "0.21", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3444e6ed78763f9f13aaa39f2481eb34", + "Repository": "CRAN", + "Hash": "45fa28dbf288cd606e13ca35d3d72437", "Requirements": [ "crosstalk", "htmltools", @@ -31,10 +31,10 @@ }, "R.cache": { "Package": "R.cache", - "Version": "0.16.0", + "Version": "0.15.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8", + "Repository": "CRAN", + "Hash": "e92a8ea8388c47c82ed8aa435ed3be50", "Requirements": [ "R.methodsS3", "R.oo", @@ -44,28 +44,28 @@ }, "R.methodsS3": { "Package": "R.methodsS3", - "Version": "1.8.2", + "Version": "1.8.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "278c286fd6e9e75d0c2e8f731ea445c8", + "Repository": "CRAN", + "Hash": "4bf6453323755202d5909697b6f7c109", "Requirements": [] }, "R.oo": { "Package": "R.oo", - "Version": "1.25.0", + "Version": "1.24.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a0900a114f4f0194cf4aa8cd4a700681", + "Repository": "CRAN", + "Hash": "5709328352717e2f0a9c012be8a97554", "Requirements": [ "R.methodsS3" ] }, "R.utils": { "Package": "R.utils", - "Version": "2.12.2", + "Version": "2.11.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "325f01db13da12c04d8f6e7be36ff514", + "Repository": "CRAN", + "Hash": "a7ecb8e60815c7a18648e84cd121b23a", "Requirements": [ "R.methodsS3", "R.oo" @@ -75,23 +75,23 @@ "Package": "R6", "Version": "2.5.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "470851b6d5d0ac559e9d01bb352b4021", "Requirements": [] }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.10", + "Version": "1.0.8", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e749cae40fa9ef469b6050959517453c", + "Repository": "CRAN", + "Hash": "22b546dd7e337f6c0c58a39983a496bc", "Requirements": [] }, "askpass": { "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "e8a22846fff485f0be3770c2da758713", "Requirements": [ "sys" @@ -101,7 +101,7 @@ "Package": "backports", "Version": "1.4.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "c39fbec8a30d23e721980b8afb31984c", "Requirements": [] }, @@ -109,40 +109,36 @@ "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, "brew": { "Package": "brew", - "Version": "1.0-8", + "Version": "1.0-7", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d69a786e85775b126bddbee185ae6084", + "Repository": "CRAN", + "Hash": "38875ea52350ff4b4c03849fc69736c8", "Requirements": [] }, "brio": { "Package": "brio", "Version": "1.1.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "976cf154dfb043c012d87cddd8bca363", "Requirements": [] }, "bslib": { "Package": "bslib", - "Version": "0.4.2", + "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a7fbf03946ad741129dc81098722fca1", + "Repository": "CRAN", + "Hash": "56ae7e1987b340186a8a5a157c2ec358", "Requirements": [ - "base64enc", - "cachem", "htmltools", "jquerylib", "jsonlite", - "memoise", - "mime", "rlang", "sass" ] @@ -151,7 +147,7 @@ "Package": "cachem", "Version": "1.0.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "648c5b3d71e6a37e3043617489a0a0e9", "Requirements": [ "fastmap", @@ -162,7 +158,7 @@ "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "9b2191ede20fa29828139b9900922e51", "Requirements": [ "R6", @@ -171,17 +167,17 @@ }, "cli": { "Package": "cli", - "Version": "3.6.0", + "Version": "3.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3177a5a16c243adc199ba33117bd9657", + "Repository": "CRAN", + "Hash": "0d297d01734d2bcea40197bd4971a764", "Requirements": [] }, "clipr": { "Package": "clipr", "Version": "0.8.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", "Requirements": [] }, @@ -195,18 +191,18 @@ }, "commonmark": { "Package": "commonmark", - "Version": "1.8.1", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b6e3e947d1d7ebf3d2bdcea1bde63fe7", + "Repository": "CRAN", + "Hash": "2ba81b120c1655ab696c935ef33ea716", "Requirements": [] }, "covr": { "Package": "covr", - "Version": "3.6.1", + "Version": "3.5.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a861cee34fbb4b107a73dd414ef56724", + "Repository": "CRAN", + "Hash": "6d80a9fc3c0c8473153b54fa54719dfd", "Requirements": [ "crayon", "digest", @@ -219,25 +215,25 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.4.3", + "Version": "0.4.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ed588261931ee3be2c700d22e94a29ab", + "Repository": "CRAN", + "Hash": "fa53ce256cd280f468c080a58ea5ba8c", "Requirements": [] }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e8a1e41acf02548751f45c718d55aa6a", + "Repository": "CRAN", + "Hash": "741c2e098e98afe3dc26a7b0e5489f4e", "Requirements": [] }, "credentials": { "Package": "credentials", "Version": "1.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "93762d0a34d78e6a025efdbfb5c6bb41", "Requirements": [ "askpass", @@ -251,7 +247,7 @@ "Package": "crosstalk", "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6aa54f69598c32177e920eb3402e8293", "Requirements": [ "R6", @@ -262,17 +258,17 @@ }, "curl": { "Package": "curl", - "Version": "5.0.0", + "Version": "4.3.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e4f97056611e8e6b8b852d13b7400cf1", + "Repository": "CRAN", + "Hash": "022c42d49c28e95d69ca60446dbabf88", "Requirements": [] }, "cyclocomp": { "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "53cbed70a2f7472d48fb6aef08442f25", "Requirements": [ "callr", @@ -284,10 +280,10 @@ }, "desc": { "Package": "desc", - "Version": "1.4.2", + "Version": "1.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", + "Repository": "CRAN", + "Hash": "eebd27ee58fcc58714eedb7aa07d8ad1", "Requirements": [ "R6", "cli", @@ -296,30 +292,29 @@ }, "devtools": { "Package": "devtools", - "Version": "2.4.5", + "Version": "2.4.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ea5bc8b4a6a01e4f12d98b58329930bb", + "Repository": "CRAN", + "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5", "Requirements": [ + "callr", "cli", "desc", "ellipsis", "fs", + "httr", "lifecycle", "memoise", - "miniUI", "pkgbuild", - "pkgdown", "pkgload", - "profvis", "rcmdcheck", "remotes", "rlang", "roxygen2", + "rstudioapi", "rversions", "sessioninfo", "testthat", - "urlchecker", "usethis", "withr" ] @@ -328,7 +323,7 @@ "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "9ddedef46959baad2080047a1b0117fe", "Requirements": [ "tibble" @@ -338,7 +333,7 @@ "Package": "diffobj", "Version": "0.3.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8", "Requirements": [ "crayon" @@ -346,18 +341,18 @@ }, "digest": { "Package": "digest", - "Version": "0.6.31", + "Version": "0.6.29", "Source": "Repository", - "Repository": "RSPM", - "Hash": "8b708f296afd9ae69f450f9640be8990", + "Repository": "CRAN", + "Hash": "cf6b206a045a684728c3267ef7596190", "Requirements": [] }, "downlit": { "Package": "downlit", - "Version": "0.4.2", + "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "79bf3f66590752ffbba20f8d2da94c7c", + "Repository": "CRAN", + "Hash": "ba63dc9ab5a31f3209892437e40c5f60", "Requirements": [ "brio", "desc", @@ -367,19 +362,17 @@ "memoise", "rlang", "vctrs", - "withr", "yaml" ] }, "dplyr": { "Package": "dplyr", - "Version": "1.1.0", + "Version": "1.0.8", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d3c34618017e7ae252d46d79a1b9ec32", + "Repository": "CRAN", + "Hash": "ef47665e64228a17609d6df877bf86f2", "Requirements": [ "R6", - "cli", "generics", "glue", "lifecycle", @@ -395,7 +388,7 @@ "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", "Requirements": [ "rlang" @@ -403,34 +396,34 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.20", + "Version": "0.15", "Source": "Repository", - "Repository": "RSPM", - "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c", + "Repository": "CRAN", + "Hash": "699a7a93d08c962d9f8950b2d7a227f1", "Requirements": [] }, "fansi": { "Package": "fansi", - "Version": "1.0.4", + "Version": "1.0.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1d9e7ad3c8312a192dea7d3db0274fde", + "Repository": "CRAN", + "Hash": "f28149c2d7a1342a834b314e95e67260", "Requirements": [] }, "fastmap": { "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, "fontawesome": { "Package": "fontawesome", - "Version": "0.5.0", + "Version": "0.2.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e80750aec5717dedc019ad7ee40e4a7c", + "Repository": "CRAN", + "Hash": "55624ed409e46c5f358b2c060be87f67", "Requirements": [ "htmltools", "rlang" @@ -438,26 +431,26 @@ }, "fs": { "Package": "fs", - "Version": "1.6.0", + "Version": "1.5.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "0120e8c933bace1141e0b0d376b0c010", + "Repository": "CRAN", + "Hash": "7c89603d81793f0d5486d91ab1fc6f1d", "Requirements": [] }, "generics": { "Package": "generics", - "Version": "0.1.3", + "Version": "0.1.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "15e9634c0fcd294799e9b2e929ed1b86", + "Repository": "CRAN", + "Hash": "177475892cf4a55865868527654a7741", "Requirements": [] }, "gert": { "Package": "gert", - "Version": "1.9.2", + "Version": "1.5.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "9122b3958e749badb5c939f498038b57", + "Repository": "CRAN", + "Hash": "8fddce7cbd59467106266a6e93e253b4", "Requirements": [ "askpass", "credentials", @@ -469,10 +462,10 @@ }, "gh": { "Package": "gh", - "Version": "1.3.1", + "Version": "1.3.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b6a12054ee13dce0f6696c019c10e539", + "Repository": "CRAN", + "Hash": "38c2580abbda249bd6afeec00d14f531", "Requirements": [ "cli", "gitcreds", @@ -483,44 +476,44 @@ }, "git2r": { "Package": "git2r", - "Version": "0.31.0", + "Version": "0.29.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "acb972e0be37f83b9c762d962d75a188", + "Repository": "CRAN", + "Hash": "b114135c4749076bd5ef74a5827b6f62", "Requirements": [] }, "gitcreds": { "Package": "gitcreds", - "Version": "0.1.2", + "Version": "0.1.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe", + "Repository": "CRAN", + "Hash": "f3aefccc1cc50de6338146b62f115de8", "Requirements": [] }, "glue": { "Package": "glue", "Version": "1.6.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", "Requirements": [] }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.9", "Source": "Repository", - "Repository": "RSPM", - "Hash": "06230136b2d2b9ba5805e1963fa6e890", + "Repository": "CRAN", + "Hash": "8eb36c8125038e648e5d111c0d7b2ed4", "Requirements": [ "xfun" ] }, "hms": { "Package": "hms", - "Version": "1.1.2", + "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "41100392191e1244b887878b533eea91", + "Repository": "CRAN", + "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca", "Requirements": [ "ellipsis", "lifecycle", @@ -531,38 +524,35 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.4", + "Version": "0.5.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7", + "Repository": "CRAN", + "Hash": "526c484233f42522278ab06fb185cb26", "Requirements": [ "base64enc", "digest", - "ellipsis", "fastmap", "rlang" ] }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.6.1", + "Version": "1.5.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b677ee5954471eaa974c0d099a343a1a", + "Repository": "CRAN", + "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb", "Requirements": [ "htmltools", "jsonlite", - "knitr", - "rmarkdown", "yaml" ] }, "httpuv": { "Package": "httpuv", - "Version": "1.6.8", + "Version": "1.6.5", "Source": "Repository", - "Repository": "RSPM", - "Hash": "08e611aee165b27f8ff18770285fb535", + "Repository": "CRAN", + "Hash": "97fe71f0a4a1c9890e6c2128afa04bc0", "Requirements": [ "R6", "Rcpp", @@ -572,10 +562,10 @@ }, "httr": { "Package": "httr", - "Version": "1.4.4", + "Version": "1.4.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "57557fac46471f0dbbf44705cc6a5c8c", + "Repository": "CRAN", + "Hash": "a525aba14184fec243f9eaec62fbed43", "Requirements": [ "R6", "curl", @@ -586,10 +576,10 @@ }, "hunspell": { "Package": "hunspell", - "Version": "3.0.2", + "Version": "3.0.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "656219b6f3f605499d7cdbe208656639", + "Repository": "CRAN", + "Hash": "3987784c19192ad0f2261c456d936df1", "Requirements": [ "Rcpp", "digest" @@ -599,7 +589,7 @@ "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, @@ -607,7 +597,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "5aab57a3bd297eee1c1d862735972182", "Requirements": [ "htmltools" @@ -615,21 +605,22 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.4", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a4269a09a9b865579b2635c77e572374", + "Repository": "CRAN", + "Hash": "d07e729b27b372429d42d24d503613a0", "Requirements": [] }, "knitr": { "Package": "knitr", - "Version": "1.42", + "Version": "1.37", "Source": "Repository", - "Repository": "RSPM", - "Hash": "8329a9bcc82943c8069104d4be3ee22d", + "Repository": "CRAN", + "Hash": "a4ec675eb332a33fe7b7fe26f70e1f98", "Requirements": [ "evaluate", "highr", + "stringr", "xfun", "yaml" ] @@ -638,7 +629,7 @@ "Package": "later", "Version": "1.3.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e", "Requirements": [ "Rcpp", @@ -649,18 +640,17 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "d908914ae53b04d4c0c0fd72ecc35370", "Requirements": [] }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "001cecbeac1cff9301bdc3775ee46a86", + "Repository": "CRAN", + "Hash": "a6b6d352e3ed897373ab19d8395c98d0", "Requirements": [ - "cli", "glue", "rlang" ] @@ -669,7 +659,7 @@ "Package": "lintr", "Version": "3.0.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b21ebd652d940f099915221f3328ab7b", "Requirements": [ "backports", @@ -687,28 +677,28 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.9.1", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "88ad585eb49669b7f2db3f5ef3c8307d", + "Repository": "CRAN", + "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a", "Requirements": [ - "generics", - "timechange" + "cpp11", + "generics" ] }, "magrittr": { "Package": "magrittr", - "Version": "2.0.3", + "Version": "2.0.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7ce2733a9826b3aeb1775d56fd305472", + "Repository": "CRAN", + "Hash": "cdc87ecd81934679d1557633d8e1fe51", "Requirements": [] }, "memoise": { "Package": "memoise", "Version": "2.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c", "Requirements": [ "cachem", @@ -719,7 +709,7 @@ "Package": "mime", "Version": "0.12", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "18e9c28c1d3ca1560ce30658b22ce104", "Requirements": [] }, @@ -727,7 +717,7 @@ "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "fec5f52652d60615fdb3957b3d74324a", "Requirements": [ "htmltools", @@ -736,22 +726,24 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.5", + "Version": "2.0.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b04c27110bf367b4daa93f34f3d58e75", + "Repository": "CRAN", + "Hash": "cf4329aac12c2c44089974559c18e446", "Requirements": [ "askpass" ] }, "pillar": { "Package": "pillar", - "Version": "1.8.1", + "Version": "1.7.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "f2316df30902c81729ae9de95ad5a608", + "Repository": "CRAN", + "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e", "Requirements": [ "cli", + "crayon", + "ellipsis", "fansi", "glue", "lifecycle", @@ -762,10 +754,10 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.4.0", + "Version": "1.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d6c3008d79653a0f267703288230105e", + "Repository": "CRAN", + "Hash": "66d2adfed274daf81ccfe77d974c3b9b", "Requirements": [ "R6", "callr", @@ -773,7 +765,6 @@ "crayon", "desc", "prettyunits", - "processx", "rprojroot", "withr" ] @@ -782,7 +773,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "01f28d4278f15c76cddbea05899c5d6f", "Requirements": [] }, @@ -790,7 +781,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "16fa15449c930bf3a7761d3c68f8abf9", "Requirements": [ "bslib", @@ -817,18 +808,17 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.2", + "Version": "1.2.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2", + "Repository": "CRAN", + "Hash": "7533cd805940821bf23eaf3c8d4c1735", "Requirements": [ "cli", "crayon", "desc", - "fs", - "glue", "rlang", "rprojroot", + "rstudioapi", "withr" ] }, @@ -836,7 +826,7 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a555924add98c99d2f411e37e7d25e9f", "Requirements": [] }, @@ -844,37 +834,26 @@ "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", "Requirements": [] }, "processx": { "Package": "processx", - "Version": "3.8.0", + "Version": "3.6.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a33ee2d9bf07564efb888ad98410da84", + "Repository": "CRAN", + "Hash": "a11891e28c1f1e5ddd773ba1b8c07cf6", "Requirements": [ "R6", "ps" ] }, - "profvis": { - "Package": "profvis", - "Version": "0.3.7", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "e9d21e79848e02e524bea6f5bd53e7e4", - "Requirements": [ - "htmlwidgets", - "stringr" - ] - }, "promises": { "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4ab2c43adb4d4699cf3690acd378d75d", "Requirements": [ "R6", @@ -886,32 +865,29 @@ }, "ps": { "Package": "ps", - "Version": "1.7.2", + "Version": "1.6.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "68dd03d98a5efd1eb3012436de45ba83", + "Repository": "CRAN", + "Hash": "32620e2001c1dce1af49c49dccbb9420", "Requirements": [] }, "purrr": { "Package": "purrr", - "Version": "1.0.1", + "Version": "0.3.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d71c815267c640f17ddbf7f16144b4bb", + "Repository": "CRAN", + "Hash": "97def703420c8ab10d8f0e6c72101e02", "Requirements": [ - "cli", - "lifecycle", "magrittr", - "rlang", - "vctrs" + "rlang" ] }, "ragg": { "Package": "ragg", - "Version": "1.2.5", + "Version": "1.2.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9", + "Repository": "CRAN", + "Hash": "14932bb6f2739c771ca4ceaba6b4248e", "Requirements": [ "systemfonts", "textshaping" @@ -921,7 +897,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, @@ -929,7 +905,7 @@ "Package": "rcmdcheck", "Version": "1.4.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4", "Requirements": [ "R6", @@ -950,7 +926,7 @@ "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ "tibble" @@ -960,7 +936,7 @@ "Package": "remotes", "Version": "2.4.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "227045be9aee47e6dda9bb38ac870d67", "Requirements": [] }, @@ -968,7 +944,7 @@ "Package": "rex", "Version": "1.2.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "ae34cd56890607370665bee5bd17812f", "Requirements": [ "lazyeval" @@ -978,16 +954,16 @@ "Package": "rlang", "Version": "1.0.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", "Requirements": [] }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.20", + "Version": "2.12", "Source": "Repository", - "Repository": "RSPM", - "Hash": "716fde5382293cc94a71f68c85b78d19", + "Repository": "CRAN", + "Hash": "354da5088ddfdffb73c11cc952885d88", "Requirements": [ "bslib", "evaluate", @@ -1003,10 +979,10 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.3", + "Version": "7.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7b153c746193b143c14baa072bae4e27", + "Repository": "CRAN", + "Hash": "da1f278262e563c835345872f2fef537", "Requirements": [ "R6", "brew", @@ -1014,6 +990,7 @@ "commonmark", "cpp11", "desc", + "digest", "knitr", "pkgload", "purrr", @@ -1026,26 +1003,26 @@ }, "rprojroot": { "Package": "rprojroot", - "Version": "2.0.3", + "Version": "2.0.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1de7ab598047a87bba48434ba35d497d", + "Repository": "CRAN", + "Hash": "249d8cd1e74a8f6a26194a91b47f21d1", "Requirements": [] }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.14", + "Version": "0.13", "Source": "Repository", - "Repository": "RSPM", - "Hash": "690bd2acc42a9166ce34845884459320", + "Repository": "CRAN", + "Hash": "06c85365a03fdaf699966cc1d3cf53ea", "Requirements": [] }, "rversions": { "Package": "rversions", - "Version": "2.1.2", + "Version": "2.1.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a9881dfed103e83f9de151dc17002cd1", + "Repository": "CRAN", + "Hash": "f88fab00907b312f8b23ec13e2d437cb", "Requirements": [ "curl", "xml2" @@ -1053,10 +1030,10 @@ }, "sass": { "Package": "sass", - "Version": "0.4.5", + "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "2bb4371a4c80115518261866eab6ab11", + "Repository": "CRAN", + "Hash": "50cf822feb64bb3977bda0b7091be623", "Requirements": [ "R6", "fs", @@ -1069,7 +1046,7 @@ "Package": "sessioninfo", "Version": "1.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", "Requirements": [ "cli" @@ -1077,10 +1054,10 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.4", + "Version": "1.7.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5", + "Repository": "CRAN", + "Hash": "00344c227c7bd0ab5d78052c5d736c44", "Requirements": [ "R6", "bslib", @@ -1106,17 +1083,17 @@ }, "sourcetools": { "Package": "sourcetools", - "Version": "0.1.7-1", + "Version": "0.1.7", "Source": "Repository", - "Repository": "RSPM", - "Hash": "5f5a7629f956619d519205ec475fe647", + "Repository": "CRAN", + "Hash": "947e4e02a79effa5d512473e10f41797", "Requirements": [] }, "spelling": { "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", @@ -1156,58 +1133,58 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.12", + "Version": "1.7.6", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ca8bd84263c77310739d2cf64d84d7c9", + "Repository": "CRAN", + "Hash": "bba431031d30789535745a9627ac9271", "Requirements": [] }, "stringr": { "Package": "stringr", - "Version": "1.5.0", + "Version": "1.4.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8", + "Repository": "CRAN", + "Hash": "0759e6b6c0957edb1311028a49a35e76", "Requirements": [ - "cli", "glue", - "lifecycle", "magrittr", - "rlang", - "stringi", - "vctrs" + "stringi" ] }, "styler": { "Package": "styler", - "Version": "1.9.0", + "Version": "1.6.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1c038945a5e14cce208f5214c1dd167c", + "Repository": "CRAN", + "Hash": "d9e85c794c5a723aabed32a49926186a", "Requirements": [ "R.cache", + "backports", "cli", + "glue", "magrittr", "purrr", + "rematch2", "rlang", "rprojroot", - "vctrs", - "withr" + "tibble", + "withr", + "xfun" ] }, "sys": { "Package": "sys", - "Version": "3.4.1", + "Version": "3.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "34c16f1ef796057bfa06d3f4ff818a5d", + "Repository": "CRAN", + "Hash": "b227d13e29222b4574486cfcbde077fa", "Requirements": [] }, "systemfonts": { "Package": "systemfonts", "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "90b28393209827327de889f49935140a", "Requirements": [ "cpp11" @@ -1215,15 +1192,16 @@ }, "testthat": { "Package": "testthat", - "Version": "3.1.6", + "Version": "3.1.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7910146255835c66e9eb272fb215248d", + "Repository": "CRAN", + "Hash": "32454e5780e8dbe31e4b61b13d8918fe", "Requirements": [ "R6", "brio", "callr", "cli", + "crayon", "desc", "digest", "ellipsis", @@ -1244,7 +1222,7 @@ "Package": "textshaping", "Version": "0.3.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "1ab6223d3670fac7143202cb6a2d43d5", "Requirements": [ "cpp11", @@ -1253,11 +1231,12 @@ }, "tibble": { "Package": "tibble", - "Version": "3.1.8", + "Version": "3.1.6", "Source": "Repository", - "Repository": "RSPM", - "Hash": "56b6934ef0f8c68225949a8672fe1a8f", + "Repository": "CRAN", + "Hash": "8a8f02d1934dfd6431c671361510dd0b", "Requirements": [ + "ellipsis", "fansi", "lifecycle", "magrittr", @@ -1269,20 +1248,19 @@ }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf", + "Repository": "CRAN", + "Hash": "d8b95b7fee945d7da6888cf7eb71a49c", "Requirements": [ - "cli", "cpp11", "dplyr", + "ellipsis", "glue", "lifecycle", "magrittr", "purrr", "rlang", - "stringr", "tibble", "tidyselect", "vctrs" @@ -1290,57 +1268,34 @@ }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.1.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "79540e5fcd9e0435af547d885f184fd5", + "Repository": "CRAN", + "Hash": "17f6da8cfd7002760a859915ce7eef8f", "Requirements": [ - "cli", + "ellipsis", "glue", - "lifecycle", + "purrr", "rlang", - "vctrs", - "withr" - ] - }, - "timechange": { - "Package": "timechange", - "Version": "0.2.0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "8548b44f79a35ba1791308b61e6012d7", - "Requirements": [ - "cpp11" + "vctrs" ] }, "tinytex": { "Package": "tinytex", - "Version": "0.44", + "Version": "0.37", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c0f007e2eeed7722ce13d42b84a22e07", + "Repository": "CRAN", + "Hash": "a80abeb527a977e4bef21873d29222dd", "Requirements": [ "xfun" ] }, - "urlchecker": { - "Package": "urlchecker", - "Version": "1.0.1", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "409328b8e1253c8d729a7836fe7f7a16", - "Requirements": [ - "cli", - "curl", - "xml2" - ] - }, "usethis": { "Package": "usethis", - "Version": "2.1.6", + "Version": "2.1.5", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a67a22c201832b12c036cc059f1d137d", + "Repository": "CRAN", + "Hash": "c499f488e6dd7718accffaee5bc5a79b", "Requirements": [ "cli", "clipr", @@ -1365,31 +1320,30 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1fe17157424bb09c48a8b3b550c753bc", + "Repository": "CRAN", + "Hash": "c9c462b759a5cc844ae25b5942654d13", "Requirements": [] }, "vctrs": { "Package": "vctrs", - "Version": "0.5.2", + "Version": "0.3.8", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e4ffa94ceed5f124d429a5a5f0f5b378", + "Repository": "CRAN", + "Hash": "ecf749a1b39ea72bd9b51b76292261f1", "Requirements": [ - "cli", + "ellipsis", "glue", - "lifecycle", "rlang" ] }, "waldo": { "Package": "waldo", - "Version": "0.4.0", + "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "035fba89d0c86e2113120f93301b98ad", + "Repository": "CRAN", + "Hash": "ad8cfff5694ac5b3c354f8f2044bd976", "Requirements": [ "cli", "diffobj", @@ -1402,33 +1356,33 @@ }, "whisker": { "Package": "whisker", - "Version": "0.4.1", + "Version": "0.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c6abfa47a46d281a7d5159d0a8891e88", + "Repository": "CRAN", + "Hash": "ca970b96d894e90397ed20637a0c1bbe", "Requirements": [] }, "withr": { "Package": "withr", "Version": "2.5.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "c0e49a9760983e81e55cdd9be92e7182", "Requirements": [] }, "xfun": { "Package": "xfun", - "Version": "0.37", + "Version": "0.30", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a6860e1400a8fd1ddb6d9b4230cc34ab", + "Repository": "CRAN", + "Hash": "e83f48136b041845e50a6658feffb197", "Requirements": [] }, "xml2": { "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "40682ed6a969ea5abfd351eb67833adc", "Requirements": [] }, @@ -1436,7 +1390,7 @@ "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "45e4bf3c46476896e821fc0a408fb4fc", "Requirements": [] }, @@ -1444,7 +1398,7 @@ "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" @@ -1454,24 +1408,24 @@ "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, "yaml": { "Package": "yaml", - "Version": "2.3.7", + "Version": "2.3.5", "Source": "Repository", - "Repository": "RSPM", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436", + "Repository": "CRAN", + "Hash": "458bb38374d73bf83b1bb85e353da200", "Requirements": [] }, "zip": { "Package": "zip", - "Version": "2.2.2", + "Version": "2.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88", + "Repository": "CRAN", + "Hash": "c7eef2996ac270a18c2715c997a727c5", "Requirements": [] } } diff --git a/renv/profiles/4.1.0/renv/.gitignore b/renv/profiles/4.1/renv/.gitignore similarity index 100% rename from renv/profiles/4.1.0/renv/.gitignore rename to renv/profiles/4.1/renv/.gitignore diff --git a/renv/profiles/4.1.0/renv/settings.dcf b/renv/profiles/4.1/renv/settings.dcf similarity index 100% rename from renv/profiles/4.1.0/renv/settings.dcf rename to renv/profiles/4.1/renv/settings.dcf diff --git a/renv/profiles/4.0.5/renv.lock b/renv/profiles/4.2/renv.lock similarity index 79% rename from renv/profiles/4.0.5/renv.lock rename to renv/profiles/4.2/renv.lock index a77db8d4..5becab33 100644 --- a/renv/profiles/4.0.5/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.0.5", + "Version": "4.2.2", "Repositories": [ { "Name": "CRAN", @@ -8,17 +8,17 @@ }, { "Name": "MRAN", - "URL": "https://cran.microsoft.com/snapshot/2021-03-31" + "URL": "https://cran.microsoft.com/snapshot/2022-10-31" } ] }, "Packages": { "DT": { "Package": "DT", - "Version": "0.27", + "Version": "0.26", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3444e6ed78763f9f13aaa39f2481eb34", + "Repository": "CRAN", + "Hash": "c66a72c4d3499e14ae179ccb742e740a", "Requirements": [ "crosstalk", "htmltools", @@ -33,7 +33,7 @@ "Package": "R.cache", "Version": "0.16.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8", "Requirements": [ "R.methodsS3", @@ -46,7 +46,7 @@ "Package": "R.methodsS3", "Version": "1.8.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "278c286fd6e9e75d0c2e8f731ea445c8", "Requirements": [] }, @@ -54,7 +54,7 @@ "Package": "R.oo", "Version": "1.25.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a0900a114f4f0194cf4aa8cd4a700681", "Requirements": [ "R.methodsS3" @@ -62,10 +62,10 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.12.2", + "Version": "2.12.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "325f01db13da12c04d8f6e7be36ff514", + "Repository": "CRAN", + "Hash": "1ed133420fcd2b93cf55a383b38fe27c", "Requirements": [ "R.methodsS3", "R.oo" @@ -75,23 +75,23 @@ "Package": "R6", "Version": "2.5.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "470851b6d5d0ac559e9d01bb352b4021", "Requirements": [] }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.10", + "Version": "1.0.9", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e749cae40fa9ef469b6050959517453c", + "Repository": "CRAN", + "Hash": "e9c08b94391e9f3f97355841229124f2", "Requirements": [] }, "askpass": { "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "e8a22846fff485f0be3770c2da758713", "Requirements": [ "sys" @@ -101,7 +101,7 @@ "Package": "backports", "Version": "1.4.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "c39fbec8a30d23e721980b8afb31984c", "Requirements": [] }, @@ -109,7 +109,7 @@ "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, @@ -117,7 +117,7 @@ "Package": "brew", "Version": "1.0-8", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "d69a786e85775b126bddbee185ae6084", "Requirements": [] }, @@ -125,24 +125,22 @@ "Package": "brio", "Version": "1.1.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "976cf154dfb043c012d87cddd8bca363", "Requirements": [] }, "bslib": { "Package": "bslib", - "Version": "0.4.2", + "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a7fbf03946ad741129dc81098722fca1", + "Repository": "CRAN", + "Hash": "be5ee090716ce1671be6cd5d7c34d091", "Requirements": [ - "base64enc", "cachem", "htmltools", "jquerylib", "jsonlite", "memoise", - "mime", "rlang", "sass" ] @@ -151,7 +149,7 @@ "Package": "cachem", "Version": "1.0.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "648c5b3d71e6a37e3043617489a0a0e9", "Requirements": [ "fastmap", @@ -162,7 +160,7 @@ "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "9b2191ede20fa29828139b9900922e51", "Requirements": [ "R6", @@ -171,17 +169,17 @@ }, "cli": { "Package": "cli", - "Version": "3.6.0", + "Version": "3.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3177a5a16c243adc199ba33117bd9657", + "Repository": "CRAN", + "Hash": "0d297d01734d2bcea40197bd4971a764", "Requirements": [] }, "clipr": { "Package": "clipr", "Version": "0.8.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", "Requirements": [] }, @@ -197,7 +195,7 @@ "Package": "commonmark", "Version": "1.8.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b6e3e947d1d7ebf3d2bdcea1bde63fe7", "Requirements": [] }, @@ -205,7 +203,7 @@ "Package": "covr", "Version": "3.6.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a861cee34fbb4b107a73dd414ef56724", "Requirements": [ "crayon", @@ -221,7 +219,7 @@ "Package": "cpp11", "Version": "0.4.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "ed588261931ee3be2c700d22e94a29ab", "Requirements": [] }, @@ -229,7 +227,7 @@ "Package": "crayon", "Version": "1.5.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "e8a1e41acf02548751f45c718d55aa6a", "Requirements": [] }, @@ -237,7 +235,7 @@ "Package": "credentials", "Version": "1.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "93762d0a34d78e6a025efdbfb5c6bb41", "Requirements": [ "askpass", @@ -251,7 +249,7 @@ "Package": "crosstalk", "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6aa54f69598c32177e920eb3402e8293", "Requirements": [ "R6", @@ -262,17 +260,17 @@ }, "curl": { "Package": "curl", - "Version": "5.0.0", + "Version": "4.3.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e4f97056611e8e6b8b852d13b7400cf1", + "Repository": "CRAN", + "Hash": "0eb86baa62f06e8855258fa5a8048667", "Requirements": [] }, "cyclocomp": { "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "53cbed70a2f7472d48fb6aef08442f25", "Requirements": [ "callr", @@ -286,7 +284,7 @@ "Package": "desc", "Version": "1.4.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", "Requirements": [ "R6", @@ -298,7 +296,7 @@ "Package": "devtools", "Version": "2.4.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "ea5bc8b4a6a01e4f12d98b58329930bb", "Requirements": [ "cli", @@ -328,7 +326,7 @@ "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "9ddedef46959baad2080047a1b0117fe", "Requirements": [ "tibble" @@ -338,7 +336,7 @@ "Package": "diffobj", "Version": "0.3.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8", "Requirements": [ "crayon" @@ -346,17 +344,17 @@ }, "digest": { "Package": "digest", - "Version": "0.6.31", + "Version": "0.6.30", "Source": "Repository", - "Repository": "RSPM", - "Hash": "8b708f296afd9ae69f450f9640be8990", + "Repository": "CRAN", + "Hash": "bf1cd206a5d170d132ef75c7537b9bdb", "Requirements": [] }, "downlit": { "Package": "downlit", "Version": "0.4.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "79bf3f66590752ffbba20f8d2da94c7c", "Requirements": [ "brio", @@ -373,13 +371,12 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.1.0", + "Version": "1.0.10", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d3c34618017e7ae252d46d79a1b9ec32", + "Repository": "CRAN", + "Hash": "539412282059f7f0c07295723d23f987", "Requirements": [ "R6", - "cli", "generics", "glue", "lifecycle", @@ -395,7 +392,7 @@ "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", "Requirements": [ "rlang" @@ -403,34 +400,34 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.20", + "Version": "0.17", "Source": "Repository", - "Repository": "RSPM", - "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c", + "Repository": "CRAN", + "Hash": "9171b012a55a1ef53f1442b1d798a3b4", "Requirements": [] }, "fansi": { "Package": "fansi", - "Version": "1.0.4", + "Version": "1.0.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1d9e7ad3c8312a192dea7d3db0274fde", + "Repository": "CRAN", + "Hash": "83a8afdbe71839506baa9f90eebad7ec", "Requirements": [] }, "fastmap": { "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, "fontawesome": { "Package": "fontawesome", - "Version": "0.5.0", + "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e80750aec5717dedc019ad7ee40e4a7c", + "Repository": "CRAN", + "Hash": "c5a628c2570aa86a96cc6ef739d8bfda", "Requirements": [ "htmltools", "rlang" @@ -438,26 +435,26 @@ }, "fs": { "Package": "fs", - "Version": "1.6.0", + "Version": "1.5.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "0120e8c933bace1141e0b0d376b0c010", + "Repository": "CRAN", + "Hash": "7c89603d81793f0d5486d91ab1fc6f1d", "Requirements": [] }, "generics": { "Package": "generics", "Version": "0.1.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "15e9634c0fcd294799e9b2e929ed1b86", "Requirements": [] }, "gert": { "Package": "gert", - "Version": "1.9.2", + "Version": "1.9.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "9122b3958e749badb5c939f498038b57", + "Repository": "CRAN", + "Hash": "9a091a6d2fb91e43afd4337e2dcef2e7", "Requirements": [ "askpass", "credentials", @@ -471,7 +468,7 @@ "Package": "gh", "Version": "1.3.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b6a12054ee13dce0f6696c019c10e539", "Requirements": [ "cli", @@ -483,17 +480,17 @@ }, "git2r": { "Package": "git2r", - "Version": "0.31.0", + "Version": "0.30.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "acb972e0be37f83b9c762d962d75a188", + "Repository": "CRAN", + "Hash": "e0c6a04a3e7b90e64213d09128f74f1b", "Requirements": [] }, "gitcreds": { "Package": "gitcreds", "Version": "0.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe", "Requirements": [] }, @@ -501,16 +498,16 @@ "Package": "glue", "Version": "1.6.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", "Requirements": [] }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.9", "Source": "Repository", - "Repository": "RSPM", - "Hash": "06230136b2d2b9ba5805e1963fa6e890", + "Repository": "CRAN", + "Hash": "8eb36c8125038e648e5d111c0d7b2ed4", "Requirements": [ "xfun" ] @@ -519,7 +516,7 @@ "Package": "hms", "Version": "1.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "41100392191e1244b887878b533eea91", "Requirements": [ "ellipsis", @@ -531,38 +528,35 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.4", + "Version": "0.5.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7", + "Repository": "CRAN", + "Hash": "6496090a9e00f8354b811d1a2d47b566", "Requirements": [ "base64enc", "digest", - "ellipsis", "fastmap", "rlang" ] }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.6.1", + "Version": "1.5.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b677ee5954471eaa974c0d099a343a1a", + "Repository": "CRAN", + "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb", "Requirements": [ "htmltools", "jsonlite", - "knitr", - "rmarkdown", "yaml" ] }, "httpuv": { "Package": "httpuv", - "Version": "1.6.8", + "Version": "1.6.6", "Source": "Repository", - "Repository": "RSPM", - "Hash": "08e611aee165b27f8ff18770285fb535", + "Repository": "CRAN", + "Hash": "fd090e236ae2dc0f0cdf33a9ec83afb6", "Requirements": [ "R6", "Rcpp", @@ -574,7 +568,7 @@ "Package": "httr", "Version": "1.4.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "57557fac46471f0dbbf44705cc6a5c8c", "Requirements": [ "R6", @@ -588,7 +582,7 @@ "Package": "hunspell", "Version": "3.0.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "656219b6f3f605499d7cdbe208656639", "Requirements": [ "Rcpp", @@ -599,7 +593,7 @@ "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, @@ -607,7 +601,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "5aab57a3bd297eee1c1d862735972182", "Requirements": [ "htmltools" @@ -615,21 +609,22 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.4", + "Version": "1.8.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a4269a09a9b865579b2635c77e572374", + "Repository": "CRAN", + "Hash": "8b1bd0be62956f2a6b91ce84fac79a45", "Requirements": [] }, "knitr": { "Package": "knitr", - "Version": "1.42", + "Version": "1.40", "Source": "Repository", - "Repository": "RSPM", - "Hash": "8329a9bcc82943c8069104d4be3ee22d", + "Repository": "CRAN", + "Hash": "caea8b0f899a0b1738444b9bc47067e7", "Requirements": [ "evaluate", "highr", + "stringr", "xfun", "yaml" ] @@ -638,7 +633,7 @@ "Package": "later", "Version": "1.3.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e", "Requirements": [ "Rcpp", @@ -649,7 +644,7 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "d908914ae53b04d4c0c0fd72ecc35370", "Requirements": [] }, @@ -657,7 +652,7 @@ "Package": "lifecycle", "Version": "1.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "001cecbeac1cff9301bdc3775ee46a86", "Requirements": [ "cli", @@ -669,7 +664,7 @@ "Package": "lintr", "Version": "3.0.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b21ebd652d940f099915221f3328ab7b", "Requirements": [ "backports", @@ -687,20 +682,20 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.9.1", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "88ad585eb49669b7f2db3f5ef3c8307d", + "Repository": "CRAN", + "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a", "Requirements": [ - "generics", - "timechange" + "cpp11", + "generics" ] }, "magrittr": { "Package": "magrittr", "Version": "2.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "7ce2733a9826b3aeb1775d56fd305472", "Requirements": [] }, @@ -708,7 +703,7 @@ "Package": "memoise", "Version": "2.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c", "Requirements": [ "cachem", @@ -719,7 +714,7 @@ "Package": "mime", "Version": "0.12", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "18e9c28c1d3ca1560ce30658b22ce104", "Requirements": [] }, @@ -727,7 +722,7 @@ "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "fec5f52652d60615fdb3957b3d74324a", "Requirements": [ "htmltools", @@ -736,10 +731,10 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.5", + "Version": "2.0.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "b04c27110bf367b4daa93f34f3d58e75", + "Repository": "CRAN", + "Hash": "e86c5ffeb8474a9e03d75f5d2919683e", "Requirements": [ "askpass" ] @@ -748,7 +743,7 @@ "Package": "pillar", "Version": "1.8.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "f2316df30902c81729ae9de95ad5a608", "Requirements": [ "cli", @@ -762,10 +757,10 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.4.0", + "Version": "1.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d6c3008d79653a0f267703288230105e", + "Repository": "CRAN", + "Hash": "66d2adfed274daf81ccfe77d974c3b9b", "Requirements": [ "R6", "callr", @@ -773,7 +768,6 @@ "crayon", "desc", "prettyunits", - "processx", "rprojroot", "withr" ] @@ -782,7 +776,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "01f28d4278f15c76cddbea05899c5d6f", "Requirements": [] }, @@ -790,7 +784,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "16fa15449c930bf3a7761d3c68f8abf9", "Requirements": [ "bslib", @@ -817,10 +811,10 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.2", + "Version": "1.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2", + "Repository": "CRAN", + "Hash": "3c0918b1792c75de2e640d1d8d12dead", "Requirements": [ "cli", "crayon", @@ -836,7 +830,7 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a555924add98c99d2f411e37e7d25e9f", "Requirements": [] }, @@ -844,7 +838,7 @@ "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", "Requirements": [] }, @@ -852,7 +846,7 @@ "Package": "processx", "Version": "3.8.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a33ee2d9bf07564efb888ad98410da84", "Requirements": [ "R6", @@ -863,7 +857,7 @@ "Package": "profvis", "Version": "0.3.7", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "e9d21e79848e02e524bea6f5bd53e7e4", "Requirements": [ "htmlwidgets", @@ -874,7 +868,7 @@ "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4ab2c43adb4d4699cf3690acd378d75d", "Requirements": [ "R6", @@ -888,30 +882,27 @@ "Package": "ps", "Version": "1.7.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "68dd03d98a5efd1eb3012436de45ba83", "Requirements": [] }, "purrr": { "Package": "purrr", - "Version": "1.0.1", + "Version": "0.3.5", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d71c815267c640f17ddbf7f16144b4bb", + "Repository": "CRAN", + "Hash": "54842a2443c76267152eface28d9e90a", "Requirements": [ - "cli", - "lifecycle", "magrittr", - "rlang", - "vctrs" + "rlang" ] }, "ragg": { "Package": "ragg", - "Version": "1.2.5", + "Version": "1.2.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9", + "Repository": "CRAN", + "Hash": "0db17bd5a1d4abfec76487b6f5dd957b", "Requirements": [ "systemfonts", "textshaping" @@ -921,7 +912,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, @@ -929,7 +920,7 @@ "Package": "rcmdcheck", "Version": "1.4.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4", "Requirements": [ "R6", @@ -950,7 +941,7 @@ "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ "tibble" @@ -960,7 +951,7 @@ "Package": "remotes", "Version": "2.4.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "227045be9aee47e6dda9bb38ac870d67", "Requirements": [] }, @@ -968,7 +959,7 @@ "Package": "rex", "Version": "1.2.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "ae34cd56890607370665bee5bd17812f", "Requirements": [ "lazyeval" @@ -978,16 +969,16 @@ "Package": "rlang", "Version": "1.0.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", "Requirements": [] }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.20", + "Version": "2.17", "Source": "Repository", - "Repository": "RSPM", - "Hash": "716fde5382293cc94a71f68c85b78d19", + "Repository": "CRAN", + "Hash": "e97c8be593e010f93520e8215c0f9189", "Requirements": [ "bslib", "evaluate", @@ -1003,10 +994,10 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.3", + "Version": "7.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7b153c746193b143c14baa072bae4e27", + "Repository": "CRAN", + "Hash": "da1f278262e563c835345872f2fef537", "Requirements": [ "R6", "brew", @@ -1014,6 +1005,7 @@ "commonmark", "cpp11", "desc", + "digest", "knitr", "pkgload", "purrr", @@ -1028,7 +1020,7 @@ "Package": "rprojroot", "Version": "2.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "1de7ab598047a87bba48434ba35d497d", "Requirements": [] }, @@ -1036,7 +1028,7 @@ "Package": "rstudioapi", "Version": "0.14", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "690bd2acc42a9166ce34845884459320", "Requirements": [] }, @@ -1044,7 +1036,7 @@ "Package": "rversions", "Version": "2.1.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a9881dfed103e83f9de151dc17002cd1", "Requirements": [ "curl", @@ -1053,10 +1045,10 @@ }, "sass": { "Package": "sass", - "Version": "0.4.5", + "Version": "0.4.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "2bb4371a4c80115518261866eab6ab11", + "Repository": "CRAN", + "Hash": "1b191143d7d3444d504277843f3a95fe", "Requirements": [ "R6", "fs", @@ -1069,7 +1061,7 @@ "Package": "sessioninfo", "Version": "1.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", "Requirements": [ "cli" @@ -1077,10 +1069,10 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.4", + "Version": "1.7.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5", + "Repository": "CRAN", + "Hash": "fe12df67fdb3b1142325cc54f100cc06", "Requirements": [ "R6", "bslib", @@ -1106,17 +1098,17 @@ }, "sourcetools": { "Package": "sourcetools", - "Version": "0.1.7-1", + "Version": "0.1.7", "Source": "Repository", - "Repository": "RSPM", - "Hash": "5f5a7629f956619d519205ec475fe647", + "Repository": "CRAN", + "Hash": "947e4e02a79effa5d512473e10f41797", "Requirements": [] }, "spelling": { "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", @@ -1156,34 +1148,30 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.12", + "Version": "1.7.8", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ca8bd84263c77310739d2cf64d84d7c9", + "Repository": "CRAN", + "Hash": "a68b980681bcbc84c7a67003fa796bfb", "Requirements": [] }, "stringr": { "Package": "stringr", - "Version": "1.5.0", + "Version": "1.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8", + "Repository": "CRAN", + "Hash": "a66ad12140cd34d4f9dfcc19e84fc2a5", "Requirements": [ - "cli", "glue", - "lifecycle", "magrittr", - "rlang", - "stringi", - "vctrs" + "stringi" ] }, "styler": { "Package": "styler", - "Version": "1.9.0", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1c038945a5e14cce208f5214c1dd167c", + "Repository": "CRAN", + "Hash": "c855e70eb69b3dd8883660b7110e0c44", "Requirements": [ "R.cache", "cli", @@ -1199,7 +1187,7 @@ "Package": "sys", "Version": "3.4.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "34c16f1ef796057bfa06d3f4ff818a5d", "Requirements": [] }, @@ -1207,7 +1195,7 @@ "Package": "systemfonts", "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "90b28393209827327de889f49935140a", "Requirements": [ "cpp11" @@ -1215,10 +1203,10 @@ }, "testthat": { "Package": "testthat", - "Version": "3.1.6", + "Version": "3.1.5", "Source": "Repository", - "Repository": "RSPM", - "Hash": "7910146255835c66e9eb272fb215248d", + "Repository": "CRAN", + "Hash": "6e3c4843f1ed0d3d90f35498671a001c", "Requirements": [ "R6", "brio", @@ -1244,7 +1232,7 @@ "Package": "textshaping", "Version": "0.3.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "1ab6223d3670fac7143202cb6a2d43d5", "Requirements": [ "cpp11", @@ -1255,7 +1243,7 @@ "Package": "tibble", "Version": "3.1.8", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "56b6934ef0f8c68225949a8672fe1a8f", "Requirements": [ "fansi", @@ -1269,20 +1257,19 @@ }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf", + "Repository": "CRAN", + "Hash": "cdb403db0de33ccd1b6f53b83736efa8", "Requirements": [ - "cli", "cpp11", "dplyr", + "ellipsis", "glue", "lifecycle", "magrittr", "purrr", "rlang", - "stringr", "tibble", "tidyselect", "vctrs" @@ -1292,7 +1279,7 @@ "Package": "tidyselect", "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "79540e5fcd9e0435af547d885f184fd5", "Requirements": [ "cli", @@ -1303,22 +1290,12 @@ "withr" ] }, - "timechange": { - "Package": "timechange", - "Version": "0.2.0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "8548b44f79a35ba1791308b61e6012d7", - "Requirements": [ - "cpp11" - ] - }, "tinytex": { "Package": "tinytex", - "Version": "0.44", + "Version": "0.42", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c0f007e2eeed7722ce13d42b84a22e07", + "Repository": "CRAN", + "Hash": "7629c6c1540835d5248e6e7df265fa74", "Requirements": [ "xfun" ] @@ -1327,7 +1304,7 @@ "Package": "urlchecker", "Version": "1.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "409328b8e1253c8d729a7836fe7f7a16", "Requirements": [ "cli", @@ -1339,7 +1316,7 @@ "Package": "usethis", "Version": "2.1.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "a67a22c201832b12c036cc059f1d137d", "Requirements": [ "cli", @@ -1365,18 +1342,18 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1fe17157424bb09c48a8b3b550c753bc", + "Repository": "CRAN", + "Hash": "c9c462b759a5cc844ae25b5942654d13", "Requirements": [] }, "vctrs": { "Package": "vctrs", - "Version": "0.5.2", + "Version": "0.5.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e4ffa94ceed5f124d429a5a5f0f5b378", + "Repository": "CRAN", + "Hash": "001fd6a5ebfff8316baf9fb2b5516dc9", "Requirements": [ "cli", "glue", @@ -1388,7 +1365,7 @@ "Package": "waldo", "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "035fba89d0c86e2113120f93301b98ad", "Requirements": [ "cli", @@ -1402,33 +1379,33 @@ }, "whisker": { "Package": "whisker", - "Version": "0.4.1", + "Version": "0.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c6abfa47a46d281a7d5159d0a8891e88", + "Repository": "CRAN", + "Hash": "ca970b96d894e90397ed20637a0c1bbe", "Requirements": [] }, "withr": { "Package": "withr", "Version": "2.5.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "c0e49a9760983e81e55cdd9be92e7182", "Requirements": [] }, "xfun": { "Package": "xfun", - "Version": "0.37", + "Version": "0.34", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a6860e1400a8fd1ddb6d9b4230cc34ab", + "Repository": "CRAN", + "Hash": "9eba2411b0b1f879797141bd24df7407", "Requirements": [] }, "xml2": { "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "40682ed6a969ea5abfd351eb67833adc", "Requirements": [] }, @@ -1436,7 +1413,7 @@ "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "45e4bf3c46476896e821fc0a408fb4fc", "Requirements": [] }, @@ -1444,7 +1421,7 @@ "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" @@ -1454,23 +1431,23 @@ "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, "yaml": { "Package": "yaml", - "Version": "2.3.7", + "Version": "2.3.6", "Source": "Repository", - "Repository": "RSPM", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436", + "Repository": "CRAN", + "Hash": "9b570515751dcbae610f29885e025b41", "Requirements": [] }, "zip": { "Package": "zip", "Version": "2.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88", "Requirements": [] } diff --git a/renv/profiles/4.2/renv/.gitignore b/renv/profiles/4.2/renv/.gitignore new file mode 100644 index 00000000..0ec0cbba --- /dev/null +++ b/renv/profiles/4.2/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/profiles/4.2/renv/settings.dcf b/renv/profiles/4.2/renv/settings.dcf new file mode 100644 index 00000000..c4ab61bd --- /dev/null +++ b/renv/profiles/4.2/renv/settings.dcf @@ -0,0 +1,10 @@ +bioconductor.version: +external.libraries: +ignored.packages: admiral, admiraldev, admiral.test, admiralci +package.dependency.fields: Imports, Depends, LinkingTo +r.version: +snapshot.type: custom +use.cache: TRUE +vcs.ignore.cellar: TRUE +vcs.ignore.library: TRUE +vcs.ignore.local: TRUE From c11bc647030d4d4fcae3aa8676401e537a6c2128 Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 14 Feb 2023 14:56:08 +0000 Subject: [PATCH 009/100] renv update from pharmaverse/admiralci --- renv.lock | 10 ++++++---- renv/profiles/4.0/renv.lock | 10 ++++++---- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/renv.lock b/renv.lock index f51a6fd8..b1ccb0c6 100644 --- a/renv.lock +++ b/renv.lock @@ -359,15 +359,17 @@ }, "downlit": { "Package": "downlit", - "Version": "0.2.1", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f24f1e44320a978c03050b8403a83793", + "Hash": "ba63dc9ab5a31f3209892437e40c5f60", "Requirements": [ "brio", + "desc", "digest", "evaluate", "fansi", + "memoise", "rlang", "vctrs", "yaml" @@ -1371,10 +1373,10 @@ }, "withr": { "Package": "withr", - "Version": "2.4.1", + "Version": "2.4.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "caf4781c674ffa549a4676d2d77b13cc", + "Hash": "a376b424c4817cda4920bbbeb3364e85", "Requirements": [] }, "xfun": { diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index f51a6fd8..b1ccb0c6 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -359,15 +359,17 @@ }, "downlit": { "Package": "downlit", - "Version": "0.2.1", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f24f1e44320a978c03050b8403a83793", + "Hash": "ba63dc9ab5a31f3209892437e40c5f60", "Requirements": [ "brio", + "desc", "digest", "evaluate", "fansi", + "memoise", "rlang", "vctrs", "yaml" @@ -1371,10 +1373,10 @@ }, "withr": { "Package": "withr", - "Version": "2.4.1", + "Version": "2.4.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "caf4781c674ffa549a4676d2d77b13cc", + "Hash": "a376b424c4817cda4920bbbeb3364e85", "Requirements": [] }, "xfun": { From de7e7188b001ebc946d2574824fcc48603d91a0e Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 16 Feb 2023 15:18:16 +0000 Subject: [PATCH 010/100] renv update from pharmaverse/admiralci --- renv.lock | 8 ++++++++ renv/profiles/4.0/renv.lock | 8 ++++++++ renv/profiles/4.1/renv.lock | 8 ++++++++ renv/profiles/4.2/renv.lock | 8 ++++++++ 4 files changed, 32 insertions(+) diff --git a/renv.lock b/renv.lock index b1ccb0c6..3dfb4dc9 100644 --- a/renv.lock +++ b/renv.lock @@ -104,6 +104,14 @@ "sys" ] }, + "assertthat": { + "Package": "assertthat", + "Version": "0.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "50c838a310445e954bc13f26f26a6ecf", + "Requirements": [] + }, "backports": { "Package": "backports", "Version": "1.2.1", diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index b1ccb0c6..3dfb4dc9 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -104,6 +104,14 @@ "sys" ] }, + "assertthat": { + "Package": "assertthat", + "Version": "0.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "50c838a310445e954bc13f26f26a6ecf", + "Requirements": [] + }, "backports": { "Package": "backports", "Version": "1.2.1", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 818d838b..3f3f23cc 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -97,6 +97,14 @@ "sys" ] }, + "assertthat": { + "Package": "assertthat", + "Version": "0.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "50c838a310445e954bc13f26f26a6ecf", + "Requirements": [] + }, "backports": { "Package": "backports", "Version": "1.4.1", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 5becab33..e91579fa 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -97,6 +97,14 @@ "sys" ] }, + "assertthat": { + "Package": "assertthat", + "Version": "0.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "50c838a310445e954bc13f26f26a6ecf", + "Requirements": [] + }, "backports": { "Package": "backports", "Version": "1.4.1", From 94b03a5dc8b4d15f704cacf29b629bff7c31b474 Mon Sep 17 00:00:00 2001 From: galachad Date: Fri, 17 Feb 2023 11:48:47 +0000 Subject: [PATCH 011/100] renv update from pharmaverse/admiralci --- renv.lock | 6 +++--- renv/profiles/4.0/renv.lock | 6 +++--- renv/profiles/4.1/renv.lock | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/renv.lock b/renv.lock index 3dfb4dc9..49efd83f 100644 --- a/renv.lock +++ b/renv.lock @@ -297,13 +297,13 @@ }, "desc": { "Package": "desc", - "Version": "1.3.0", + "Version": "1.4.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "b6963166f7f10b970af1006c462ce6cd", + "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", "Requirements": [ "R6", - "crayon", + "cli", "rprojroot" ] }, diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index 3dfb4dc9..49efd83f 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -297,13 +297,13 @@ }, "desc": { "Package": "desc", - "Version": "1.3.0", + "Version": "1.4.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "b6963166f7f10b970af1006c462ce6cd", + "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", "Requirements": [ "R6", - "crayon", + "cli", "rprojroot" ] }, diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 3f3f23cc..0de19238 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -288,10 +288,10 @@ }, "desc": { "Package": "desc", - "Version": "1.4.1", + "Version": "1.4.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "eebd27ee58fcc58714eedb7aa07d8ad1", + "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", "Requirements": [ "R6", "cli", From 288457c8f0e36d714e2d7b96c165d81a148220a2 Mon Sep 17 00:00:00 2001 From: galachad Date: Mon, 20 Feb 2023 03:06:52 +0000 Subject: [PATCH 012/100] renv update from pharmaverse/admiralci --- renv.lock | 4 ++-- renv/profiles/4.0/renv.lock | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/renv.lock b/renv.lock index 49efd83f..f14c1f46 100644 --- a/renv.lock +++ b/renv.lock @@ -1397,10 +1397,10 @@ }, "xml2": { "Package": "xml2", - "Version": "1.3.2", + "Version": "1.3.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "d4d71a75dd3ea9eb5fa28cc21f9585e2", + "Hash": "40682ed6a969ea5abfd351eb67833adc", "Requirements": [] }, "xmlparsedata": { diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index 49efd83f..f14c1f46 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -1397,10 +1397,10 @@ }, "xml2": { "Package": "xml2", - "Version": "1.3.2", + "Version": "1.3.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "d4d71a75dd3ea9eb5fa28cc21f9585e2", + "Hash": "40682ed6a969ea5abfd351eb67833adc", "Requirements": [] }, "xmlparsedata": { From f6db65d372e0b768a149dad242e9ccd1363fcfb3 Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Mon, 20 Feb 2023 06:29:43 +0000 Subject: [PATCH 013/100] Upgrade lintr and add new checks --- .lintr | 13 +++++++++++-- R/addin_format_testthat.R | 2 +- R/assertions.R | 8 ++++---- R/dataset_vignette.R | 2 +- tests/testthat.R | 4 ++-- tests/testthat/test-dataset_vignette.R | 8 ++++---- 6 files changed, 23 insertions(+), 14 deletions(-) diff --git a/.lintr b/.lintr index 5c286fe8..b2a0a879 100644 --- a/.lintr +++ b/.lintr @@ -1,2 +1,11 @@ -linters: with_defaults(line_length_linter(100), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20)) -exclusions: list("R/data.R") +linters: linters_with_defaults( + line_length_linter(100), + object_usage_linter=NULL, + cyclocomp_linter(complexity_limit = 20), + undesirable_function_linter = undesirable_function_linter() + ) +exclusions: list( + "R/data.R" = Inf, + "inst" = list(undesirable_function_linter = Inf), + "vignettes" = list(undesirable_function_linter = Inf) + ) diff --git a/R/addin_format_testthat.R b/R/addin_format_testthat.R index 6de0674c..2aae2443 100644 --- a/R/addin_format_testthat.R +++ b/R/addin_format_testthat.R @@ -13,7 +13,7 @@ prepare_test_that_file <- function(path) { } # check that testthat is used and testing file is opened - uses_test_file <- grepl("tests/testthat/test-", path, fixed = T) + uses_test_file <- grepl("tests/testthat/test-", path, fixed = TRUE) if (!uses_test_file) { stop("This Addin works only on unit test files that follow a testthat structure.") } diff --git a/R/assertions.R b/R/assertions.R index 788f4bc3..c375274e 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -465,12 +465,12 @@ assert_filter_cond <- function(arg, optional = FALSE) { } provided <- !rlang::quo_is_missing(arg) - if (!provided & !optional) { + if (!provided && !optional) { err_msg <- sprintf("Argument `%s` is missing, with no default", arg_name(substitute(arg))) abort(err_msg) } - if (provided & !(quo_is_call(arg) | is_logical(quo_get_expr(arg)))) { + if (provided && !(quo_is_call(arg) || is_logical(quo_get_expr(arg)))) { err_msg <- sprintf( "`%s` must be a filter condition but is %s", arg_name(substitute(arg)), @@ -1273,7 +1273,7 @@ assert_varval_list <- function(arg, # nolint valid_vals <- "a symbol, character scalar, numeric scalar, or `NA`" } - if (!accept_var & (!is_quosures(arg) || !is_named(arg))) { + if (!accept_var && (!is_quosures(arg) || !is_named(arg))) { err_msg <- sprintf( paste0( "`%s` must be a named list of quosures where each element is ", @@ -1287,7 +1287,7 @@ assert_varval_list <- function(arg, # nolint abort(err_msg) } - if (accept_var & (!contains_vars(arg))) { + if (accept_var && (!contains_vars(arg))) { err_msg <- sprintf( paste0( "`%s` must be a list of quosures where each element is ", diff --git a/R/dataset_vignette.R b/R/dataset_vignette.R index b4fd606e..34b2ef28 100644 --- a/R/dataset_vignette.R +++ b/R/dataset_vignette.R @@ -75,7 +75,7 @@ dataset_vignette <- function(dataset, display_vars = NULL, filter = NULL) { buttons = list(list( extend = "colvis", text = "Choose the columns to display", - scroller = T, + scroller = TRUE, collectionLayout = "fixed two-column" )), colReorder = TRUE diff --git a/tests/testthat.R b/tests/testthat.R index 20b68db6..0416049e 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,4 +1,4 @@ -library(testthat) -library(admiraldev) +library(testthat) # nolint: undesirable_function_linter +library(admiraldev) # nolint: undesirable_function_linter test_check("admiraldev") diff --git a/tests/testthat/test-dataset_vignette.R b/tests/testthat/test-dataset_vignette.R index cb47647b..696f26bd 100644 --- a/tests/testthat/test-dataset_vignette.R +++ b/tests/testthat/test-dataset_vignette.R @@ -1,8 +1,8 @@ # dataset_vignette ---- ## Test 1: A 'knitr_kable' object is outputted when run outside pkgdown ---- test_that("dataset_vignette Test 1: A 'knitr_kable' object is outputted when run outside pkgdown", { - Sys.setenv(IN_PKGDOWN = "false") - on.exit(Sys.setenv(IN_PKGDOWN = "")) + Sys.setenv(IN_PKGDOWN = "false") # nolint: undesirable_function_linter + on.exit(Sys.setenv(IN_PKGDOWN = "")) # nolint: undesirable_function_linter dm <- tibble::tribble( ~STUDYID, ~USUBJID, ~COUNTRY, @@ -18,8 +18,8 @@ test_that("dataset_vignette Test 1: A 'knitr_kable' object is outputted when run ## Test 2: A 'datatables' object is outputted when run inside pkgdown ---- test_that("dataset_vignette Test 2: A 'shiny.tag.list' is outputted when run inside pkgdown", { - Sys.setenv(IN_PKGDOWN = "true") - on.exit(Sys.setenv(IN_PKGDOWN = "")) + Sys.setenv(IN_PKGDOWN = "true") # nolint: undesirable_function_linter + on.exit(Sys.setenv(IN_PKGDOWN = "")) # nolint: undesirable_function_linter dm <- tibble::tribble( ~STUDYID, ~USUBJID, ~COUNTRY, From 5400e955ec8e6e7a66c2dfebabd7a642e4af71b0 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 22 Feb 2023 07:16:32 +0000 Subject: [PATCH 014/100] renv update from pharmaverse/admiralci --- renv/activate.R | 478 ++++++++++++++++++++++++------------------------ 1 file changed, 240 insertions(+), 238 deletions(-) diff --git a/renv/activate.R b/renv/activate.R index e52e2dae..019b5a66 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -1,4 +1,6 @@ + local({ + # the requested version of renv version <- "0.16.0" @@ -56,100 +58,100 @@ local({ if ("renv" %in% loadedNamespaces()) unloadNamespace("renv") - # load bootstrap tools + # load bootstrap tools `%||%` <- function(x, y) { if (is.environment(x) || length(x)) x else y } - + bootstrap <- function(version, library) { - + # attempt to download renv tarball <- tryCatch(renv_bootstrap_download(version), error = identity) if (inherits(tarball, "error")) stop("failed to download renv ", version) - + # now attempt to install status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) if (inherits(status, "error")) stop("failed to install renv ", version) - + } - + renv_bootstrap_tests_running <- function() { getOption("renv.tests.running", default = FALSE) } - + renv_bootstrap_repos <- function() { - + # check for repos override repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) if (!is.na(repos)) return(repos) - + # check for lockfile repositories repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) if (!inherits(repos, "error") && length(repos)) return(repos) - + # if we're testing, re-use the test repositories if (renv_bootstrap_tests_running()) return(getOption("renv.tests.repos")) - + # retrieve current repos repos <- getOption("repos") - + # ensure @CRAN@ entries are resolved repos[repos == "@CRAN@"] <- getOption( "renv.repos.cran", "https://cloud.r-project.org" ) - + # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") extra <- getOption("renv.bootstrap.repos", default = default) repos <- c(repos, extra) - + # remove duplicates that might've snuck in dupes <- duplicated(repos) | duplicated(names(repos)) repos[!dupes] - + } - + renv_bootstrap_repos_lockfile <- function() { - + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") if (!file.exists(lockpath)) return(NULL) - + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) if (inherits(lockfile, "error")) { warning(lockfile) return(NULL) } - + repos <- lockfile$R$Repositories if (length(repos) == 0) return(NULL) - + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) names(vals) <- keys - + return(vals) - + } - + renv_bootstrap_download <- function(version) { - + # if the renv version number has 4 components, assume it must # be retrieved via github nv <- numeric_version(version) components <- unclass(nv)[[1]] - + # if this appears to be a development version of 'renv', we'll # try to restore from github dev <- length(components) == 4L - + # begin collecting different methods for finding renv methods <- c( renv_bootstrap_download_tarball, @@ -160,79 +162,79 @@ local({ renv_bootstrap_download_cran_archive ) ) - + for (method in methods) { path <- tryCatch(method(version), error = identity) if (is.character(path) && file.exists(path)) return(path) } - + stop("failed to download renv ", version) - + } - + renv_bootstrap_download_impl <- function(url, destfile) { - + mode <- "wb" - + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 fixup <- Sys.info()[["sysname"]] == "Windows" && substring(url, 1L, 5L) == "file:" - + if (fixup) mode <- "w+b" - + args <- list( url = url, destfile = destfile, mode = mode, quiet = TRUE ) - + if ("headers" %in% names(formals(utils::download.file))) args$headers <- renv_bootstrap_download_custom_headers(url) - + do.call(utils::download.file, args) - + } - + renv_bootstrap_download_custom_headers <- function(url) { - + headers <- getOption("renv.download.headers") if (is.null(headers)) return(character()) - + if (!is.function(headers)) stopf("'renv.download.headers' is not a function") - + headers <- headers(url) if (length(headers) == 0L) return(character()) - + if (is.list(headers)) headers <- unlist(headers, recursive = FALSE, use.names = TRUE) - + ok <- is.character(headers) && is.character(names(headers)) && all(nzchar(names(headers))) - + if (!ok) stop("invocation of 'renv.download.headers' did not return a named character vector") - + headers - + } - + renv_bootstrap_download_cran_latest <- function(version) { - + spec <- renv_bootstrap_download_cran_latest_find(version) type <- spec$type repos <- spec$repos - + message("* Downloading renv ", version, " ... ", appendLF = FALSE) - + baseurl <- utils::contrib.url(repos = repos, type = type) ext <- if (identical(type, "source")) ".tar.gz" @@ -242,39 +244,39 @@ local({ ".tgz" name <- sprintf("renv_%s%s", version, ext) url <- paste(baseurl, name, sep = "/") - + destfile <- file.path(tempdir(), name) status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (inherits(status, "condition")) { message("FAILED") return(FALSE) } - + # report success and return message("OK (downloaded ", type, ")") destfile - + } - + renv_bootstrap_download_cran_latest_find <- function(version) { - + # check whether binaries are supported on this system binary <- getOption("renv.bootstrap.binary", default = TRUE) && !identical(.Platform$pkgType, "source") && !identical(getOption("pkgType"), "source") && Sys.info()[["sysname"]] %in% c("Darwin", "Windows") - + types <- c(if (binary) "binary", "source") - + # iterate over types + repositories for (type in types) { for (repos in renv_bootstrap_repos()) { - + # retrieve package database db <- tryCatch( as.data.frame( @@ -283,98 +285,98 @@ local({ ), error = identity ) - + if (inherits(db, "error")) next - + # check for compatible entry entry <- db[db$Package %in% "renv" & db$Version %in% version, ] if (nrow(entry) == 0) next - + # found it; return spec to caller spec <- list(entry = entry, type = type, repos = repos) return(spec) - + } } - + # if we got here, we failed to find renv fmt <- "renv %s is not available from your declared package repositories" stop(sprintf(fmt, version)) - + } - + renv_bootstrap_download_cran_archive <- function(version) { - + name <- sprintf("renv_%s.tar.gz", version) repos <- renv_bootstrap_repos() urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - + message("* Downloading renv ", version, " ... ", appendLF = FALSE) - + for (url in urls) { - + status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (identical(status, 0L)) { message("OK") return(destfile) } - + } - + message("FAILED") return(FALSE) - + } - + renv_bootstrap_download_tarball <- function(version) { - + # if the user has provided the path to a tarball via # an environment variable, then use it tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) if (is.na(tarball)) return() - + # allow directories info <- file.info(tarball, extra_cols = FALSE) if (identical(info$isdir, TRUE)) { name <- sprintf("renv_%s.tar.gz", version) tarball <- file.path(tarball, name) } - + # bail if it doesn't exist if (!file.exists(tarball)) { - + # let the user know we weren't able to honour their request fmt <- "* RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." msg <- sprintf(fmt, tarball) warning(msg) - + # bail return() - + } - + fmt <- "* Bootstrapping with tarball at path '%s'." msg <- sprintf(fmt, tarball) message(msg) - + tarball - + } - + renv_bootstrap_download_github <- function(version) { - + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") if (!identical(enabled, "TRUE")) return(FALSE) - + # prepare download options pat <- Sys.getenv("GITHUB_PAT") if (nzchar(Sys.which("curl")) && nzchar(pat)) { @@ -390,48 +392,48 @@ local({ options(download.file.method = "wget", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) } - + message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) - + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) - + status <- tryCatch( renv_bootstrap_download_impl(url, destfile), condition = identity ) - + if (!identical(status, 0L)) { message("FAILED") return(FALSE) } - + message("OK") return(destfile) - + } - + renv_bootstrap_install <- function(version, tarball, library) { - + # attempt to install it into project library message("* Installing renv ", version, " ... ", appendLF = FALSE) dir.create(library, showWarnings = FALSE, recursive = TRUE) - + # invoke using system2 so we can capture and report output bin <- R.home("bin") exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" r <- file.path(bin, exe) - + args <- c( "--vanilla", "CMD", "INSTALL", "--no-multiarch", "-l", shQuote(path.expand(library)), shQuote(path.expand(tarball)) ) - + output <- system2(r, args, stdout = TRUE, stderr = TRUE) message("Done!") - + # check for successful install status <- attr(output, "status") if (is.numeric(status) && !identical(status, 0L)) { @@ -440,101 +442,101 @@ local({ text <- c(header, lines, output) writeLines(text, con = stderr()) } - + status - + } - + renv_bootstrap_platform_prefix <- function() { - + # construct version prefix version <- paste(R.version$major, R.version$minor, sep = ".") prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") - + # include SVN revision for development versions of R # (to avoid sharing platform-specific artefacts with released versions of R) devel <- identical(R.version[["status"]], "Under development (unstable)") || identical(R.version[["nickname"]], "Unsuffered Consequences") - + if (devel) prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") - + # build list of path components components <- c(prefix, R.version$platform) - + # include prefix if provided by user prefix <- renv_bootstrap_platform_prefix_impl() if (!is.na(prefix) && nzchar(prefix)) components <- c(prefix, components) - + # build prefix paste(components, collapse = "/") - + } - + renv_bootstrap_platform_prefix_impl <- function() { - + # if an explicit prefix has been supplied, use it prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) if (!is.na(prefix)) return(prefix) - + # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) - + # empty string on failure "" - + } - + renv_bootstrap_platform_prefix_auto <- function() { - + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) if (inherits(prefix, "error") || prefix %in% "unknown") { - + msg <- paste( "failed to infer current operating system", "please file a bug report at https://github.com/rstudio/renv/issues", sep = "; " ) - + warning(msg) - + } - + prefix - + } - + renv_bootstrap_platform_os <- function() { - + sysinfo <- Sys.info() sysname <- sysinfo[["sysname"]] - + # handle Windows + macOS up front if (sysname == "Windows") return("windows") else if (sysname == "Darwin") return("macos") - + # check for os-release files for (file in c("/etc/os-release", "/usr/lib/os-release")) if (file.exists(file)) return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) - + # check for redhat-release files if (file.exists("/etc/redhat-release")) return(renv_bootstrap_platform_os_via_redhat_release()) - + "unknown" - + } - + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { - + # read /etc/os-release release <- utils::read.table( file = file, @@ -544,13 +546,13 @@ local({ comment.char = "#", stringsAsFactors = FALSE ) - + vars <- as.list(release$Value) names(vars) <- release$Key - + # get os name os <- tolower(sysinfo[["sysname"]]) - + # read id id <- "unknown" for (field in c("ID", "ID_LIKE")) { @@ -559,7 +561,7 @@ local({ break } } - + # read version version <- "unknown" for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { @@ -568,17 +570,17 @@ local({ 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" @@ -586,77 +588,77 @@ local({ "redhat" else "unknown" - + # try to find a version component (very hacky) version <- "unknown" - + parts <- strsplit(contents, "[[:space:]]")[[1L]] for (part in parts) { - + nv <- tryCatch(numeric_version(part), error = identity) if (inherits(nv, "error")) next - + version <- nv[1, 1] break - + } - + paste(c("linux", id, version), collapse = "-") - + } - + renv_bootstrap_library_root_name <- function(project) { - + # use project name as-is if requested asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") if (asis) return(basename(project)) - + # otherwise, disambiguate based on project's path id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) paste(basename(project), id, sep = "-") - + } - + renv_bootstrap_library_root <- function(project) { - + prefix <- renv_bootstrap_profile_prefix() - + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) if (!is.na(path)) return(paste(c(path, prefix), collapse = "/")) - + path <- renv_bootstrap_library_root_impl(project) if (!is.null(path)) { name <- renv_bootstrap_library_root_name(project) return(paste(c(path, prefix, name), collapse = "/")) } - + renv_bootstrap_paths_renv("library", project = project) - + } - + renv_bootstrap_library_root_impl <- function(project) { - + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) if (!is.na(root)) return(root) - + type <- renv_bootstrap_project_type(project) if (identical(type, "package")) { userdir <- renv_bootstrap_user_dir() return(file.path(userdir, "library")) } - + } - + renv_bootstrap_validate_version <- function(version) { - + loadedversion <- utils::packageDescription("renv", fields = "Version") if (version == loadedversion) return(TRUE) - + # assume four-component versions are from GitHub; three-component # versions are from CRAN components <- strsplit(loadedversion, "[.-]")[[1]] @@ -664,84 +666,84 @@ local({ paste("rstudio/renv", loadedversion, sep = "@") else paste("renv", loadedversion, sep = "@") - + fmt <- paste( "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", sep = "\n" ) - + msg <- sprintf(fmt, loadedversion, version, remote) warning(msg, call. = FALSE) - + FALSE - + } - + renv_bootstrap_hash_text <- function(text) { - + hashfile <- tempfile("renv-hash-") on.exit(unlink(hashfile), add = TRUE) - + writeLines(text, con = hashfile) tools::md5sum(hashfile) - + } - + renv_bootstrap_load <- function(project, libpath, version) { - + # try to load renv from the project library if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) return(FALSE) - + # warn if the version of renv loaded does not match renv_bootstrap_validate_version(version) - + # load the project renv::load(project) - + TRUE - + } - + renv_bootstrap_profile_load <- function(project) { - + # if RENV_PROFILE is already set, just use that profile <- Sys.getenv("RENV_PROFILE", unset = NA) if (!is.na(profile) && nzchar(profile)) return(profile) - + # check for a profile file (nothing to do if it doesn't exist) path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) if (!file.exists(path)) return(NULL) - + # read the profile, and set it if it exists contents <- readLines(path, warn = FALSE) if (length(contents) == 0L) return(NULL) - + # set RENV_PROFILE profile <- contents[[1L]] if (!profile %in% c("", "default")) Sys.setenv(RENV_PROFILE = profile) - + profile - + } - + renv_bootstrap_profile_prefix <- function() { profile <- renv_bootstrap_profile_get() if (!is.null(profile)) return(file.path("profiles", profile, "renv")) } - + renv_bootstrap_profile_get <- function() { profile <- Sys.getenv("RENV_PROFILE", unset = "") renv_bootstrap_profile_normalize(profile) } - + renv_bootstrap_profile_set <- function(profile) { profile <- renv_bootstrap_profile_normalize(profile) if (is.null(profile)) @@ -749,25 +751,25 @@ local({ 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 @@ -775,50 +777,50 @@ local({ 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) { @@ -826,7 +828,7 @@ local({ 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") @@ -834,57 +836,57 @@ local({ "~/Library/Caches/org.R-project.R/R/renv" else "~/.cache/R/renv" - + } - - + + renv_json_read <- function(file = NULL, text = NULL) { - + # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) renv_json_read_jsonlite(file, text) else renv_json_read_default(file, text) - + } - + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { text <- paste(text %||% read(file), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } - + renv_json_read_default <- function(file = NULL, text = NULL) { - + # find strings in the JSON text <- paste(text %||% read(file), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] - + # if any are found, replace them with placeholders replaced <- text strings <- character() replacements <- character() - + if (!identical(c(locs), -1L)) { - + # get the string values starts <- locs ends <- locs + attr(locs, "match.length") - 1L strings <- substring(text, starts, ends) - + # only keep those requiring escaping strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) - + # compute replacements replacements <- sprintf('"\032%i\032"', seq_along(strings)) - + # replace the strings mapply(function(string, replacement) { replaced <<- sub(string, replacement, replaced, fixed = TRUE) }, strings, replacements) - + } - + # transform the JSON into something the R parser understands transformed <- replaced transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) @@ -892,38 +894,38 @@ local({ transformed <- gsub("[]}]", ")", transformed, perl = TRUE) transformed <- gsub(":", "=", transformed, fixed = TRUE) text <- paste(transformed, collapse = "\n") - + # parse it json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] - + # construct map between source strings, replaced strings map <- as.character(parse(text = strings)) names(map) <- as.character(parse(text = replacements)) - + # convert to list map <- as.list(map) - + # remap strings in object remapped <- renv_json_remap(json, map) - + # evaluate eval(remapped, envir = baseenv()) - + } - + renv_json_remap <- function(json, map) { - + # fix names if (!is.null(names(json))) { lhs <- match(names(json), names(map), nomatch = 0L) rhs <- match(names(map), names(json), nomatch = 0L) names(json)[rhs] <- map[lhs] } - + # fix values if (is.character(json)) return(map[[json]] %||% json) - + # handle true, false, null if (is.name(json)) { text <- as.character(json) @@ -934,16 +936,16 @@ local({ else if (text == "null") return(NULL) } - + # recurse if (is.recursive(json)) { for (i in seq_along(json)) { json[i] <- list(renv_json_remap(json[[i]], map)) } } - + json - + } # load the renv profile, if any From bddcc89c0b914720919ce06168ac39a38f447336 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 22 Feb 2023 07:58:09 +0000 Subject: [PATCH 015/100] renv update from pharmaverse/admiralci --- renv.lock | 223 ++++++++++++++++----------------- renv/profiles/4.0/renv.lock | 223 ++++++++++++++++----------------- renv/profiles/4.1/renv.lock | 222 ++++++++++++++++----------------- renv/profiles/4.2/renv.lock | 238 ++++++++++++++++++------------------ 4 files changed, 454 insertions(+), 452 deletions(-) diff --git a/renv.lock b/renv.lock index f14c1f46..19f2bf92 100644 --- a/renv.lock +++ b/renv.lock @@ -7,8 +7,8 @@ "URL": "https://cloud.r-project.org" }, { - "Name": "MRAN", - "URL": "https://cran.microsoft.com/snapshot/2021-03-31" + "Name": "RSPM", + "URL": "https://packagemanager.posit.co/cran/2021-03-31" } ] }, @@ -17,7 +17,7 @@ "Package": "BH", "Version": "1.75.0-0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e4c04affc2cac20c8fec18385cd14691", "Requirements": [] }, @@ -25,7 +25,7 @@ "Package": "DT", "Version": "0.17", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0", "Requirements": [ "crosstalk", @@ -40,7 +40,7 @@ "Package": "R.cache", "Version": "0.14.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1ca02d43e1a4d49e616bd23bb39b17e6", "Requirements": [ "R.methodsS3", @@ -53,7 +53,7 @@ "Package": "R.methodsS3", "Version": "1.8.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4bf6453323755202d5909697b6f7c109", "Requirements": [] }, @@ -61,7 +61,7 @@ "Package": "R.oo", "Version": "1.24.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5709328352717e2f0a9c012be8a97554", "Requirements": [ "R.methodsS3" @@ -71,7 +71,7 @@ "Package": "R.utils", "Version": "2.10.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a9e316277ff12a43997266f2f6567780", "Requirements": [ "R.methodsS3", @@ -82,7 +82,7 @@ "Package": "R6", "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b203113193e70978a696b2809525649d", "Requirements": [] }, @@ -90,7 +90,7 @@ "Package": "Rcpp", "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "dbb5e436998a7eba5a9d682060533338", "Requirements": [] }, @@ -98,7 +98,7 @@ "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e8a22846fff485f0be3770c2da758713", "Requirements": [ "sys" @@ -108,7 +108,7 @@ "Package": "assertthat", "Version": "0.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "50c838a310445e954bc13f26f26a6ecf", "Requirements": [] }, @@ -116,7 +116,7 @@ "Package": "backports", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "644043219fc24e190c2f620c1a380a69", "Requirements": [] }, @@ -124,7 +124,7 @@ "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, @@ -132,7 +132,7 @@ "Package": "brew", "Version": "1.0-6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "92a5f887f9ae3035ac7afde22ba73ee9", "Requirements": [] }, @@ -140,7 +140,7 @@ "Package": "brio", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "36758510e65a457efeefa50e1e7f0576", "Requirements": [] }, @@ -148,7 +148,7 @@ "Package": "bslib", "Version": "0.2.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4830a372b241d78ed6f53731ee3023ac", "Requirements": [ "digest", @@ -164,7 +164,7 @@ "Package": "cachem", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2703a46dcabfb902f10060b2bca9f708", "Requirements": [ "fastmap", @@ -194,7 +194,7 @@ "Package": "clipr", "Version": "0.7.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7", "Requirements": [] }, @@ -210,7 +210,7 @@ "Package": "commonmark", "Version": "1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0f22be39ec1d141fd03683c06f3a6e67", "Requirements": [] }, @@ -218,7 +218,7 @@ "Package": "covr", "Version": "3.5.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6d80a9fc3c0c8473153b54fa54719dfd", "Requirements": [ "crayon", @@ -234,7 +234,7 @@ "Package": "cpp11", "Version": "0.2.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "730eebcc741a5c36761f7d4d0f5e37b8", "Requirements": [] }, @@ -242,7 +242,7 @@ "Package": "crayon", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e75525c55c70e5f4f78c9960a4b402e9", "Requirements": [] }, @@ -250,7 +250,7 @@ "Package": "credentials", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a96728288c75a814c900af9da84387be", "Requirements": [ "askpass", @@ -264,7 +264,7 @@ "Package": "crosstalk", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2b06f9e415a62b6762e4b8098d2aecbc", "Requirements": [ "R6", @@ -277,7 +277,7 @@ "Package": "curl", "Version": "4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2b7d10581cc730804e9ed178c8374bd6", "Requirements": [] }, @@ -285,7 +285,7 @@ "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "53cbed70a2f7472d48fb6aef08442f25", "Requirements": [ "callr", @@ -311,7 +311,7 @@ "Package": "devtools", "Version": "2.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "415656f50722f5b6e6bcf80855ce11b9", "Requirements": [ "DT", @@ -341,7 +341,7 @@ "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9ddedef46959baad2080047a1b0117fe", "Requirements": [ "tibble" @@ -351,7 +351,7 @@ "Package": "diffobj", "Version": "0.3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "feb5b7455eba422a2c110bb89852e6a3", "Requirements": [ "crayon" @@ -361,7 +361,7 @@ "Package": "digest", "Version": "0.6.27", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a0cbe758a531d054b537d16dff4d58a1", "Requirements": [] }, @@ -387,7 +387,7 @@ "Package": "dplyr", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68", "Requirements": [ "R6", @@ -406,7 +406,7 @@ "Package": "ellipsis", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a", "Requirements": [ "rlang" @@ -416,7 +416,7 @@ "Package": "evaluate", "Version": "0.14", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ec8ca05cffcc70569eaaad8469d2a3a7", "Requirements": [] }, @@ -424,7 +424,7 @@ "Package": "fansi", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fea074fb67fe4c25d47ad09087da847d", "Requirements": [] }, @@ -432,7 +432,7 @@ "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, @@ -440,7 +440,7 @@ "Package": "fs", "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "44594a07a42e5f91fac9f93fda6d0109", "Requirements": [] }, @@ -448,7 +448,7 @@ "Package": "generics", "Version": "0.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4d243a9c10b00589889fe32314ffd902", "Requirements": [] }, @@ -456,7 +456,7 @@ "Package": "gert", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "56f398846cd40937be6b435a66bd3f37", "Requirements": [ "askpass", @@ -471,7 +471,7 @@ "Package": "gh", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "05129b4387282404780d2f8593636388", "Requirements": [ "cli", @@ -485,7 +485,7 @@ "Package": "git2r", "Version": "0.28.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "f64fd34026f6025de71a4354800e6d79", "Requirements": [] }, @@ -493,7 +493,7 @@ "Package": "gitcreds", "Version": "0.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "f3aefccc1cc50de6338146b62f115de8", "Requirements": [] }, @@ -501,7 +501,7 @@ "Package": "glue", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6efd734b14c6471cfe443345f3e35e29", "Requirements": [] }, @@ -509,7 +509,7 @@ "Package": "highr", "Version": "0.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4dc5bb88961e347a0f4d8aad597cbfac", "Requirements": [] }, @@ -517,7 +517,7 @@ "Package": "hms", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bf552cdd96f5969873afdac7311c7d0d", "Requirements": [ "ellipsis", @@ -529,13 +529,14 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.1.1", + "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "af2c2531e55df5cf230c4b5444fc973c", + "Hash": "526c484233f42522278ab06fb185cb26", "Requirements": [ "base64enc", "digest", + "fastmap", "rlang" ] }, @@ -543,7 +544,7 @@ "Package": "htmlwidgets", "Version": "1.5.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6fdaa86d0700f8b3e92ee3c445a5a10d", "Requirements": [ "htmltools", @@ -555,7 +556,7 @@ "Package": "httpuv", "Version": "1.5.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b9d5d39be2150cf86538b8488334b8f8", "Requirements": [ "BH", @@ -569,7 +570,7 @@ "Package": "httr", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a525aba14184fec243f9eaec62fbed43", "Requirements": [ "R6", @@ -583,7 +584,7 @@ "Package": "hunspell", "Version": "3.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3987784c19192ad0f2261c456d936df1", "Requirements": [ "Rcpp", @@ -594,7 +595,7 @@ "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, @@ -602,7 +603,7 @@ "Package": "jquerylib", "Version": "0.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5ff50b36f7f0832f8421745af333e73c", "Requirements": [ "htmltools" @@ -612,7 +613,7 @@ "Package": "jsonlite", "Version": "1.7.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "98138e0994d41508c7a6b84a0600cfcb", "Requirements": [] }, @@ -620,7 +621,7 @@ "Package": "knitr", "Version": "1.31", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c3994c036d19fc22c5e2a209c8298bfb", "Requirements": [ "evaluate", @@ -635,7 +636,7 @@ "Package": "later", "Version": "1.1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d0a62b247165aabf397fded504660d8a", "Requirements": [ "BH", @@ -647,7 +648,7 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d908914ae53b04d4c0c0fd72ecc35370", "Requirements": [] }, @@ -655,7 +656,7 @@ "Package": "lifecycle", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3471fb65971f1a7b2d4ae7848cf2db8d", "Requirements": [ "glue", @@ -686,7 +687,7 @@ "Package": "lubridate", "Version": "1.7.10", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1ebfdc8a3cfe8fe19184f5481972b092", "Requirements": [ "Rcpp", @@ -697,7 +698,7 @@ "Package": "magrittr", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "41287f1ac7d28a92f0a286ed507928d3", "Requirements": [] }, @@ -705,7 +706,7 @@ "Package": "markdown", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "61e4a10781dd00d7d81dd06ca9b94e95", "Requirements": [ "mime", @@ -716,7 +717,7 @@ "Package": "memoise", "Version": "2.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a0bc51650201a56d00a4798523cc91b3", "Requirements": [ "cachem", @@ -727,7 +728,7 @@ "Package": "mime", "Version": "0.10", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "26fa77e707223e1ce042b2b5d09993dc", "Requirements": [] }, @@ -735,7 +736,7 @@ "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fec5f52652d60615fdb3957b3d74324a", "Requirements": [ "htmltools", @@ -746,7 +747,7 @@ "Package": "openssl", "Version": "1.4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a399e4773075fc2375b71f45fca186c4", "Requirements": [ "askpass" @@ -756,7 +757,7 @@ "Package": "pillar", "Version": "1.5.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "24622aa4a0d3de3463c34513edca99b2", "Requirements": [ "cli", @@ -773,7 +774,7 @@ "Package": "pkgbuild", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "725fcc30222d4d11ec68efb8ff11a9af", "Requirements": [ "R6", @@ -790,7 +791,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "01f28d4278f15c76cddbea05899c5d6f", "Requirements": [] }, @@ -827,7 +828,7 @@ "Package": "pkgload", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "cb57de933545960a86f03513e4bd2911", "Requirements": [ "cli", @@ -844,7 +845,7 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a555924add98c99d2f411e37e7d25e9f", "Requirements": [] }, @@ -852,7 +853,7 @@ "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", "Requirements": [] }, @@ -871,7 +872,7 @@ "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4ab2c43adb4d4699cf3690acd378d75d", "Requirements": [ "R6", @@ -885,7 +886,7 @@ "Package": "ps", "Version": "1.6.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "32620e2001c1dce1af49c49dccbb9420", "Requirements": [] }, @@ -893,7 +894,7 @@ "Package": "purrr", "Version": "0.3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "97def703420c8ab10d8f0e6c72101e02", "Requirements": [ "magrittr", @@ -904,7 +905,7 @@ "Package": "ragg", "Version": "1.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3f0ac98597bebdc31b747def3eb9b6ca", "Requirements": [ "systemfonts", @@ -915,7 +916,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, @@ -923,7 +924,7 @@ "Package": "rcmdcheck", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ed95895886dab6d2a584da45503555da", "Requirements": [ "R6", @@ -944,7 +945,7 @@ "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ "tibble" @@ -954,7 +955,7 @@ "Package": "remotes", "Version": "2.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "430a0908aee75b1fcba0e62857cab0ce", "Requirements": [] }, @@ -962,7 +963,7 @@ "Package": "rex", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "093584b944440c5cd07a696b3c8e0e4c", "Requirements": [ "lazyeval" @@ -980,7 +981,7 @@ "Package": "rmarkdown", "Version": "2.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "edbf4cb1aefae783fd8d3a008ae51943", "Requirements": [ "evaluate", @@ -1021,7 +1022,7 @@ "Package": "rprojroot", "Version": "2.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "249d8cd1e74a8f6a26194a91b47f21d1", "Requirements": [] }, @@ -1029,7 +1030,7 @@ "Package": "rstudioapi", "Version": "0.13", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "06c85365a03fdaf699966cc1d3cf53ea", "Requirements": [] }, @@ -1037,7 +1038,7 @@ "Package": "rversions", "Version": "2.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0ec41191f744d0f5afad8c6f35cc36e4", "Requirements": [ "curl", @@ -1048,7 +1049,7 @@ "Package": "sass", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3ef1adfe46b7b144b970d74ce33ab0d6", "Requirements": [ "R6", @@ -1063,7 +1064,7 @@ "Package": "sessioninfo", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "308013098befe37484df72c39cf90d6e", "Requirements": [ "cli", @@ -1074,7 +1075,7 @@ "Package": "shiny", "Version": "1.6.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6e3b6ae7fe02b5859e4bb277f218b8ae", "Requirements": [ "R6", @@ -1103,7 +1104,7 @@ "Package": "sourcetools", "Version": "0.1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "947e4e02a79effa5d512473e10f41797", "Requirements": [] }, @@ -1111,7 +1112,7 @@ "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", @@ -1153,7 +1154,7 @@ "Package": "stringi", "Version": "1.5.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a063ebea753c92910a4cca7b18bc1f05", "Requirements": [] }, @@ -1161,7 +1162,7 @@ "Package": "stringr", "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0759e6b6c0957edb1311028a49a35e76", "Requirements": [ "glue", @@ -1173,7 +1174,7 @@ "Package": "styler", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2ec6308547ffe73208cef3ef3766fc33", "Requirements": [ "R.cache", @@ -1193,7 +1194,7 @@ "Package": "sys", "Version": "3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b227d13e29222b4574486cfcbde077fa", "Requirements": [] }, @@ -1201,7 +1202,7 @@ "Package": "systemfonts", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6e899d7c097698d50ec87b1d8e65f246", "Requirements": [ "cpp11" @@ -1211,7 +1212,7 @@ "Package": "testthat", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "495e0434d9305716b6a87031570ce109", "Requirements": [ "R6", @@ -1239,7 +1240,7 @@ "Package": "textshaping", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fff317575e7191e2d077292309bed575", "Requirements": [ "cpp11", @@ -1250,7 +1251,7 @@ "Package": "tibble", "Version": "3.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4d894a114dbd4ecafeda5074e7c538e6", "Requirements": [ "ellipsis", @@ -1267,7 +1268,7 @@ "Package": "tidyr", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "450d7dfaedde58e28586b854eeece4fa", "Requirements": [ "cpp11", @@ -1287,7 +1288,7 @@ "Package": "tidyselect", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6ea435c354e8448819627cf686f66e0a", "Requirements": [ "ellipsis", @@ -1301,7 +1302,7 @@ "Package": "tinytex", "Version": "0.31", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "25b572f764f3c19fef9aac33b5724f3d", "Requirements": [ "xfun" @@ -1311,7 +1312,7 @@ "Package": "usethis", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "360e904f9e623286e1a0c6ca0a98c5f6", "Requirements": [ "cli", @@ -1339,7 +1340,7 @@ "Package": "utf8", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7", "Requirements": [] }, @@ -1347,7 +1348,7 @@ "Package": "vctrs", "Version": "0.3.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5540dc30a203a43a1ce5dc6a89532b3b", "Requirements": [ "ellipsis", @@ -1359,7 +1360,7 @@ "Package": "waldo", "Version": "0.2.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "20c45f1d511a3f730b7b469f4d11e104", "Requirements": [ "cli", @@ -1375,7 +1376,7 @@ "Package": "whisker", "Version": "0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ca970b96d894e90397ed20637a0c1bbe", "Requirements": [] }, @@ -1391,7 +1392,7 @@ "Package": "xfun", "Version": "0.22", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "eab2f8ba53809c321813e72ecbbd19ba", "Requirements": [] }, @@ -1407,7 +1408,7 @@ "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "45e4bf3c46476896e821fc0a408fb4fc", "Requirements": [] }, @@ -1415,7 +1416,7 @@ "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" @@ -1425,7 +1426,7 @@ "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, @@ -1433,7 +1434,7 @@ "Package": "yaml", "Version": "2.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2826c5d9efb0a88f657c7a679c7106db", "Requirements": [] }, @@ -1441,7 +1442,7 @@ "Package": "zip", "Version": "2.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3bc8405c637d988801ec5ea88372d0c2", "Requirements": [] } diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index f14c1f46..19f2bf92 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -7,8 +7,8 @@ "URL": "https://cloud.r-project.org" }, { - "Name": "MRAN", - "URL": "https://cran.microsoft.com/snapshot/2021-03-31" + "Name": "RSPM", + "URL": "https://packagemanager.posit.co/cran/2021-03-31" } ] }, @@ -17,7 +17,7 @@ "Package": "BH", "Version": "1.75.0-0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e4c04affc2cac20c8fec18385cd14691", "Requirements": [] }, @@ -25,7 +25,7 @@ "Package": "DT", "Version": "0.17", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0", "Requirements": [ "crosstalk", @@ -40,7 +40,7 @@ "Package": "R.cache", "Version": "0.14.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1ca02d43e1a4d49e616bd23bb39b17e6", "Requirements": [ "R.methodsS3", @@ -53,7 +53,7 @@ "Package": "R.methodsS3", "Version": "1.8.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4bf6453323755202d5909697b6f7c109", "Requirements": [] }, @@ -61,7 +61,7 @@ "Package": "R.oo", "Version": "1.24.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5709328352717e2f0a9c012be8a97554", "Requirements": [ "R.methodsS3" @@ -71,7 +71,7 @@ "Package": "R.utils", "Version": "2.10.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a9e316277ff12a43997266f2f6567780", "Requirements": [ "R.methodsS3", @@ -82,7 +82,7 @@ "Package": "R6", "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b203113193e70978a696b2809525649d", "Requirements": [] }, @@ -90,7 +90,7 @@ "Package": "Rcpp", "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "dbb5e436998a7eba5a9d682060533338", "Requirements": [] }, @@ -98,7 +98,7 @@ "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e8a22846fff485f0be3770c2da758713", "Requirements": [ "sys" @@ -108,7 +108,7 @@ "Package": "assertthat", "Version": "0.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "50c838a310445e954bc13f26f26a6ecf", "Requirements": [] }, @@ -116,7 +116,7 @@ "Package": "backports", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "644043219fc24e190c2f620c1a380a69", "Requirements": [] }, @@ -124,7 +124,7 @@ "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, @@ -132,7 +132,7 @@ "Package": "brew", "Version": "1.0-6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "92a5f887f9ae3035ac7afde22ba73ee9", "Requirements": [] }, @@ -140,7 +140,7 @@ "Package": "brio", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "36758510e65a457efeefa50e1e7f0576", "Requirements": [] }, @@ -148,7 +148,7 @@ "Package": "bslib", "Version": "0.2.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4830a372b241d78ed6f53731ee3023ac", "Requirements": [ "digest", @@ -164,7 +164,7 @@ "Package": "cachem", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2703a46dcabfb902f10060b2bca9f708", "Requirements": [ "fastmap", @@ -194,7 +194,7 @@ "Package": "clipr", "Version": "0.7.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7", "Requirements": [] }, @@ -210,7 +210,7 @@ "Package": "commonmark", "Version": "1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0f22be39ec1d141fd03683c06f3a6e67", "Requirements": [] }, @@ -218,7 +218,7 @@ "Package": "covr", "Version": "3.5.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6d80a9fc3c0c8473153b54fa54719dfd", "Requirements": [ "crayon", @@ -234,7 +234,7 @@ "Package": "cpp11", "Version": "0.2.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "730eebcc741a5c36761f7d4d0f5e37b8", "Requirements": [] }, @@ -242,7 +242,7 @@ "Package": "crayon", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e75525c55c70e5f4f78c9960a4b402e9", "Requirements": [] }, @@ -250,7 +250,7 @@ "Package": "credentials", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a96728288c75a814c900af9da84387be", "Requirements": [ "askpass", @@ -264,7 +264,7 @@ "Package": "crosstalk", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2b06f9e415a62b6762e4b8098d2aecbc", "Requirements": [ "R6", @@ -277,7 +277,7 @@ "Package": "curl", "Version": "4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2b7d10581cc730804e9ed178c8374bd6", "Requirements": [] }, @@ -285,7 +285,7 @@ "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "53cbed70a2f7472d48fb6aef08442f25", "Requirements": [ "callr", @@ -311,7 +311,7 @@ "Package": "devtools", "Version": "2.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "415656f50722f5b6e6bcf80855ce11b9", "Requirements": [ "DT", @@ -341,7 +341,7 @@ "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9ddedef46959baad2080047a1b0117fe", "Requirements": [ "tibble" @@ -351,7 +351,7 @@ "Package": "diffobj", "Version": "0.3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "feb5b7455eba422a2c110bb89852e6a3", "Requirements": [ "crayon" @@ -361,7 +361,7 @@ "Package": "digest", "Version": "0.6.27", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a0cbe758a531d054b537d16dff4d58a1", "Requirements": [] }, @@ -387,7 +387,7 @@ "Package": "dplyr", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68", "Requirements": [ "R6", @@ -406,7 +406,7 @@ "Package": "ellipsis", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a", "Requirements": [ "rlang" @@ -416,7 +416,7 @@ "Package": "evaluate", "Version": "0.14", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ec8ca05cffcc70569eaaad8469d2a3a7", "Requirements": [] }, @@ -424,7 +424,7 @@ "Package": "fansi", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fea074fb67fe4c25d47ad09087da847d", "Requirements": [] }, @@ -432,7 +432,7 @@ "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, @@ -440,7 +440,7 @@ "Package": "fs", "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "44594a07a42e5f91fac9f93fda6d0109", "Requirements": [] }, @@ -448,7 +448,7 @@ "Package": "generics", "Version": "0.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4d243a9c10b00589889fe32314ffd902", "Requirements": [] }, @@ -456,7 +456,7 @@ "Package": "gert", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "56f398846cd40937be6b435a66bd3f37", "Requirements": [ "askpass", @@ -471,7 +471,7 @@ "Package": "gh", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "05129b4387282404780d2f8593636388", "Requirements": [ "cli", @@ -485,7 +485,7 @@ "Package": "git2r", "Version": "0.28.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "f64fd34026f6025de71a4354800e6d79", "Requirements": [] }, @@ -493,7 +493,7 @@ "Package": "gitcreds", "Version": "0.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "f3aefccc1cc50de6338146b62f115de8", "Requirements": [] }, @@ -501,7 +501,7 @@ "Package": "glue", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6efd734b14c6471cfe443345f3e35e29", "Requirements": [] }, @@ -509,7 +509,7 @@ "Package": "highr", "Version": "0.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4dc5bb88961e347a0f4d8aad597cbfac", "Requirements": [] }, @@ -517,7 +517,7 @@ "Package": "hms", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bf552cdd96f5969873afdac7311c7d0d", "Requirements": [ "ellipsis", @@ -529,13 +529,14 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.1.1", + "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "af2c2531e55df5cf230c4b5444fc973c", + "Hash": "526c484233f42522278ab06fb185cb26", "Requirements": [ "base64enc", "digest", + "fastmap", "rlang" ] }, @@ -543,7 +544,7 @@ "Package": "htmlwidgets", "Version": "1.5.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6fdaa86d0700f8b3e92ee3c445a5a10d", "Requirements": [ "htmltools", @@ -555,7 +556,7 @@ "Package": "httpuv", "Version": "1.5.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b9d5d39be2150cf86538b8488334b8f8", "Requirements": [ "BH", @@ -569,7 +570,7 @@ "Package": "httr", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a525aba14184fec243f9eaec62fbed43", "Requirements": [ "R6", @@ -583,7 +584,7 @@ "Package": "hunspell", "Version": "3.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3987784c19192ad0f2261c456d936df1", "Requirements": [ "Rcpp", @@ -594,7 +595,7 @@ "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, @@ -602,7 +603,7 @@ "Package": "jquerylib", "Version": "0.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5ff50b36f7f0832f8421745af333e73c", "Requirements": [ "htmltools" @@ -612,7 +613,7 @@ "Package": "jsonlite", "Version": "1.7.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "98138e0994d41508c7a6b84a0600cfcb", "Requirements": [] }, @@ -620,7 +621,7 @@ "Package": "knitr", "Version": "1.31", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c3994c036d19fc22c5e2a209c8298bfb", "Requirements": [ "evaluate", @@ -635,7 +636,7 @@ "Package": "later", "Version": "1.1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d0a62b247165aabf397fded504660d8a", "Requirements": [ "BH", @@ -647,7 +648,7 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d908914ae53b04d4c0c0fd72ecc35370", "Requirements": [] }, @@ -655,7 +656,7 @@ "Package": "lifecycle", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3471fb65971f1a7b2d4ae7848cf2db8d", "Requirements": [ "glue", @@ -686,7 +687,7 @@ "Package": "lubridate", "Version": "1.7.10", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1ebfdc8a3cfe8fe19184f5481972b092", "Requirements": [ "Rcpp", @@ -697,7 +698,7 @@ "Package": "magrittr", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "41287f1ac7d28a92f0a286ed507928d3", "Requirements": [] }, @@ -705,7 +706,7 @@ "Package": "markdown", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "61e4a10781dd00d7d81dd06ca9b94e95", "Requirements": [ "mime", @@ -716,7 +717,7 @@ "Package": "memoise", "Version": "2.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a0bc51650201a56d00a4798523cc91b3", "Requirements": [ "cachem", @@ -727,7 +728,7 @@ "Package": "mime", "Version": "0.10", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "26fa77e707223e1ce042b2b5d09993dc", "Requirements": [] }, @@ -735,7 +736,7 @@ "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fec5f52652d60615fdb3957b3d74324a", "Requirements": [ "htmltools", @@ -746,7 +747,7 @@ "Package": "openssl", "Version": "1.4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a399e4773075fc2375b71f45fca186c4", "Requirements": [ "askpass" @@ -756,7 +757,7 @@ "Package": "pillar", "Version": "1.5.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "24622aa4a0d3de3463c34513edca99b2", "Requirements": [ "cli", @@ -773,7 +774,7 @@ "Package": "pkgbuild", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "725fcc30222d4d11ec68efb8ff11a9af", "Requirements": [ "R6", @@ -790,7 +791,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "01f28d4278f15c76cddbea05899c5d6f", "Requirements": [] }, @@ -827,7 +828,7 @@ "Package": "pkgload", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "cb57de933545960a86f03513e4bd2911", "Requirements": [ "cli", @@ -844,7 +845,7 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a555924add98c99d2f411e37e7d25e9f", "Requirements": [] }, @@ -852,7 +853,7 @@ "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", "Requirements": [] }, @@ -871,7 +872,7 @@ "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4ab2c43adb4d4699cf3690acd378d75d", "Requirements": [ "R6", @@ -885,7 +886,7 @@ "Package": "ps", "Version": "1.6.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "32620e2001c1dce1af49c49dccbb9420", "Requirements": [] }, @@ -893,7 +894,7 @@ "Package": "purrr", "Version": "0.3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "97def703420c8ab10d8f0e6c72101e02", "Requirements": [ "magrittr", @@ -904,7 +905,7 @@ "Package": "ragg", "Version": "1.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3f0ac98597bebdc31b747def3eb9b6ca", "Requirements": [ "systemfonts", @@ -915,7 +916,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, @@ -923,7 +924,7 @@ "Package": "rcmdcheck", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ed95895886dab6d2a584da45503555da", "Requirements": [ "R6", @@ -944,7 +945,7 @@ "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ "tibble" @@ -954,7 +955,7 @@ "Package": "remotes", "Version": "2.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "430a0908aee75b1fcba0e62857cab0ce", "Requirements": [] }, @@ -962,7 +963,7 @@ "Package": "rex", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "093584b944440c5cd07a696b3c8e0e4c", "Requirements": [ "lazyeval" @@ -980,7 +981,7 @@ "Package": "rmarkdown", "Version": "2.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "edbf4cb1aefae783fd8d3a008ae51943", "Requirements": [ "evaluate", @@ -1021,7 +1022,7 @@ "Package": "rprojroot", "Version": "2.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "249d8cd1e74a8f6a26194a91b47f21d1", "Requirements": [] }, @@ -1029,7 +1030,7 @@ "Package": "rstudioapi", "Version": "0.13", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "06c85365a03fdaf699966cc1d3cf53ea", "Requirements": [] }, @@ -1037,7 +1038,7 @@ "Package": "rversions", "Version": "2.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0ec41191f744d0f5afad8c6f35cc36e4", "Requirements": [ "curl", @@ -1048,7 +1049,7 @@ "Package": "sass", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3ef1adfe46b7b144b970d74ce33ab0d6", "Requirements": [ "R6", @@ -1063,7 +1064,7 @@ "Package": "sessioninfo", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "308013098befe37484df72c39cf90d6e", "Requirements": [ "cli", @@ -1074,7 +1075,7 @@ "Package": "shiny", "Version": "1.6.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6e3b6ae7fe02b5859e4bb277f218b8ae", "Requirements": [ "R6", @@ -1103,7 +1104,7 @@ "Package": "sourcetools", "Version": "0.1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "947e4e02a79effa5d512473e10f41797", "Requirements": [] }, @@ -1111,7 +1112,7 @@ "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", @@ -1153,7 +1154,7 @@ "Package": "stringi", "Version": "1.5.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a063ebea753c92910a4cca7b18bc1f05", "Requirements": [] }, @@ -1161,7 +1162,7 @@ "Package": "stringr", "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0759e6b6c0957edb1311028a49a35e76", "Requirements": [ "glue", @@ -1173,7 +1174,7 @@ "Package": "styler", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2ec6308547ffe73208cef3ef3766fc33", "Requirements": [ "R.cache", @@ -1193,7 +1194,7 @@ "Package": "sys", "Version": "3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b227d13e29222b4574486cfcbde077fa", "Requirements": [] }, @@ -1201,7 +1202,7 @@ "Package": "systemfonts", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6e899d7c097698d50ec87b1d8e65f246", "Requirements": [ "cpp11" @@ -1211,7 +1212,7 @@ "Package": "testthat", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "495e0434d9305716b6a87031570ce109", "Requirements": [ "R6", @@ -1239,7 +1240,7 @@ "Package": "textshaping", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fff317575e7191e2d077292309bed575", "Requirements": [ "cpp11", @@ -1250,7 +1251,7 @@ "Package": "tibble", "Version": "3.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4d894a114dbd4ecafeda5074e7c538e6", "Requirements": [ "ellipsis", @@ -1267,7 +1268,7 @@ "Package": "tidyr", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "450d7dfaedde58e28586b854eeece4fa", "Requirements": [ "cpp11", @@ -1287,7 +1288,7 @@ "Package": "tidyselect", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6ea435c354e8448819627cf686f66e0a", "Requirements": [ "ellipsis", @@ -1301,7 +1302,7 @@ "Package": "tinytex", "Version": "0.31", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "25b572f764f3c19fef9aac33b5724f3d", "Requirements": [ "xfun" @@ -1311,7 +1312,7 @@ "Package": "usethis", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "360e904f9e623286e1a0c6ca0a98c5f6", "Requirements": [ "cli", @@ -1339,7 +1340,7 @@ "Package": "utf8", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7", "Requirements": [] }, @@ -1347,7 +1348,7 @@ "Package": "vctrs", "Version": "0.3.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5540dc30a203a43a1ce5dc6a89532b3b", "Requirements": [ "ellipsis", @@ -1359,7 +1360,7 @@ "Package": "waldo", "Version": "0.2.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "20c45f1d511a3f730b7b469f4d11e104", "Requirements": [ "cli", @@ -1375,7 +1376,7 @@ "Package": "whisker", "Version": "0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ca970b96d894e90397ed20637a0c1bbe", "Requirements": [] }, @@ -1391,7 +1392,7 @@ "Package": "xfun", "Version": "0.22", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "eab2f8ba53809c321813e72ecbbd19ba", "Requirements": [] }, @@ -1407,7 +1408,7 @@ "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "45e4bf3c46476896e821fc0a408fb4fc", "Requirements": [] }, @@ -1415,7 +1416,7 @@ "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" @@ -1425,7 +1426,7 @@ "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, @@ -1433,7 +1434,7 @@ "Package": "yaml", "Version": "2.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2826c5d9efb0a88f657c7a679c7106db", "Requirements": [] }, @@ -1441,7 +1442,7 @@ "Package": "zip", "Version": "2.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3bc8405c637d988801ec5ea88372d0c2", "Requirements": [] } diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 0de19238..49034e33 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -7,8 +7,8 @@ "URL": "https://cloud.r-project.org" }, { - "Name": "MRAN", - "URL": "https://cran.microsoft.com/snapshot/2022-03-10" + "Name": "RSPM", + "URL": "https://packagemanager.posit.co/cran/2022-03-10" } ] }, @@ -17,7 +17,7 @@ "Package": "DT", "Version": "0.21", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "45fa28dbf288cd606e13ca35d3d72437", "Requirements": [ "crosstalk", @@ -33,7 +33,7 @@ "Package": "R.cache", "Version": "0.15.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e92a8ea8388c47c82ed8aa435ed3be50", "Requirements": [ "R.methodsS3", @@ -46,7 +46,7 @@ "Package": "R.methodsS3", "Version": "1.8.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4bf6453323755202d5909697b6f7c109", "Requirements": [] }, @@ -54,7 +54,7 @@ "Package": "R.oo", "Version": "1.24.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5709328352717e2f0a9c012be8a97554", "Requirements": [ "R.methodsS3" @@ -64,7 +64,7 @@ "Package": "R.utils", "Version": "2.11.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a7ecb8e60815c7a18648e84cd121b23a", "Requirements": [ "R.methodsS3", @@ -75,7 +75,7 @@ "Package": "R6", "Version": "2.5.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "470851b6d5d0ac559e9d01bb352b4021", "Requirements": [] }, @@ -83,7 +83,7 @@ "Package": "Rcpp", "Version": "1.0.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "22b546dd7e337f6c0c58a39983a496bc", "Requirements": [] }, @@ -91,7 +91,7 @@ "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e8a22846fff485f0be3770c2da758713", "Requirements": [ "sys" @@ -109,7 +109,7 @@ "Package": "backports", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c39fbec8a30d23e721980b8afb31984c", "Requirements": [] }, @@ -117,7 +117,7 @@ "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, @@ -125,7 +125,7 @@ "Package": "brew", "Version": "1.0-7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "38875ea52350ff4b4c03849fc69736c8", "Requirements": [] }, @@ -133,7 +133,7 @@ "Package": "brio", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "976cf154dfb043c012d87cddd8bca363", "Requirements": [] }, @@ -141,7 +141,7 @@ "Package": "bslib", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "56ae7e1987b340186a8a5a157c2ec358", "Requirements": [ "htmltools", @@ -155,7 +155,7 @@ "Package": "cachem", "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "648c5b3d71e6a37e3043617489a0a0e9", "Requirements": [ "fastmap", @@ -185,7 +185,7 @@ "Package": "clipr", "Version": "0.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", "Requirements": [] }, @@ -201,7 +201,7 @@ "Package": "commonmark", "Version": "1.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2ba81b120c1655ab696c935ef33ea716", "Requirements": [] }, @@ -209,7 +209,7 @@ "Package": "covr", "Version": "3.5.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6d80a9fc3c0c8473153b54fa54719dfd", "Requirements": [ "crayon", @@ -225,7 +225,7 @@ "Package": "cpp11", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fa53ce256cd280f468c080a58ea5ba8c", "Requirements": [] }, @@ -233,7 +233,7 @@ "Package": "crayon", "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "741c2e098e98afe3dc26a7b0e5489f4e", "Requirements": [] }, @@ -241,7 +241,7 @@ "Package": "credentials", "Version": "1.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "93762d0a34d78e6a025efdbfb5c6bb41", "Requirements": [ "askpass", @@ -255,7 +255,7 @@ "Package": "crosstalk", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6aa54f69598c32177e920eb3402e8293", "Requirements": [ "R6", @@ -268,7 +268,7 @@ "Package": "curl", "Version": "4.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "022c42d49c28e95d69ca60446dbabf88", "Requirements": [] }, @@ -276,7 +276,7 @@ "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "53cbed70a2f7472d48fb6aef08442f25", "Requirements": [ "callr", @@ -302,7 +302,7 @@ "Package": "devtools", "Version": "2.4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5", "Requirements": [ "callr", @@ -331,7 +331,7 @@ "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9ddedef46959baad2080047a1b0117fe", "Requirements": [ "tibble" @@ -341,7 +341,7 @@ "Package": "diffobj", "Version": "0.3.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8", "Requirements": [ "crayon" @@ -351,7 +351,7 @@ "Package": "digest", "Version": "0.6.29", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "cf6b206a045a684728c3267ef7596190", "Requirements": [] }, @@ -359,7 +359,7 @@ "Package": "downlit", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ba63dc9ab5a31f3209892437e40c5f60", "Requirements": [ "brio", @@ -377,7 +377,7 @@ "Package": "dplyr", "Version": "1.0.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ef47665e64228a17609d6df877bf86f2", "Requirements": [ "R6", @@ -396,7 +396,7 @@ "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", "Requirements": [ "rlang" @@ -406,7 +406,7 @@ "Package": "evaluate", "Version": "0.15", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "699a7a93d08c962d9f8950b2d7a227f1", "Requirements": [] }, @@ -414,7 +414,7 @@ "Package": "fansi", "Version": "1.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "f28149c2d7a1342a834b314e95e67260", "Requirements": [] }, @@ -422,7 +422,7 @@ "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, @@ -430,7 +430,7 @@ "Package": "fontawesome", "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "55624ed409e46c5f358b2c060be87f67", "Requirements": [ "htmltools", @@ -441,7 +441,7 @@ "Package": "fs", "Version": "1.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7c89603d81793f0d5486d91ab1fc6f1d", "Requirements": [] }, @@ -449,7 +449,7 @@ "Package": "generics", "Version": "0.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "177475892cf4a55865868527654a7741", "Requirements": [] }, @@ -457,7 +457,7 @@ "Package": "gert", "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "8fddce7cbd59467106266a6e93e253b4", "Requirements": [ "askpass", @@ -472,7 +472,7 @@ "Package": "gh", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "38c2580abbda249bd6afeec00d14f531", "Requirements": [ "cli", @@ -486,7 +486,7 @@ "Package": "git2r", "Version": "0.29.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b114135c4749076bd5ef74a5827b6f62", "Requirements": [] }, @@ -494,7 +494,7 @@ "Package": "gitcreds", "Version": "0.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "f3aefccc1cc50de6338146b62f115de8", "Requirements": [] }, @@ -502,7 +502,7 @@ "Package": "glue", "Version": "1.6.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", "Requirements": [] }, @@ -510,7 +510,7 @@ "Package": "highr", "Version": "0.9", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "8eb36c8125038e648e5d111c0d7b2ed4", "Requirements": [ "xfun" @@ -520,7 +520,7 @@ "Package": "hms", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca", "Requirements": [ "ellipsis", @@ -534,7 +534,7 @@ "Package": "htmltools", "Version": "0.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "526c484233f42522278ab06fb185cb26", "Requirements": [ "base64enc", @@ -547,7 +547,7 @@ "Package": "htmlwidgets", "Version": "1.5.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb", "Requirements": [ "htmltools", @@ -559,7 +559,7 @@ "Package": "httpuv", "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "97fe71f0a4a1c9890e6c2128afa04bc0", "Requirements": [ "R6", @@ -572,7 +572,7 @@ "Package": "httr", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a525aba14184fec243f9eaec62fbed43", "Requirements": [ "R6", @@ -586,7 +586,7 @@ "Package": "hunspell", "Version": "3.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3987784c19192ad0f2261c456d936df1", "Requirements": [ "Rcpp", @@ -597,7 +597,7 @@ "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, @@ -605,7 +605,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5aab57a3bd297eee1c1d862735972182", "Requirements": [ "htmltools" @@ -615,7 +615,7 @@ "Package": "jsonlite", "Version": "1.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d07e729b27b372429d42d24d503613a0", "Requirements": [] }, @@ -623,7 +623,7 @@ "Package": "knitr", "Version": "1.37", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a4ec675eb332a33fe7b7fe26f70e1f98", "Requirements": [ "evaluate", @@ -637,7 +637,7 @@ "Package": "later", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e", "Requirements": [ "Rcpp", @@ -648,7 +648,7 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d908914ae53b04d4c0c0fd72ecc35370", "Requirements": [] }, @@ -656,7 +656,7 @@ "Package": "lifecycle", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a6b6d352e3ed897373ab19d8395c98d0", "Requirements": [ "glue", @@ -687,7 +687,7 @@ "Package": "lubridate", "Version": "1.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a", "Requirements": [ "cpp11", @@ -698,7 +698,7 @@ "Package": "magrittr", "Version": "2.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "cdc87ecd81934679d1557633d8e1fe51", "Requirements": [] }, @@ -706,7 +706,7 @@ "Package": "memoise", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c", "Requirements": [ "cachem", @@ -717,7 +717,7 @@ "Package": "mime", "Version": "0.12", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "18e9c28c1d3ca1560ce30658b22ce104", "Requirements": [] }, @@ -725,7 +725,7 @@ "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fec5f52652d60615fdb3957b3d74324a", "Requirements": [ "htmltools", @@ -736,7 +736,7 @@ "Package": "openssl", "Version": "2.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "cf4329aac12c2c44089974559c18e446", "Requirements": [ "askpass" @@ -746,7 +746,7 @@ "Package": "pillar", "Version": "1.7.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e", "Requirements": [ "cli", @@ -764,7 +764,7 @@ "Package": "pkgbuild", "Version": "1.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "66d2adfed274daf81ccfe77d974c3b9b", "Requirements": [ "R6", @@ -781,7 +781,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "01f28d4278f15c76cddbea05899c5d6f", "Requirements": [] }, @@ -818,7 +818,7 @@ "Package": "pkgload", "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7533cd805940821bf23eaf3c8d4c1735", "Requirements": [ "cli", @@ -834,7 +834,7 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a555924add98c99d2f411e37e7d25e9f", "Requirements": [] }, @@ -842,7 +842,7 @@ "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", "Requirements": [] }, @@ -861,7 +861,7 @@ "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4ab2c43adb4d4699cf3690acd378d75d", "Requirements": [ "R6", @@ -875,7 +875,7 @@ "Package": "ps", "Version": "1.6.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "32620e2001c1dce1af49c49dccbb9420", "Requirements": [] }, @@ -883,7 +883,7 @@ "Package": "purrr", "Version": "0.3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "97def703420c8ab10d8f0e6c72101e02", "Requirements": [ "magrittr", @@ -894,7 +894,7 @@ "Package": "ragg", "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "14932bb6f2739c771ca4ceaba6b4248e", "Requirements": [ "systemfonts", @@ -905,7 +905,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, @@ -913,7 +913,7 @@ "Package": "rcmdcheck", "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4", "Requirements": [ "R6", @@ -934,7 +934,7 @@ "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ "tibble" @@ -944,7 +944,7 @@ "Package": "remotes", "Version": "2.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "227045be9aee47e6dda9bb38ac870d67", "Requirements": [] }, @@ -952,7 +952,7 @@ "Package": "rex", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ae34cd56890607370665bee5bd17812f", "Requirements": [ "lazyeval" @@ -970,7 +970,7 @@ "Package": "rmarkdown", "Version": "2.12", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "354da5088ddfdffb73c11cc952885d88", "Requirements": [ "bslib", @@ -1013,7 +1013,7 @@ "Package": "rprojroot", "Version": "2.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "249d8cd1e74a8f6a26194a91b47f21d1", "Requirements": [] }, @@ -1021,7 +1021,7 @@ "Package": "rstudioapi", "Version": "0.13", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "06c85365a03fdaf699966cc1d3cf53ea", "Requirements": [] }, @@ -1029,7 +1029,7 @@ "Package": "rversions", "Version": "2.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "f88fab00907b312f8b23ec13e2d437cb", "Requirements": [ "curl", @@ -1040,7 +1040,7 @@ "Package": "sass", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "50cf822feb64bb3977bda0b7091be623", "Requirements": [ "R6", @@ -1054,7 +1054,7 @@ "Package": "sessioninfo", "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", "Requirements": [ "cli" @@ -1064,7 +1064,7 @@ "Package": "shiny", "Version": "1.7.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "00344c227c7bd0ab5d78052c5d736c44", "Requirements": [ "R6", @@ -1093,7 +1093,7 @@ "Package": "sourcetools", "Version": "0.1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "947e4e02a79effa5d512473e10f41797", "Requirements": [] }, @@ -1101,7 +1101,7 @@ "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", @@ -1143,7 +1143,7 @@ "Package": "stringi", "Version": "1.7.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bba431031d30789535745a9627ac9271", "Requirements": [] }, @@ -1151,7 +1151,7 @@ "Package": "stringr", "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0759e6b6c0957edb1311028a49a35e76", "Requirements": [ "glue", @@ -1163,7 +1163,7 @@ "Package": "styler", "Version": "1.6.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d9e85c794c5a723aabed32a49926186a", "Requirements": [ "R.cache", @@ -1184,7 +1184,7 @@ "Package": "sys", "Version": "3.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b227d13e29222b4574486cfcbde077fa", "Requirements": [] }, @@ -1192,7 +1192,7 @@ "Package": "systemfonts", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "90b28393209827327de889f49935140a", "Requirements": [ "cpp11" @@ -1202,7 +1202,7 @@ "Package": "testthat", "Version": "3.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "32454e5780e8dbe31e4b61b13d8918fe", "Requirements": [ "R6", @@ -1230,7 +1230,7 @@ "Package": "textshaping", "Version": "0.3.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1ab6223d3670fac7143202cb6a2d43d5", "Requirements": [ "cpp11", @@ -1241,7 +1241,7 @@ "Package": "tibble", "Version": "3.1.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "8a8f02d1934dfd6431c671361510dd0b", "Requirements": [ "ellipsis", @@ -1258,7 +1258,7 @@ "Package": "tidyr", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d8b95b7fee945d7da6888cf7eb71a49c", "Requirements": [ "cpp11", @@ -1278,7 +1278,7 @@ "Package": "tidyselect", "Version": "1.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "17f6da8cfd7002760a859915ce7eef8f", "Requirements": [ "ellipsis", @@ -1292,7 +1292,7 @@ "Package": "tinytex", "Version": "0.37", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a80abeb527a977e4bef21873d29222dd", "Requirements": [ "xfun" @@ -1302,7 +1302,7 @@ "Package": "usethis", "Version": "2.1.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c499f488e6dd7718accffaee5bc5a79b", "Requirements": [ "cli", @@ -1330,7 +1330,7 @@ "Package": "utf8", "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c9c462b759a5cc844ae25b5942654d13", "Requirements": [] }, @@ -1338,7 +1338,7 @@ "Package": "vctrs", "Version": "0.3.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ecf749a1b39ea72bd9b51b76292261f1", "Requirements": [ "ellipsis", @@ -1350,7 +1350,7 @@ "Package": "waldo", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ad8cfff5694ac5b3c354f8f2044bd976", "Requirements": [ "cli", @@ -1366,7 +1366,7 @@ "Package": "whisker", "Version": "0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ca970b96d894e90397ed20637a0c1bbe", "Requirements": [] }, @@ -1374,7 +1374,7 @@ "Package": "withr", "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c0e49a9760983e81e55cdd9be92e7182", "Requirements": [] }, @@ -1382,7 +1382,7 @@ "Package": "xfun", "Version": "0.30", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e83f48136b041845e50a6658feffb197", "Requirements": [] }, @@ -1390,7 +1390,7 @@ "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "40682ed6a969ea5abfd351eb67833adc", "Requirements": [] }, @@ -1398,7 +1398,7 @@ "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "45e4bf3c46476896e821fc0a408fb4fc", "Requirements": [] }, @@ -1406,7 +1406,7 @@ "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" @@ -1416,7 +1416,7 @@ "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, @@ -1424,7 +1424,7 @@ "Package": "yaml", "Version": "2.3.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "458bb38374d73bf83b1bb85e353da200", "Requirements": [] }, @@ -1432,7 +1432,7 @@ "Package": "zip", "Version": "2.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c7eef2996ac270a18c2715c997a727c5", "Requirements": [] } diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index e91579fa..ae9feba5 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -7,8 +7,8 @@ "URL": "https://cloud.r-project.org" }, { - "Name": "MRAN", - "URL": "https://cran.microsoft.com/snapshot/2022-10-31" + "Name": "RSPM", + "URL": "https://packagemanager.posit.co/cran/2022-10-31" } ] }, @@ -17,7 +17,7 @@ "Package": "DT", "Version": "0.26", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c66a72c4d3499e14ae179ccb742e740a", "Requirements": [ "crosstalk", @@ -33,7 +33,7 @@ "Package": "R.cache", "Version": "0.16.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8", "Requirements": [ "R.methodsS3", @@ -46,7 +46,7 @@ "Package": "R.methodsS3", "Version": "1.8.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "278c286fd6e9e75d0c2e8f731ea445c8", "Requirements": [] }, @@ -54,7 +54,7 @@ "Package": "R.oo", "Version": "1.25.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a0900a114f4f0194cf4aa8cd4a700681", "Requirements": [ "R.methodsS3" @@ -64,7 +64,7 @@ "Package": "R.utils", "Version": "2.12.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1ed133420fcd2b93cf55a383b38fe27c", "Requirements": [ "R.methodsS3", @@ -75,7 +75,7 @@ "Package": "R6", "Version": "2.5.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "470851b6d5d0ac559e9d01bb352b4021", "Requirements": [] }, @@ -83,7 +83,7 @@ "Package": "Rcpp", "Version": "1.0.9", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e9c08b94391e9f3f97355841229124f2", "Requirements": [] }, @@ -91,7 +91,7 @@ "Package": "askpass", "Version": "1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e8a22846fff485f0be3770c2da758713", "Requirements": [ "sys" @@ -109,7 +109,7 @@ "Package": "backports", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c39fbec8a30d23e721980b8afb31984c", "Requirements": [] }, @@ -117,7 +117,7 @@ "Package": "base64enc", "Version": "0.1-3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, @@ -125,7 +125,7 @@ "Package": "brew", "Version": "1.0-8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d69a786e85775b126bddbee185ae6084", "Requirements": [] }, @@ -133,7 +133,7 @@ "Package": "brio", "Version": "1.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "976cf154dfb043c012d87cddd8bca363", "Requirements": [] }, @@ -141,7 +141,7 @@ "Package": "bslib", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "be5ee090716ce1671be6cd5d7c34d091", "Requirements": [ "cachem", @@ -157,7 +157,7 @@ "Package": "cachem", "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "648c5b3d71e6a37e3043617489a0a0e9", "Requirements": [ "fastmap", @@ -179,7 +179,7 @@ "Package": "cli", "Version": "3.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0d297d01734d2bcea40197bd4971a764", "Requirements": [] }, @@ -187,7 +187,7 @@ "Package": "clipr", "Version": "0.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", "Requirements": [] }, @@ -203,7 +203,7 @@ "Package": "commonmark", "Version": "1.8.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b6e3e947d1d7ebf3d2bdcea1bde63fe7", "Requirements": [] }, @@ -211,7 +211,7 @@ "Package": "covr", "Version": "3.6.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a861cee34fbb4b107a73dd414ef56724", "Requirements": [ "crayon", @@ -227,7 +227,7 @@ "Package": "cpp11", "Version": "0.4.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ed588261931ee3be2c700d22e94a29ab", "Requirements": [] }, @@ -235,7 +235,7 @@ "Package": "crayon", "Version": "1.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e8a1e41acf02548751f45c718d55aa6a", "Requirements": [] }, @@ -243,7 +243,7 @@ "Package": "credentials", "Version": "1.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "93762d0a34d78e6a025efdbfb5c6bb41", "Requirements": [ "askpass", @@ -257,7 +257,7 @@ "Package": "crosstalk", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6aa54f69598c32177e920eb3402e8293", "Requirements": [ "R6", @@ -270,7 +270,7 @@ "Package": "curl", "Version": "4.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0eb86baa62f06e8855258fa5a8048667", "Requirements": [] }, @@ -278,7 +278,7 @@ "Package": "cyclocomp", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "53cbed70a2f7472d48fb6aef08442f25", "Requirements": [ "callr", @@ -292,7 +292,7 @@ "Package": "desc", "Version": "1.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21", "Requirements": [ "R6", @@ -304,7 +304,7 @@ "Package": "devtools", "Version": "2.4.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ea5bc8b4a6a01e4f12d98b58329930bb", "Requirements": [ "cli", @@ -334,7 +334,7 @@ "Package": "diffdf", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9ddedef46959baad2080047a1b0117fe", "Requirements": [ "tibble" @@ -344,7 +344,7 @@ "Package": "diffobj", "Version": "0.3.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8", "Requirements": [ "crayon" @@ -354,7 +354,7 @@ "Package": "digest", "Version": "0.6.30", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bf1cd206a5d170d132ef75c7537b9bdb", "Requirements": [] }, @@ -362,7 +362,7 @@ "Package": "downlit", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "79bf3f66590752ffbba20f8d2da94c7c", "Requirements": [ "brio", @@ -381,7 +381,7 @@ "Package": "dplyr", "Version": "1.0.10", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "539412282059f7f0c07295723d23f987", "Requirements": [ "R6", @@ -400,7 +400,7 @@ "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", "Requirements": [ "rlang" @@ -410,7 +410,7 @@ "Package": "evaluate", "Version": "0.17", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9171b012a55a1ef53f1442b1d798a3b4", "Requirements": [] }, @@ -418,7 +418,7 @@ "Package": "fansi", "Version": "1.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "83a8afdbe71839506baa9f90eebad7ec", "Requirements": [] }, @@ -426,7 +426,7 @@ "Package": "fastmap", "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, @@ -434,7 +434,7 @@ "Package": "fontawesome", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c5a628c2570aa86a96cc6ef739d8bfda", "Requirements": [ "htmltools", @@ -445,7 +445,7 @@ "Package": "fs", "Version": "1.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7c89603d81793f0d5486d91ab1fc6f1d", "Requirements": [] }, @@ -453,7 +453,7 @@ "Package": "generics", "Version": "0.1.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "15e9634c0fcd294799e9b2e929ed1b86", "Requirements": [] }, @@ -461,7 +461,7 @@ "Package": "gert", "Version": "1.9.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9a091a6d2fb91e43afd4337e2dcef2e7", "Requirements": [ "askpass", @@ -476,7 +476,7 @@ "Package": "gh", "Version": "1.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b6a12054ee13dce0f6696c019c10e539", "Requirements": [ "cli", @@ -490,7 +490,7 @@ "Package": "git2r", "Version": "0.30.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e0c6a04a3e7b90e64213d09128f74f1b", "Requirements": [] }, @@ -498,7 +498,7 @@ "Package": "gitcreds", "Version": "0.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe", "Requirements": [] }, @@ -506,7 +506,7 @@ "Package": "glue", "Version": "1.6.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", "Requirements": [] }, @@ -514,7 +514,7 @@ "Package": "highr", "Version": "0.9", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "8eb36c8125038e648e5d111c0d7b2ed4", "Requirements": [ "xfun" @@ -524,7 +524,7 @@ "Package": "hms", "Version": "1.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "41100392191e1244b887878b533eea91", "Requirements": [ "ellipsis", @@ -538,7 +538,7 @@ "Package": "htmltools", "Version": "0.5.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6496090a9e00f8354b811d1a2d47b566", "Requirements": [ "base64enc", @@ -551,7 +551,7 @@ "Package": "htmlwidgets", "Version": "1.5.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb", "Requirements": [ "htmltools", @@ -563,7 +563,7 @@ "Package": "httpuv", "Version": "1.6.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fd090e236ae2dc0f0cdf33a9ec83afb6", "Requirements": [ "R6", @@ -576,7 +576,7 @@ "Package": "httr", "Version": "1.4.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "57557fac46471f0dbbf44705cc6a5c8c", "Requirements": [ "R6", @@ -590,7 +590,7 @@ "Package": "hunspell", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "656219b6f3f605499d7cdbe208656639", "Requirements": [ "Rcpp", @@ -601,7 +601,7 @@ "Package": "ini", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, @@ -609,7 +609,7 @@ "Package": "jquerylib", "Version": "0.1.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5aab57a3bd297eee1c1d862735972182", "Requirements": [ "htmltools" @@ -619,7 +619,7 @@ "Package": "jsonlite", "Version": "1.8.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "8b1bd0be62956f2a6b91ce84fac79a45", "Requirements": [] }, @@ -627,7 +627,7 @@ "Package": "knitr", "Version": "1.40", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "caea8b0f899a0b1738444b9bc47067e7", "Requirements": [ "evaluate", @@ -641,7 +641,7 @@ "Package": "later", "Version": "1.3.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e", "Requirements": [ "Rcpp", @@ -652,7 +652,7 @@ "Package": "lazyeval", "Version": "0.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "d908914ae53b04d4c0c0fd72ecc35370", "Requirements": [] }, @@ -660,7 +660,7 @@ "Package": "lifecycle", "Version": "1.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "001cecbeac1cff9301bdc3775ee46a86", "Requirements": [ "cli", @@ -672,7 +672,7 @@ "Package": "lintr", "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b21ebd652d940f099915221f3328ab7b", "Requirements": [ "backports", @@ -692,7 +692,7 @@ "Package": "lubridate", "Version": "1.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a", "Requirements": [ "cpp11", @@ -703,7 +703,7 @@ "Package": "magrittr", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7ce2733a9826b3aeb1775d56fd305472", "Requirements": [] }, @@ -711,7 +711,7 @@ "Package": "memoise", "Version": "2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c", "Requirements": [ "cachem", @@ -722,7 +722,7 @@ "Package": "mime", "Version": "0.12", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "18e9c28c1d3ca1560ce30658b22ce104", "Requirements": [] }, @@ -730,7 +730,7 @@ "Package": "miniUI", "Version": "0.1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fec5f52652d60615fdb3957b3d74324a", "Requirements": [ "htmltools", @@ -741,7 +741,7 @@ "Package": "openssl", "Version": "2.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e86c5ffeb8474a9e03d75f5d2919683e", "Requirements": [ "askpass" @@ -751,7 +751,7 @@ "Package": "pillar", "Version": "1.8.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "f2316df30902c81729ae9de95ad5a608", "Requirements": [ "cli", @@ -767,7 +767,7 @@ "Package": "pkgbuild", "Version": "1.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "66d2adfed274daf81ccfe77d974c3b9b", "Requirements": [ "R6", @@ -784,7 +784,7 @@ "Package": "pkgconfig", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "01f28d4278f15c76cddbea05899c5d6f", "Requirements": [] }, @@ -821,7 +821,7 @@ "Package": "pkgload", "Version": "1.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3c0918b1792c75de2e640d1d8d12dead", "Requirements": [ "cli", @@ -838,7 +838,7 @@ "Package": "praise", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a555924add98c99d2f411e37e7d25e9f", "Requirements": [] }, @@ -846,7 +846,7 @@ "Package": "prettyunits", "Version": "1.1.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", "Requirements": [] }, @@ -854,7 +854,7 @@ "Package": "processx", "Version": "3.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a33ee2d9bf07564efb888ad98410da84", "Requirements": [ "R6", @@ -865,7 +865,7 @@ "Package": "profvis", "Version": "0.3.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e9d21e79848e02e524bea6f5bd53e7e4", "Requirements": [ "htmlwidgets", @@ -876,7 +876,7 @@ "Package": "promises", "Version": "1.2.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4ab2c43adb4d4699cf3690acd378d75d", "Requirements": [ "R6", @@ -890,7 +890,7 @@ "Package": "ps", "Version": "1.7.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "68dd03d98a5efd1eb3012436de45ba83", "Requirements": [] }, @@ -898,7 +898,7 @@ "Package": "purrr", "Version": "0.3.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "54842a2443c76267152eface28d9e90a", "Requirements": [ "magrittr", @@ -909,7 +909,7 @@ "Package": "ragg", "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "0db17bd5a1d4abfec76487b6f5dd957b", "Requirements": [ "systemfonts", @@ -920,7 +920,7 @@ "Package": "rappdirs", "Version": "0.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, @@ -928,7 +928,7 @@ "Package": "rcmdcheck", "Version": "1.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4", "Requirements": [ "R6", @@ -949,7 +949,7 @@ "Package": "rematch2", "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "76c9e04c712a05848ae7a23d2f170a40", "Requirements": [ "tibble" @@ -959,7 +959,7 @@ "Package": "remotes", "Version": "2.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "227045be9aee47e6dda9bb38ac870d67", "Requirements": [] }, @@ -967,7 +967,7 @@ "Package": "rex", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ae34cd56890607370665bee5bd17812f", "Requirements": [ "lazyeval" @@ -977,7 +977,7 @@ "Package": "rlang", "Version": "1.0.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", "Requirements": [] }, @@ -985,7 +985,7 @@ "Package": "rmarkdown", "Version": "2.17", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "e97c8be593e010f93520e8215c0f9189", "Requirements": [ "bslib", @@ -1004,7 +1004,7 @@ "Package": "roxygen2", "Version": "7.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "da1f278262e563c835345872f2fef537", "Requirements": [ "R6", @@ -1028,7 +1028,7 @@ "Package": "rprojroot", "Version": "2.0.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1de7ab598047a87bba48434ba35d497d", "Requirements": [] }, @@ -1036,7 +1036,7 @@ "Package": "rstudioapi", "Version": "0.14", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "690bd2acc42a9166ce34845884459320", "Requirements": [] }, @@ -1044,7 +1044,7 @@ "Package": "rversions", "Version": "2.1.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a9881dfed103e83f9de151dc17002cd1", "Requirements": [ "curl", @@ -1055,7 +1055,7 @@ "Package": "sass", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1b191143d7d3444d504277843f3a95fe", "Requirements": [ "R6", @@ -1069,7 +1069,7 @@ "Package": "sessioninfo", "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", "Requirements": [ "cli" @@ -1079,7 +1079,7 @@ "Package": "shiny", "Version": "1.7.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "fe12df67fdb3b1142325cc54f100cc06", "Requirements": [ "R6", @@ -1108,7 +1108,7 @@ "Package": "sourcetools", "Version": "0.1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "947e4e02a79effa5d512473e10f41797", "Requirements": [] }, @@ -1116,7 +1116,7 @@ "Package": "spelling", "Version": "2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", @@ -1158,7 +1158,7 @@ "Package": "stringi", "Version": "1.7.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a68b980681bcbc84c7a67003fa796bfb", "Requirements": [] }, @@ -1166,7 +1166,7 @@ "Package": "stringr", "Version": "1.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a66ad12140cd34d4f9dfcc19e84fc2a5", "Requirements": [ "glue", @@ -1178,7 +1178,7 @@ "Package": "styler", "Version": "1.8.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c855e70eb69b3dd8883660b7110e0c44", "Requirements": [ "R.cache", @@ -1195,7 +1195,7 @@ "Package": "sys", "Version": "3.4.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "34c16f1ef796057bfa06d3f4ff818a5d", "Requirements": [] }, @@ -1203,7 +1203,7 @@ "Package": "systemfonts", "Version": "1.0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "90b28393209827327de889f49935140a", "Requirements": [ "cpp11" @@ -1213,7 +1213,7 @@ "Package": "testthat", "Version": "3.1.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6e3c4843f1ed0d3d90f35498671a001c", "Requirements": [ "R6", @@ -1240,7 +1240,7 @@ "Package": "textshaping", "Version": "0.3.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "1ab6223d3670fac7143202cb6a2d43d5", "Requirements": [ "cpp11", @@ -1251,7 +1251,7 @@ "Package": "tibble", "Version": "3.1.8", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "56b6934ef0f8c68225949a8672fe1a8f", "Requirements": [ "fansi", @@ -1267,7 +1267,7 @@ "Package": "tidyr", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "cdb403db0de33ccd1b6f53b83736efa8", "Requirements": [ "cpp11", @@ -1287,7 +1287,7 @@ "Package": "tidyselect", "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "79540e5fcd9e0435af547d885f184fd5", "Requirements": [ "cli", @@ -1302,7 +1302,7 @@ "Package": "tinytex", "Version": "0.42", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "7629c6c1540835d5248e6e7df265fa74", "Requirements": [ "xfun" @@ -1312,7 +1312,7 @@ "Package": "urlchecker", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "409328b8e1253c8d729a7836fe7f7a16", "Requirements": [ "cli", @@ -1324,7 +1324,7 @@ "Package": "usethis", "Version": "2.1.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "a67a22c201832b12c036cc059f1d137d", "Requirements": [ "cli", @@ -1352,7 +1352,7 @@ "Package": "utf8", "Version": "1.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c9c462b759a5cc844ae25b5942654d13", "Requirements": [] }, @@ -1360,7 +1360,7 @@ "Package": "vctrs", "Version": "0.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "001fd6a5ebfff8316baf9fb2b5516dc9", "Requirements": [ "cli", @@ -1373,7 +1373,7 @@ "Package": "waldo", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "035fba89d0c86e2113120f93301b98ad", "Requirements": [ "cli", @@ -1389,7 +1389,7 @@ "Package": "whisker", "Version": "0.4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "ca970b96d894e90397ed20637a0c1bbe", "Requirements": [] }, @@ -1397,7 +1397,7 @@ "Package": "withr", "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c0e49a9760983e81e55cdd9be92e7182", "Requirements": [] }, @@ -1405,7 +1405,7 @@ "Package": "xfun", "Version": "0.34", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9eba2411b0b1f879797141bd24df7407", "Requirements": [] }, @@ -1413,7 +1413,7 @@ "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "40682ed6a969ea5abfd351eb67833adc", "Requirements": [] }, @@ -1421,7 +1421,7 @@ "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "45e4bf3c46476896e821fc0a408fb4fc", "Requirements": [] }, @@ -1429,7 +1429,7 @@ "Package": "xopen", "Version": "1.0.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ "processx" @@ -1439,7 +1439,7 @@ "Package": "xtable", "Version": "1.8-4", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", "Requirements": [] }, @@ -1447,7 +1447,7 @@ "Package": "yaml", "Version": "2.3.6", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "9b570515751dcbae610f29885e025b41", "Requirements": [] }, @@ -1455,7 +1455,7 @@ "Package": "zip", "Version": "2.2.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88", "Requirements": [] } From 3fa38589b363c5545e2739ec1cbff9d0d496dbf6 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 22 Feb 2023 09:29:21 +0000 Subject: [PATCH 016/100] renv update from pharmaverse/admiralci --- renv.lock | 39 ++++++++++++------------------------- renv/profiles/4.0/renv.lock | 39 ++++++++++++------------------------- renv/profiles/4.1/renv.lock | 12 ++++++------ 3 files changed, 30 insertions(+), 60 deletions(-) diff --git a/renv.lock b/renv.lock index 19f2bf92..f84948ba 100644 --- a/renv.lock +++ b/renv.lock @@ -146,16 +146,14 @@ }, "bslib": { "Package": "bslib", - "Version": "0.2.4", + "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "4830a372b241d78ed6f53731ee3023ac", + "Repository": "CRAN", + "Hash": "56ae7e1987b340186a8a5a157c2ec358", "Requirements": [ - "digest", "htmltools", "jquerylib", "jsonlite", - "magrittr", "rlang", "sass" ] @@ -619,14 +617,13 @@ }, "knitr": { "Package": "knitr", - "Version": "1.31", + "Version": "1.40", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c3994c036d19fc22c5e2a209c8298bfb", + "Repository": "CRAN", + "Hash": "caea8b0f899a0b1738444b9bc47067e7", "Requirements": [ "evaluate", "highr", - "markdown", "stringr", "xfun", "yaml" @@ -702,17 +699,6 @@ "Hash": "41287f1ac7d28a92f0a286ed507928d3", "Requirements": [] }, - "markdown": { - "Package": "markdown", - "Version": "1.1", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "61e4a10781dd00d7d81dd06ca9b94e95", - "Requirements": [ - "mime", - "xfun" - ] - }, "memoise": { "Package": "memoise", "Version": "2.0.0", @@ -1047,13 +1033,12 @@ }, "sass": { "Package": "sass", - "Version": "0.3.1", + "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3ef1adfe46b7b144b970d74ce33ab0d6", + "Repository": "CRAN", + "Hash": "50cf822feb64bb3977bda0b7091be623", "Requirements": [ "R6", - "digest", "fs", "htmltools", "rappdirs", @@ -1390,10 +1375,10 @@ }, "xfun": { "Package": "xfun", - "Version": "0.22", + "Version": "0.34", "Source": "Repository", - "Repository": "RSPM", - "Hash": "eab2f8ba53809c321813e72ecbbd19ba", + "Repository": "CRAN", + "Hash": "9eba2411b0b1f879797141bd24df7407", "Requirements": [] }, "xml2": { diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index 19f2bf92..f84948ba 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -146,16 +146,14 @@ }, "bslib": { "Package": "bslib", - "Version": "0.2.4", + "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "4830a372b241d78ed6f53731ee3023ac", + "Repository": "CRAN", + "Hash": "56ae7e1987b340186a8a5a157c2ec358", "Requirements": [ - "digest", "htmltools", "jquerylib", "jsonlite", - "magrittr", "rlang", "sass" ] @@ -619,14 +617,13 @@ }, "knitr": { "Package": "knitr", - "Version": "1.31", + "Version": "1.40", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c3994c036d19fc22c5e2a209c8298bfb", + "Repository": "CRAN", + "Hash": "caea8b0f899a0b1738444b9bc47067e7", "Requirements": [ "evaluate", "highr", - "markdown", "stringr", "xfun", "yaml" @@ -702,17 +699,6 @@ "Hash": "41287f1ac7d28a92f0a286ed507928d3", "Requirements": [] }, - "markdown": { - "Package": "markdown", - "Version": "1.1", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "61e4a10781dd00d7d81dd06ca9b94e95", - "Requirements": [ - "mime", - "xfun" - ] - }, "memoise": { "Package": "memoise", "Version": "2.0.0", @@ -1047,13 +1033,12 @@ }, "sass": { "Package": "sass", - "Version": "0.3.1", + "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "3ef1adfe46b7b144b970d74ce33ab0d6", + "Repository": "CRAN", + "Hash": "50cf822feb64bb3977bda0b7091be623", "Requirements": [ "R6", - "digest", "fs", "htmltools", "rappdirs", @@ -1390,10 +1375,10 @@ }, "xfun": { "Package": "xfun", - "Version": "0.22", + "Version": "0.34", "Source": "Repository", - "Repository": "RSPM", - "Hash": "eab2f8ba53809c321813e72ecbbd19ba", + "Repository": "CRAN", + "Hash": "9eba2411b0b1f879797141bd24df7407", "Requirements": [] }, "xml2": { diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 49034e33..6b4041ed 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -621,10 +621,10 @@ }, "knitr": { "Package": "knitr", - "Version": "1.37", + "Version": "1.40", "Source": "Repository", - "Repository": "RSPM", - "Hash": "a4ec675eb332a33fe7b7fe26f70e1f98", + "Repository": "CRAN", + "Hash": "caea8b0f899a0b1738444b9bc47067e7", "Requirements": [ "evaluate", "highr", @@ -1380,10 +1380,10 @@ }, "xfun": { "Package": "xfun", - "Version": "0.30", + "Version": "0.34", "Source": "Repository", - "Repository": "RSPM", - "Hash": "e83f48136b041845e50a6658feffb197", + "Repository": "CRAN", + "Hash": "9eba2411b0b1f879797141bd24df7407", "Requirements": [] }, "xml2": { From 0aa48e8be078c0b61bf400eda866b998f3491a3d Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 22 Feb 2023 10:17:31 +0000 Subject: [PATCH 017/100] renv update from pharmaverse/admiralci --- renv.lock | 13 +++++-------- renv/profiles/4.0/renv.lock | 13 +++++-------- renv/profiles/4.1/renv.lock | 14 +++++--------- 3 files changed, 15 insertions(+), 25 deletions(-) diff --git a/renv.lock b/renv.lock index f84948ba..fa6cee31 100644 --- a/renv.lock +++ b/renv.lock @@ -1157,22 +1157,19 @@ }, "styler": { "Package": "styler", - "Version": "1.4.1", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "2ec6308547ffe73208cef3ef3766fc33", + "Repository": "CRAN", + "Hash": "c855e70eb69b3dd8883660b7110e0c44", "Requirements": [ "R.cache", - "backports", "cli", "magrittr", "purrr", - "rematch2", "rlang", "rprojroot", - "tibble", - "withr", - "xfun" + "vctrs", + "withr" ] }, "sys": { diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index f84948ba..fa6cee31 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -1157,22 +1157,19 @@ }, "styler": { "Package": "styler", - "Version": "1.4.1", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "2ec6308547ffe73208cef3ef3766fc33", + "Repository": "CRAN", + "Hash": "c855e70eb69b3dd8883660b7110e0c44", "Requirements": [ "R.cache", - "backports", "cli", "magrittr", "purrr", - "rematch2", "rlang", "rprojroot", - "tibble", - "withr", - "xfun" + "vctrs", + "withr" ] }, "sys": { diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 6b4041ed..2e7355df 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -1161,23 +1161,19 @@ }, "styler": { "Package": "styler", - "Version": "1.6.2", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "d9e85c794c5a723aabed32a49926186a", + "Repository": "CRAN", + "Hash": "c855e70eb69b3dd8883660b7110e0c44", "Requirements": [ "R.cache", - "backports", "cli", - "glue", "magrittr", "purrr", - "rematch2", "rlang", "rprojroot", - "tibble", - "withr", - "xfun" + "vctrs", + "withr" ] }, "sys": { From 3062108d712160e252433fee01ef06c037c2e0da Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 22 Feb 2023 11:46:30 +0000 Subject: [PATCH 018/100] renv update from pharmaverse/admiralci --- renv.lock | 20 ++++++++++---------- renv/profiles/4.0/renv.lock | 20 ++++++++++---------- renv/profiles/4.1/renv.lock | 8 ++++---- 3 files changed, 24 insertions(+), 24 deletions(-) diff --git a/renv.lock b/renv.lock index fa6cee31..10b5d185 100644 --- a/renv.lock +++ b/renv.lock @@ -38,10 +38,10 @@ }, "R.cache": { "Package": "R.cache", - "Version": "0.14.0", + "Version": "0.15.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1ca02d43e1a4d49e616bd23bb39b17e6", + "Repository": "CRAN", + "Hash": "e92a8ea8388c47c82ed8aa435ed3be50", "Requirements": [ "R.methodsS3", "R.oo", @@ -412,10 +412,10 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.14", + "Version": "0.15", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ec8ca05cffcc70569eaaad8469d2a3a7", + "Repository": "CRAN", + "Hash": "699a7a93d08c962d9f8950b2d7a227f1", "Requirements": [] }, "fansi": { @@ -1328,12 +1328,12 @@ }, "vctrs": { "Package": "vctrs", - "Version": "0.3.7", + "Version": "0.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "5540dc30a203a43a1ce5dc6a89532b3b", + "Repository": "CRAN", + "Hash": "8b54f22e2a58c4f275479c92ce041a57", "Requirements": [ - "ellipsis", + "cli", "glue", "rlang" ] diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index fa6cee31..10b5d185 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -38,10 +38,10 @@ }, "R.cache": { "Package": "R.cache", - "Version": "0.14.0", + "Version": "0.15.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "1ca02d43e1a4d49e616bd23bb39b17e6", + "Repository": "CRAN", + "Hash": "e92a8ea8388c47c82ed8aa435ed3be50", "Requirements": [ "R.methodsS3", "R.oo", @@ -412,10 +412,10 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.14", + "Version": "0.15", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ec8ca05cffcc70569eaaad8469d2a3a7", + "Repository": "CRAN", + "Hash": "699a7a93d08c962d9f8950b2d7a227f1", "Requirements": [] }, "fansi": { @@ -1328,12 +1328,12 @@ }, "vctrs": { "Package": "vctrs", - "Version": "0.3.7", + "Version": "0.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "5540dc30a203a43a1ce5dc6a89532b3b", + "Repository": "CRAN", + "Hash": "8b54f22e2a58c4f275479c92ce041a57", "Requirements": [ - "ellipsis", + "cli", "glue", "rlang" ] diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 2e7355df..a0028252 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -1332,12 +1332,12 @@ }, "vctrs": { "Package": "vctrs", - "Version": "0.3.8", + "Version": "0.4.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ecf749a1b39ea72bd9b51b76292261f1", + "Repository": "CRAN", + "Hash": "8b54f22e2a58c4f275479c92ce041a57", "Requirements": [ - "ellipsis", + "cli", "glue", "rlang" ] From 658008e16711fc9c5a279107911f5e211f8a5488 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Fri, 10 Mar 2023 14:56:49 +0100 Subject: [PATCH 019/100] 241_allow_expressions: accept expressions by default in assert_varval_list() --- R/assertions.R | 2 +- man/assert_varval_list.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/assertions.R b/R/assertions.R index 4cdd9a37..f8ce0943 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -1200,7 +1200,7 @@ assert_param_does_not_exist <- function(dataset, param) { #' try(example_fun(exprs("AE", DTSEQ = AESEQ))) assert_varval_list <- function(arg, # nolint required_elements = NULL, - accept_expr = FALSE, + accept_expr = TRUE, accept_var = FALSE, optional = FALSE) { assert_logical_scalar(accept_expr) diff --git a/man/assert_varval_list.Rd b/man/assert_varval_list.Rd index 82461851..ba08f7d6 100644 --- a/man/assert_varval_list.Rd +++ b/man/assert_varval_list.Rd @@ -7,7 +7,7 @@ assert_varval_list( arg, required_elements = NULL, - accept_expr = FALSE, + accept_expr = TRUE, accept_var = FALSE, optional = FALSE ) From 476c79ff973c562a8869b8352686f15754a041e3 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Mon, 13 Mar 2023 17:44:17 +0100 Subject: [PATCH 020/100] 241_allow_expressions: fix expr_c() --- R/quo.R | 12 +++++++- tests/testthat/test-quo.R | 61 +++++++++++++++++++++++++-------------- 2 files changed, 50 insertions(+), 23 deletions(-) diff --git a/R/quo.R b/R/quo.R index 17055e66..b5d5506e 100644 --- a/R/quo.R +++ b/R/quo.R @@ -40,7 +40,17 @@ quo_c <- function(...) { #' #' @export expr_c <- function(...) { - inputs <- unlist(list(...), recursive = TRUE) + # transform single expression into list of expression + inputs <- map( + list(...), + function(x) + if (typeof(x) != "list") { + list(x) + } else { + x + } + ) + inputs <- purrr::flatten(inputs) stopifnot(all(map_lgl(inputs, is_expression))) is_null <- map_lgl(inputs, is.null) inputs[!is_null] diff --git a/tests/testthat/test-quo.R b/tests/testthat/test-quo.R index 3811feb3..56ca99bc 100644 --- a/tests/testthat/test-quo.R +++ b/tests/testthat/test-quo.R @@ -47,16 +47,33 @@ test_that("expr_c Test 4: concatenating and indexing expressions", { ) }) -## Test 5: returns error if non-expressions are input ---- -test_that("expr_c Test 5: returns error if non-expressions are input", { +## Test 5: concatenating named list of expressions ---- +test_that("expr_c Test 5: concatenating named list of expressions", { + expect_equal( + expected = exprs(PARAMCD = "DOSE", PARAMN = 1), + object = expr_c(exprs(PARAMCD = "DOSE", PARAMN = 1, NULL)) + ) +} +) + +## Test 6: concatenating list and single expression ---- +test_that("expr_c Test 6: concatenating list and single expression", { + expect_equal( + expected = exprs(PARAMCD, PARAM, AVAL), + object = expr_c(exprs(PARAMCD, PARAM), expr(AVAL)) + ) +}) + +## Test 7: returns error if non-expressions are input ---- +test_that("expr_c Test 7: returns error if non-expressions are input", { expect_error( object = expr_c(expr(USUBJID), mean) ) }) # quo_not_missing ---- -## Test 6: issues deprecation warning ---- -test_that("quo_not_missing Test 6: issues deprecation warning", { +## Test 8: issues deprecation warning ---- +test_that("quo_not_missing Test 8: issues deprecation warning", { test_fun <- function(x) { x <- enquo(x) !isTRUE(quo_not_missing(x)) @@ -67,8 +84,8 @@ test_that("quo_not_missing Test 6: issues deprecation warning", { ) }) -## Test 7: `quo_not_missing` throws an Error if missing argument ---- -test_that("quo_not_missing Test 7: `quo_not_missing` throws an Error if missing argument", { +## Test 9: `quo_not_missing` throws an Error if missing argument ---- +test_that("quo_not_missing Test 9: `quo_not_missing` throws an Error if missing argument", { test_fun <- function(x) { x <- enquo(x) isTrue(quo_not_missing(x)) @@ -77,8 +94,8 @@ test_that("quo_not_missing Test 7: `quo_not_missing` throws an Error if missing }) # replace_values_by_names ---- -## Test 8: names of quosures replace value ---- -test_that("replace_values_by_names Test 8: names of quosures replace value", { +## Test 10: names of quosures replace value ---- +test_that("replace_values_by_names Test 10: names of quosures replace value", { z <- exprs(USUBJID, STUDYID) z_noname <- replace_values_by_names(z) @@ -105,8 +122,8 @@ test_that("replace_values_by_names Test 8: names of quosures replace value", { ) }) -## Test 9: warning if quosures argument is used ---- -test_that("replace_values_by_names Test 9: warning if quosures argument is used", { +## Test 11: warning if quosures argument is used ---- +test_that("replace_values_by_names Test 11: warning if quosures argument is used", { expect_warning( replace_values_by_names(quosures = rlang::quos(STUDYID, USUBJID)), class = "lifecycle_warning_deprecated" @@ -114,8 +131,8 @@ test_that("replace_values_by_names Test 9: warning if quosures argument is used" }) # replace_symbol_in_quo ---- -## Test 10: error if called ---- -test_that("replace_symbol_in_quo Test 10: error if called", { +## Test 12: error if called ---- +test_that("replace_symbol_in_quo Test 12: error if called", { expect_error( replace_symbol_in_quo(), class = "lifecycle_error_deprecated" @@ -123,8 +140,8 @@ test_that("replace_symbol_in_quo Test 10: error if called", { }) # replace_symbol_in_expr ---- -## Test 11: symbol is replaced ---- -test_that("replace_symbol_in_expr Test 11: symbol is replaced", { +## Test 13: symbol is replaced ---- +test_that("replace_symbol_in_expr Test 13: symbol is replaced", { expect_equal( expected = expr(AVAL.join), object = replace_symbol_in_expr( @@ -135,8 +152,8 @@ test_that("replace_symbol_in_expr Test 11: symbol is replaced", { ) }) -## Test 12: partial match is not replaced ---- -test_that("replace_symbol_in_expr Test 12: partial match is not replaced", { +## Test 14: partial match is not replaced ---- +test_that("replace_symbol_in_expr Test 14: partial match is not replaced", { expect_equal( expected = expr(AVALC), object = replace_symbol_in_expr( @@ -147,8 +164,8 @@ test_that("replace_symbol_in_expr Test 12: partial match is not replaced", { ) }) -## Test 13: symbol in expression is replaced ---- -test_that("replace_symbol_in_expr Test 13: symbol in expression is replaced", { +## Test 15: symbol in expression is replaced ---- +test_that("replace_symbol_in_expr Test 15: symbol in expression is replaced", { expect_equal( expected = expr(desc(AVAL.join)), object = replace_symbol_in_expr( @@ -160,8 +177,8 @@ test_that("replace_symbol_in_expr Test 13: symbol in expression is replaced", { }) # add_suffix_to_vars ---- -## Test 14: with single variable ---- -test_that("add_suffix_to_vars Test 14: with single variable", { +## Test 16: with single variable ---- +test_that("add_suffix_to_vars Test 16: with single variable", { expect_equal( expected = exprs(ADT, desc(AVAL.join), AVALC), object = add_suffix_to_vars( @@ -172,8 +189,8 @@ test_that("add_suffix_to_vars Test 14: with single variable", { ) }) -## Test 15: with more than one variable ---- -test_that("add_suffix_to_vars Test 15: with more than one variable", { +## Test 17: with more than one variable ---- +test_that("add_suffix_to_vars Test 17: with more than one variable", { expect_equal( expected = exprs(ADT, desc(AVAL.join), AVALC.join), object = add_suffix_to_vars( From 0caa331cba138b637bfc865a0990fa0843a8a254 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Tue, 14 Mar 2023 13:23:39 +0100 Subject: [PATCH 021/100] 241_allow_expression: make set_values_to optional in process_set_values_to() --- R/process_set_values_to.R | 4 ++-- man/process_set_values_to.Rd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/process_set_values_to.R b/R/process_set_values_to.R index 9d703774..50921de9 100644 --- a/R/process_set_values_to.R +++ b/R/process_set_values_to.R @@ -56,10 +56,10 @@ #' ) #' ) process_set_values_to <- function(dataset, - set_values_to, + set_values_to = NULL, expected_types = NULL) { assert_data_frame(dataset) - assert_varval_list(set_values_to, accept_expr = TRUE) + assert_varval_list(set_values_to, optional = TRUE) assert_character_vector( expected_types, values = c("numeric", "character"), diff --git a/man/process_set_values_to.Rd b/man/process_set_values_to.Rd index 967d50b0..5ed3c567 100644 --- a/man/process_set_values_to.Rd +++ b/man/process_set_values_to.Rd @@ -4,7 +4,7 @@ \alias{process_set_values_to} \title{Process \code{set_values_to} Argument} \usage{ -process_set_values_to(dataset, set_values_to, expected_types = NULL) +process_set_values_to(dataset, set_values_to = NULL, expected_types = NULL) } \arguments{ \item{dataset}{Input dataset} From 7b9d269aee1d7af97ab4f41fed22a1ab75a461d3 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Tue, 14 Mar 2023 15:16:43 +0100 Subject: [PATCH 022/100] 241_allow_expressions: enable expressions for order --- R/assertions.R | 18 ++++++++++-------- man/assert_order_vars.Rd | 12 +++++++----- tests/testthat/test-assertions.R | 26 +++++++++++++++----------- 3 files changed, 32 insertions(+), 24 deletions(-) diff --git a/R/assertions.R b/R/assertions.R index f8ce0943..279bae19 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -533,7 +533,8 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) { #' Is an Argument a List of Order Variables? #' -#' Checks if an argument is a valid list of order variables created using `exprs()` +#' Checks if an argument is a valid list of order variables/expressions created +#' using `exprs()` #' #' @param arg A function argument to be checked #' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` @@ -541,8 +542,9 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) { #' #' #' @return -#' The function throws an error if `arg` is not a list of variables or `desc()` -#' calls created using `exprs()` and returns the input invisibly otherwise. +#' The function throws an error if `arg` is not a list of variables or +#' expressions created using `exprs()` and returns the input invisibly +#' otherwise. #' #' @export #' @@ -558,18 +560,18 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) { #' #' example_fun(exprs(USUBJID, PARAMCD, desc(AVISITN))) #' +#' example_fun(exprs(USUBJID, if_else(AVALC == "Y", 1, 0))) +#' #' try(example_fun(quos(USUBJID, PARAMCD))) #' #' try(example_fun(c("USUBJID", "PARAMCD", "VISIT"))) -#' -#' try(example_fun(exprs(USUBJID, toupper(PARAMCD), -AVAL))) assert_order_vars <- function(arg, optional = FALSE) { assert_logical_scalar(optional) default_err_msg <- paste( backquote(arg_name(substitute(arg))), - "must be a list of unquoted variable names or `desc()` calls,", - "e.g. `exprs(USUBJID, desc(VISITNUM))`" + "must be a list of unquoted variable names or expressions,", + "e.g. `exprs(USUBJID, desc(VISITNUM), -abs(AVAL))`" ) if (isTRUE(tryCatch(force(arg), error = function(e) TRUE))) { @@ -584,7 +586,7 @@ assert_order_vars <- function(arg, optional = FALSE) { abort(default_err_msg) } - if (isFALSE(is_order_vars(arg))) { + if (isFALSE(is_call(arg))) { abort(default_err_msg) } diff --git a/man/assert_order_vars.Rd b/man/assert_order_vars.Rd index b24e9794..551b8f24 100644 --- a/man/assert_order_vars.Rd +++ b/man/assert_order_vars.Rd @@ -13,11 +13,13 @@ assert_order_vars(arg, optional = FALSE) is \code{NULL} then an error is thrown} } \value{ -The function throws an error if \code{arg} is not a list of variables or \code{desc()} -calls created using \code{exprs()} and returns the input invisibly otherwise. +The function throws an error if \code{arg} is not a list of variables or +expressions created using \code{exprs()} and returns the input invisibly +otherwise. } \description{ -Checks if an argument is a valid list of order variables created using \code{exprs()} +Checks if an argument is a valid list of order variables/expressions created +using \code{exprs()} } \examples{ library(dplyr, warn.conflicts = FALSE) @@ -29,11 +31,11 @@ example_fun <- function(by_vars) { example_fun(exprs(USUBJID, PARAMCD, desc(AVISITN))) +example_fun(exprs(USUBJID, if_else(AVALC == "Y", 1, 0))) + try(example_fun(quos(USUBJID, PARAMCD))) try(example_fun(c("USUBJID", "PARAMCD", "VISIT"))) - -try(example_fun(exprs(USUBJID, toupper(PARAMCD), -AVAL))) } \seealso{ Checks for valid input and returns warning or errors messages: diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index 740ecd0b..3472f900 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -525,26 +525,30 @@ test_that("assert_vars Test 31: error if some elements of `arg` are not unquoted # assert_order_vars ---- ## Test 32: error if `arg` is not a list variable names or `desc()` ---- test_that("assert_order_vars Test 32: error if `arg` is not a list variable names or `desc()`", { - example_fun <- function(arg) { - assert_order_vars(arg) - } - expect_error( - example_fun(TRUE) + assert_order_vars(arg <- TRUE), + regexp = + paste( + "`arg` must be a list of unquoted variable names or expressions,", + "e.g. `exprs(USUBJID, desc(VISITNUM), -abs(AVAL))`" + ), + fixed = TRUE ) expect_error( - example_fun(1) + assert_order_vars(arg <- 1), + regexp = + paste( + "`arg` must be a list of unquoted variable names or expressions,", + "e.g. `exprs(USUBJID, desc(VISITNUM), -abs(AVAL))`" + ), + fixed = TRUE ) }) ## Test 33: no error if `arg` is NULL and optional is TRUE ---- test_that("assert_order_vars Test 33: no error if `arg` is NULL and optional is TRUE", { - example_fun <- function(arg) { - assert_order_vars(arg, optional = TRUE) - } - expect_invisible( - example_fun(NULL) + assert_order_vars(arg <- NULL, optional = TRUE) ) }) From 6a55dd38978871327371275037d0034dae2dced3 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Tue, 14 Mar 2023 15:25:55 +0100 Subject: [PATCH 023/100] 241_allow_expressions: enable expressions for order --- R/assertions.R | 2 +- tests/testthat/test-assertions.R | 217 ++++++++++++++++--------------- 2 files changed, 113 insertions(+), 106 deletions(-) diff --git a/R/assertions.R b/R/assertions.R index 279bae19..8c3ccc42 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -586,7 +586,7 @@ assert_order_vars <- function(arg, optional = FALSE) { abort(default_err_msg) } - if (isFALSE(is_call(arg))) { + if (isTRUE(is_call(arg))) { abort(default_err_msg) } diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index 3472f900..ad234530 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -84,7 +84,7 @@ test_that("assert_data_frame Test 5: assert_data_frame extract_vars() works as i expect_invisible(example_fun(input, order = exprs(SEQ))) }) -## Test 6: assert_data_frame throws not throw error if extract_vars() has NULL input ---- +## Test 6: assert_data_frame throws error if extract_vars() has NULL input ---- test_that("assert_data_frame Test 6: assert_data_frame throws error if extract_vars() has NULL input", { # nolint input <- tibble::tribble( ~STUDYID, ~USUBJID, ~SEQ, @@ -545,16 +545,23 @@ test_that("assert_order_vars Test 32: error if `arg` is not a list variable name ) }) -## Test 33: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_order_vars Test 33: no error if `arg` is NULL and optional is TRUE", { +## Test 33: no error if valid argument ---- +test_that("assert_order_vars Test 33: no error if valid argument", { + expect_invisible( + assert_order_vars(arg <- exprs(USUBJID, desc(PARAMCD), -abs(AVAL))) + ) +}) + +## Test 34: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_order_vars Test 34: no error if `arg` is NULL and optional is TRUE", { expect_invisible( assert_order_vars(arg <- NULL, optional = TRUE) ) }) # assert_integer_scalar ---- -## Test 34: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_integer_scalar Test 34: no error if `arg` is NULL and optional is TRUE", { +## Test 35: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_integer_scalar Test 35: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_integer_scalar(arg, optional = TRUE) } @@ -564,8 +571,8 @@ test_that("assert_integer_scalar Test 34: no error if `arg` is NULL and optional ) }) -## Test 35: error if chosen subset not in subsets ---- -test_that("assert_integer_scalar Test 35: error if chosen subset not in subsets", { +## Test 36: error if chosen subset not in subsets ---- +test_that("assert_integer_scalar Test 36: error if chosen subset not in subsets", { example_fun <- function(arg) { assert_integer_scalar(arg, subset = "infinity") } @@ -575,8 +582,8 @@ test_that("assert_integer_scalar Test 35: error if chosen subset not in subsets" ) }) -## Test 36: no error if `arg` is in selected subset ---- -test_that("assert_integer_scalar Test 36: no error if `arg` is in selected subset", { +## Test 37: no error if `arg` is in selected subset ---- +test_that("assert_integer_scalar Test 37: no error if `arg` is in selected subset", { example_fun <- function(arg) { assert_integer_scalar(arg, subset = "positive") } @@ -586,8 +593,8 @@ test_that("assert_integer_scalar Test 36: no error if `arg` is in selected subse ) }) -## Test 37: error if `arg` is not an integer scalar ---- -test_that("assert_integer_scalar Test 37: error if `arg` is not an integer scalar", { +## Test 38: error if `arg` is not an integer scalar ---- +test_that("assert_integer_scalar Test 38: error if `arg` is not an integer scalar", { example_fun <- function(arg) { assert_integer_scalar(arg) } @@ -601,8 +608,8 @@ test_that("assert_integer_scalar Test 37: error if `arg` is not an integer scala }) # assert_numeric_vector ---- -## Test 38: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_numeric_vector Test 38: no error if `arg` is NULL and optional is TRUE", { +## Test 39: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_numeric_vector Test 39: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_numeric_vector(arg, optional = TRUE) } @@ -613,8 +620,8 @@ test_that("assert_numeric_vector Test 38: no error if `arg` is NULL and optional }) # assert_integer_scalar ---- -## Test 39: error if `arg` is not an integer scalar ---- -test_that("assert_integer_scalar Test 39: error if `arg` is not an integer scalar", { +## Test 40: error if `arg` is not an integer scalar ---- +test_that("assert_integer_scalar Test 40: error if `arg` is not an integer scalar", { example_fun <- function(arg) { assert_numeric_vector(arg) } @@ -627,8 +634,8 @@ test_that("assert_integer_scalar Test 39: error if `arg` is not an integer scala }) # assert_s3_class ---- -## Test 40: error if `arg` is not an object of a specific class S3 ---- -test_that("assert_s3_class Test 40: error if `arg` is not an object of a specific class S3", { +## Test 41: error if `arg` is not an object of a specific class S3 ---- +test_that("assert_s3_class Test 41: error if `arg` is not an object of a specific class S3", { example_fun <- function(arg) { assert_s3_class(arg, "factor") } @@ -636,8 +643,8 @@ test_that("assert_s3_class Test 40: error if `arg` is not an object of a specifi expect_error(example_fun("test")) }) -## Test 41: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_s3_class Test 41: no error if `arg` is NULL and optional is TRUE", { +## Test 42: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_s3_class Test 42: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_s3_class(arg, class = "factor", optional = TRUE) } @@ -647,8 +654,8 @@ test_that("assert_s3_class Test 41: no error if `arg` is NULL and optional is TR ) }) -## Test 42: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_s3_class Test 42: error if `arg` is NULL and optional is FALSE", { +## Test 43: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_s3_class Test 43: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_s3_class(arg, class = "factor", optional = FALSE) } @@ -660,8 +667,8 @@ test_that("assert_s3_class Test 42: error if `arg` is NULL and optional is FALSE ) }) -## Test 43: no error if `arg` is an object of a specific class S3 ---- -test_that("assert_s3_class Test 43: no error if `arg` is an object of a specific class S3", { +## Test 44: no error if `arg` is an object of a specific class S3 ---- +test_that("assert_s3_class Test 44: no error if `arg` is an object of a specific class S3", { example_fun <- function(arg) { assert_s3_class(arg, "factor") } @@ -670,8 +677,8 @@ test_that("assert_s3_class Test 43: no error if `arg` is an object of a specific }) # assert_list_of ---- -## Test 44: error if `arg` is not a list of specific class S3 objects ---- -test_that("assert_list_of Test 44: error if `arg` is not a list of specific class S3 objects", { +## Test 45: error if `arg` is not a list of specific class S3 objects ---- +test_that("assert_list_of Test 45: error if `arg` is not a list of specific class S3 objects", { example_fun <- function(arg) { assert_list_of(arg, "factor") } @@ -679,8 +686,8 @@ test_that("assert_list_of Test 44: error if `arg` is not a list of specific clas expect_error(example_fun(list("test"))) }) -## Test 45: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_list_of Test 45: no error if `arg` is NULL and optional is TRUE", { +## Test 46: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_list_of Test 46: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_list_of(arg, class = "factor", optional = TRUE) } @@ -690,8 +697,8 @@ test_that("assert_list_of Test 45: no error if `arg` is NULL and optional is TRU ) }) -## Test 46: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_list_of Test 46: error if `arg` is NULL and optional is FALSE", { +## Test 47: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_list_of Test 47: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_list_of(arg, class = "factor", optional = FALSE) } @@ -703,8 +710,8 @@ test_that("assert_list_of Test 46: error if `arg` is NULL and optional is FALSE" ) }) -## Test 47: no error if `arg` is a list of specific class S3 objects ---- -test_that("assert_list_of Test 47: no error if `arg` is a list of specific class S3 objects", { +## Test 48: no error if `arg` is a list of specific class S3 objects ---- +test_that("assert_list_of Test 48: no error if `arg` is a list of specific class S3 objects", { example_fun <- function(arg) { assert_list_of(arg, "factor") } @@ -716,8 +723,8 @@ test_that("assert_list_of Test 47: no error if `arg` is a list of specific class ) }) -## Test 48: error if `arg` is not a named list (no elements named) ---- -test_that("assert_list_of Test 48: error if `arg` is not a named list (no elements named)", { +## Test 49: error if `arg` is not a named list (no elements named) ---- +test_that("assert_list_of Test 49: error if `arg` is not a named list (no elements named)", { expect_error( assert_list_of(mylist <- list(1, 2, 3), class = "numeric", named = TRUE), paste( @@ -728,8 +735,8 @@ test_that("assert_list_of Test 48: error if `arg` is not a named list (no elemen ) }) -## Test 49: error if `arg` is not a named list (some elements named) ---- -test_that("assert_list_of Test 49: error if `arg` is not a named list (some elements named)", { +## Test 50: error if `arg` is not a named list (some elements named) ---- +test_that("assert_list_of Test 50: error if `arg` is not a named list (some elements named)", { expect_error( assert_list_of(mylist <- list(1, 2, 3, d = 4), class = "numeric", named = TRUE), paste( @@ -740,16 +747,16 @@ test_that("assert_list_of Test 49: error if `arg` is not a named list (some elem ) }) -## Test 50: no error if `arg` is a named list ---- -test_that("assert_list_of Test 50: no error if `arg` is a named list", { +## Test 51: no error if `arg` is a named list ---- +test_that("assert_list_of Test 51: no error if `arg` is a named list", { expect_invisible( assert_list_of(mylist <- list(a = 1, b = 2, c = 3), class = "numeric", named = TRUE) ) }) # assert_named_exprs ---- -## Test 51: error if `arg` is not a named list of expressions ---- -test_that("assert_named_exprs Test 51: error if `arg` is not a named list of expressions", { +## Test 52: error if `arg` is not a named list of expressions ---- +test_that("assert_named_exprs Test 52: error if `arg` is not a named list of expressions", { example_fun <- function(arg) { assert_named_exprs(arg) } @@ -763,8 +770,8 @@ test_that("assert_named_exprs Test 51: error if `arg` is not a named list of exp expect_error(example_fun(arg)) }) -## Test 52: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_named_exprs Test 52: no error if `arg` is NULL and optional is TRUE", { +## Test 53: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_named_exprs Test 53: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_named_exprs(arg, optional = TRUE) } @@ -774,8 +781,8 @@ test_that("assert_named_exprs Test 52: no error if `arg` is NULL and optional is ) }) -## Test 53: no error if `arg` is a named list of expressions ---- -test_that("assert_named_exprs Test 53: no error if `arg` is a named list of expressions", { +## Test 54: no error if `arg` is a named list of expressions ---- +test_that("assert_named_exprs Test 54: no error if `arg` is a named list of expressions", { example_fun <- function(arg) { assert_named_exprs(arg) } @@ -788,8 +795,8 @@ test_that("assert_named_exprs Test 53: no error if `arg` is a named list of expr }) # assert_function ---- -## Test 54: error if `arg` is not a function ---- -test_that("assert_function Test 54: error if `arg` is not a function", { +## Test 55: error if `arg` is not a function ---- +test_that("assert_function Test 55: error if `arg` is not a function", { example_fun <- function(arg) { assert_function(arg) } @@ -798,8 +805,8 @@ test_that("assert_function Test 54: error if `arg` is not a function", { expect_error(example_fun()) }) -## Test 55: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_function Test 55: no error if `arg` is NULL and optional is TRUE", { +## Test 56: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_function Test 56: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_function(arg, optional = TRUE) } @@ -809,8 +816,8 @@ test_that("assert_function Test 55: no error if `arg` is NULL and optional is TR ) }) -## Test 56: no error if `arg` is a function with all parameters defined ---- -test_that("assert_function Test 56: no error if `arg` is a function with all parameters defined", { +## Test 57: no error if `arg` is a function with all parameters defined ---- +test_that("assert_function Test 57: no error if `arg` is a function with all parameters defined", { example_fun <- function(arg) { assert_function(arg, params = c("x")) } @@ -818,8 +825,8 @@ test_that("assert_function Test 56: no error if `arg` is a function with all par expect_invisible(example_fun(mean)) }) -## Test 57: error if `params` is missing with no default ---- -test_that("assert_function Test 57: error if `params` is missing with no default", { +## Test 58: error if `params` is missing with no default ---- +test_that("assert_function Test 58: error if `params` is missing with no default", { example_fun <- function(arg) { assert_function(arg, params = c("x")) } @@ -835,8 +842,8 @@ test_that("assert_function Test 57: error if `params` is missing with no defau # assert_function_param ---- -## Test 58: no error if `arg` is a parameter of a function ---- -test_that("assert_function_param Test 58: no error if `arg` is a parameter of a function", { +## Test 59: no error if `arg` is a parameter of a function ---- +test_that("assert_function_param Test 59: no error if `arg` is a parameter of a function", { hello <- function(name) { print(sprintf("Hello %s", name)) } @@ -844,8 +851,8 @@ test_that("assert_function_param Test 58: no error if `arg` is a parameter of a expect_invisible(assert_function_param("hello", "name")) }) -## Test 59: error if expected function parameters are missing ---- -test_that("assert_function_param Test 59: error if expected function parameters are missing", { +## Test 60: error if expected function parameters are missing ---- +test_that("assert_function_param Test 60: error if expected function parameters are missing", { hello <- function(name) { print(sprintf("Hello %s", name)) } @@ -855,8 +862,8 @@ test_that("assert_function_param Test 59: error if expected function parameters }) # assert_unit ---- -## Test 60: no error if the parameter is provided in the expected unit ---- -test_that("assert_unit Test 60: no error if the parameter is provided in the expected unit", { +## Test 61: no error if the parameter is provided in the expected unit ---- +test_that("assert_unit Test 61: no error if the parameter is provided in the expected unit", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -868,8 +875,8 @@ test_that("assert_unit Test 60: no error if the parameter is provided in the exp ) }) -## Test 61: error if there are multiple units in the input dataset ---- -test_that("assert_unit Test 61: error if there are multiple units in the input dataset", { +## Test 62: error if there are multiple units in the input dataset ---- +test_that("assert_unit Test 62: error if there are multiple units in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -881,8 +888,8 @@ test_that("assert_unit Test 61: error if there are multiple units in the input d ) }) -## Test 62: error if unexpected unit in the input dataset ---- -test_that("assert_unit Test 62: error if unexpected unit in the input dataset", { +## Test 63: error if unexpected unit in the input dataset ---- +test_that("assert_unit Test 63: error if unexpected unit in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -895,8 +902,8 @@ test_that("assert_unit Test 62: error if unexpected unit in the input dataset", }) # assert_param_does_not_exist ---- -## Test 63: error if parameter exists in the input dataset ---- -test_that("assert_param_does_not_exist Test 63: error if parameter exists in the input dataset", { +## Test 64: error if parameter exists in the input dataset ---- +test_that("assert_param_does_not_exist Test 64: error if parameter exists in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -908,8 +915,8 @@ test_that("assert_param_does_not_exist Test 63: error if parameter exists in the ) }) -## Test 64: no error if the parameter exists in the dataset ---- -test_that("assert_param_does_not_exist Test 64: no error if the parameter exists in the dataset", { +## Test 65: no error if the parameter exists in the dataset ---- +test_that("assert_param_does_not_exist Test 65: no error if the parameter exists in the dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -922,8 +929,8 @@ test_that("assert_param_does_not_exist Test 64: no error if the parameter exists }) # assert_varval_list ---- -## Test 65: error if `arg` is not a list of var-value expressions ---- -test_that("assert_varval_list Test 65: error if `arg` is not a list of var-value expressions", { +## Test 66: error if `arg` is not a list of var-value expressions ---- +test_that("assert_varval_list Test 66: error if `arg` is not a list of var-value expressions", { example_fun <- function(arg) { assert_varval_list(arg, accept_var = FALSE) } @@ -933,8 +940,8 @@ test_that("assert_varval_list Test 65: error if `arg` is not a list of var-value ) }) -## Test 66: error if `arg` is not a list of var-value expressions ---- -test_that("assert_varval_list Test 66: error if `arg` is not a list of var-value expressions", { +## Test 67: error if `arg` is not a list of var-value expressions ---- +test_that("assert_varval_list Test 67: error if `arg` is not a list of var-value expressions", { example_fun <- function(arg) { assert_varval_list(arg, accept_var = TRUE) } @@ -944,8 +951,8 @@ test_that("assert_varval_list Test 66: error if `arg` is not a list of var-value ) }) -## Test 67: error if `required_elements` are missing from `arg` ---- -test_that("assert_varval_list Test 67: error if `required_elements` are missing from `arg`", { +## Test 68: error if `required_elements` are missing from `arg` ---- +test_that("assert_varval_list Test 68: error if `required_elements` are missing from `arg`", { example_fun <- function(arg) { assert_varval_list(arg, required_elements = "DTHDOM") } @@ -955,8 +962,8 @@ test_that("assert_varval_list Test 67: error if `required_elements` are missing ) }) -## Test 68: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_varval_list Test 68: no error if `arg` is NULL and optional is TRUE", { +## Test 69: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_varval_list Test 69: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_varval_list(arg, optional = TRUE) } @@ -966,8 +973,8 @@ test_that("assert_varval_list Test 68: no error if `arg` is NULL and optional is ) }) -## Test 69: error if `accept_expr` is TRUE and value is invalid ---- -test_that("assert_varval_list Test 69: error if `accept_expr` is TRUE and value is invalid", { +## Test 70: error if `accept_expr` is TRUE and value is invalid ---- +test_that("assert_varval_list Test 70: error if `accept_expr` is TRUE and value is invalid", { example_fun <- function(arg) { assert_varval_list(arg, accept_expr = TRUE) } @@ -977,8 +984,8 @@ test_that("assert_varval_list Test 69: error if `accept_expr` is TRUE and value ) }) -## Test 70: error if `accept_expr` is FALSE and value is invalid ---- -test_that("assert_varval_list Test 70: error if `accept_expr` is FALSE and value is invalid", { +## Test 71: error if `accept_expr` is FALSE and value is invalid ---- +test_that("assert_varval_list Test 71: error if `accept_expr` is FALSE and value is invalid", { example_fun <- function(arg) { assert_varval_list(arg, accept_expr = FALSE) } @@ -988,8 +995,8 @@ test_that("assert_varval_list Test 70: error if `accept_expr` is FALSE and value ) }) -## Test 71: no error if an argument is a variable-value list ---- -test_that("assert_varval_list Test 71: no error if an argument is a variable-value list", { +## Test 72: no error if an argument is a variable-value list ---- +test_that("assert_varval_list Test 72: no error if an argument is a variable-value list", { example_fun <- function(arg) { assert_varval_list(arg) } @@ -1000,8 +1007,8 @@ test_that("assert_varval_list Test 71: no error if an argument is a variable-val }) # assert_list_element ---- -## Test 72: no error if the elements fulfill a certain condition ---- -test_that("assert_list_element Test 72: no error if the elements fulfill a certain condition", { +## Test 73: no error if the elements fulfill a certain condition ---- +test_that("assert_list_element Test 73: no error if the elements fulfill a certain condition", { expect_invisible( assert_list_element( list( @@ -1015,8 +1022,8 @@ test_that("assert_list_element Test 72: no error if the elements fulfill a certa ) }) -## Test 73: error if the elements do not fulfill the condition ---- -test_that("assert_list_element Test 73: error if the elements do not fulfill the condition", { +## Test 74: error if the elements do not fulfill the condition ---- +test_that("assert_list_element Test 74: error if the elements do not fulfill the condition", { expect_error( assert_list_element( input <- list( @@ -1033,23 +1040,23 @@ test_that("assert_list_element Test 73: error if the elements do not fulfill the }) # assert_one_to_one ---- -## Test 74: error if there is a one to many mapping ---- -test_that("assert_one_to_one Test 74: error if there is a one to many mapping", { +## Test 75: error if there is a one to many mapping ---- +test_that("assert_one_to_one Test 75: error if there is a one to many mapping", { expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(DOMAIN), exprs(USUBJID)) ) }) -## Test 75: error if there is a many to one mapping ---- -test_that("assert_one_to_one Test 75: error if there is a many to one mapping", { +## Test 76: error if there is a many to one mapping ---- +test_that("assert_one_to_one Test 76: error if there is a many to one mapping", { expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(USUBJID), exprs(DOMAIN)) ) }) # assert_date_var ---- -## Test 76: error if variable is not a date or datetime variable ---- -test_that("assert_date_var Test 76: error if variable is not a date or datetime variable", { +## Test 77: error if variable is not a date or datetime variable ---- +test_that("assert_date_var Test 77: error if variable is not a date or datetime variable", { example_fun <- function(dataset, var) { var <- assert_symbol(enexpr(var)) assert_date_var(dataset = dataset, var = !!var) @@ -1070,18 +1077,18 @@ test_that("assert_date_var Test 76: error if variable is not a date or datetime }) # assert_date_vector ---- -## Test 77: returns error if input vector is not a date formatted ---- -test_that("assert_date_vector Test 77: returns error if input vector is not a date formatted", { +## Test 78: returns error if input vector is not a date formatted ---- +test_that("assert_date_vector Test 78: returns error if input vector is not a date formatted", { expect_error(assert_date_vector("2018-08-23")) }) -## Test 78: returns invisible if input is date formatted ---- -test_that("assert_date_vector Test 78: returns invisible if input is date formatted", { +## Test 79: returns invisible if input is date formatted ---- +test_that("assert_date_vector Test 79: returns invisible if input is date formatted", { expect_invisible(assert_date_vector(as.Date("2022-10-25"))) }) -## Test 79: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_date_vector Test 79: no error if `arg` is NULL and optional is TRUE", { +## Test 80: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_date_vector Test 80: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_date_vector(arg, optional = TRUE) } @@ -1091,8 +1098,8 @@ test_that("assert_date_vector Test 79: no error if `arg` is NULL and optional is ) }) -## Test 80: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_date_vector Test 80: error if `arg` is NULL and optional is FALSE", { +## Test 81: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_date_vector Test 81: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_date_vector(arg, optional = FALSE) } @@ -1106,22 +1113,22 @@ test_that("assert_date_vector Test 80: error if `arg` is NULL and optional is FA # assert_atomic_vector ---- -## Test 81: error if input is not atomic vector ---- -test_that("assert_atomic_vector Test 81: error if input is not atomic vector", { +## Test 82: error if input is not atomic vector ---- +test_that("assert_atomic_vector Test 82: error if input is not atomic vector", { x <- list("a", "a", "b", "c", "d", "d", 1, 1, 4) expect_error(assert_atomic_vector(x)) }) # assert_same_type ---- -## Test 82: no error if same type ---- -test_that("assert_same_type Test 82: no error if same type", { +## Test 83: no error if same type ---- +test_that("assert_same_type Test 83: no error if same type", { true_value <- "Y" false_value <- "N" expect_invisible(assert_same_type(true_value, false_value)) }) -## Test 83: error if different type ---- -test_that("assert_same_type Test 83: error if different type", { +## Test 84: error if different type ---- +test_that("assert_same_type Test 84: error if different type", { true_value <- "Y" false_value <- "N" missing_value <- 0 @@ -1140,8 +1147,8 @@ test_that("assert_same_type Test 83: error if different type", { ) }) -## Test 84: works as intended ---- -test_that("assert_same_type Test 84: works as intended", { +## Test 85: works as intended ---- +test_that("assert_same_type Test 85: works as intended", { expect_equal( valid_time_units(), c("years", "months", "days", "hours", "minutes", "seconds") From 25ef10546386246e86728f39e3361cc0501a2a03 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 15 Mar 2023 07:50:17 +0000 Subject: [PATCH 024/100] renv update from pharmaverse/admiralci --- renv/activate.R | 46 ++++++++++++++++++++++++++++++++++++---------- 1 file changed, 36 insertions(+), 10 deletions(-) diff --git a/renv/activate.R b/renv/activate.R index 019b5a66..360dd528 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "0.16.0" + version <- "0.17.0" # the project directory project <- getwd() @@ -94,8 +94,11 @@ local({ return(repos) # if we're testing, re-use the test repositories - if (renv_bootstrap_tests_running()) - return(getOption("renv.tests.repos")) + if (renv_bootstrap_tests_running()) { + repos <- getOption("renv.tests.repos") + if (!is.null(repos)) + return(repos) + } # retrieve current repos repos <- getOption("repos") @@ -344,8 +347,7 @@ local({ return() # allow directories - info <- file.info(tarball, extra_cols = FALSE) - if (identical(info$isdir, TRUE)) { + if (dir.exists(tarball)) { name <- sprintf("renv_%s.tar.gz", version) tarball <- file.path(tarball, name) } @@ -659,8 +661,8 @@ local({ if (version == loadedversion) return(TRUE) - # assume four-component versions are from GitHub; three-component - # versions are from CRAN + # assume four-component versions are from GitHub; + # three-component versions are from CRAN components <- strsplit(loadedversion, "[.-]")[[1]] remote <- if (length(components) == 4L) paste("rstudio/renv", loadedversion, sep = "@") @@ -700,6 +702,12 @@ local({ # 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 = warning) + # load the project renv::load(project) @@ -842,11 +850,29 @@ local({ renv_json_read <- function(file = NULL, text = NULL) { + jlerr <- NULL + # if jsonlite is loaded, use that instead - if ("jsonlite" %in% loadedNamespaces()) - renv_json_read_jsonlite(file, text) + if ("jsonlite" %in% loadedNamespaces()) { + + json <- catch(renv_json_read_jsonlite(file, text)) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- catch(renv_json_read_default(file, text)) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) else - renv_json_read_default(file, text) + stop(json) } From 75cae944913e8ac6ea22a78be5bb142185747ed3 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 15 Mar 2023 08:35:11 +0000 Subject: [PATCH 025/100] renv update from pharmaverse/admiralci --- renv.lock | 704 ++++++++++++++++++++++------------- renv/profiles/4.0/renv.lock | 704 ++++++++++++++++++++++------------- renv/profiles/4.1/renv.lock | 708 ++++++++++++++++++++++------------- renv/profiles/4.2/renv.lock | 718 +++++++++++++++++++++++------------- 4 files changed, 1797 insertions(+), 1037 deletions(-) diff --git a/renv.lock b/renv.lock index 10b5d185..628cf197 100644 --- a/renv.lock +++ b/renv.lock @@ -18,15 +18,13 @@ "Version": "1.75.0-0", "Source": "Repository", "Repository": "RSPM", - "Hash": "e4c04affc2cac20c8fec18385cd14691", - "Requirements": [] + "Hash": "e4c04affc2cac20c8fec18385cd14691" }, "DT": { "Package": "DT", "Version": "0.17", "Source": "Repository", "Repository": "RSPM", - "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0", "Requirements": [ "crosstalk", "htmltools", @@ -34,285 +32,328 @@ "jsonlite", "magrittr", "promises" - ] + ], + "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0" }, "R.cache": { "Package": "R.cache", "Version": "0.15.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "e92a8ea8388c47c82ed8aa435ed3be50", "Requirements": [ + "R", "R.methodsS3", "R.oo", "R.utils", - "digest" - ] + "digest", + "utils" + ], + "Hash": "e92a8ea8388c47c82ed8aa435ed3be50" }, "R.methodsS3": { "Package": "R.methodsS3", "Version": "1.8.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "4bf6453323755202d5909697b6f7c109", - "Requirements": [] + "Requirements": [ + "R", + "utils" + ], + "Hash": "4bf6453323755202d5909697b6f7c109" }, "R.oo": { "Package": "R.oo", "Version": "1.24.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "5709328352717e2f0a9c012be8a97554", "Requirements": [ - "R.methodsS3" - ] + "R", + "R.methodsS3", + "methods", + "utils" + ], + "Hash": "5709328352717e2f0a9c012be8a97554" }, "R.utils": { "Package": "R.utils", "Version": 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"lifecycle", "magrittr", + "methods", "pillar", "pkgconfig", "rlang", + "utils", "vctrs" - ] + ], + "Hash": "4d894a114dbd4ecafeda5074e7c538e6" }, "tidyr": { "Package": "tidyr", "Version": "1.1.3", "Source": "Repository", "Repository": "RSPM", - "Hash": "450d7dfaedde58e28586b854eeece4fa", "Requirements": [ + "R", "cpp11", "dplyr", "ellipsis", @@ -1263,40 +1424,43 @@ "rlang", "tibble", "tidyselect", + "utils", "vctrs" - ] + ], + "Hash": "450d7dfaedde58e28586b854eeece4fa" }, "tidyselect": { "Package": "tidyselect", "Version": "1.1.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "6ea435c354e8448819627cf686f66e0a", "Requirements": [ + "R", "ellipsis", "glue", "purrr", "rlang", "vctrs" - ] + ], + "Hash": "6ea435c354e8448819627cf686f66e0a" }, "tinytex": { "Package": "tinytex", "Version": "0.31", "Source": "Repository", "Repository": "RSPM", - "Hash": "25b572f764f3c19fef9aac33b5724f3d", "Requirements": [ "xfun" - ] + ], + "Hash": "25b572f764f3c19fef9aac33b5724f3d" }, "usethis": { 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"ae34cd56890607370665bee5bd17812f" }, "rlang": { "Package": "rlang", "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", - "Hash": "4ed1f8336c8d52c3e750adcdc57228a7", - "Requirements": [] + "Requirements": [ + "R", + "utils" + ], + "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" }, "rmarkdown": { "Package": "rmarkdown", "Version": "2.17", "Source": "Repository", "Repository": "RSPM", - "Hash": "e97c8be593e010f93520e8215c0f9189", "Requirements": [ + "R", "bslib", "evaluate", "htmltools", "jquerylib", "jsonlite", "knitr", + "methods", "stringr", "tinytex", + "tools", + "utils", "xfun", "yaml" - ] + ], + "Hash": "e97c8be593e010f93520e8215c0f9189" }, "roxygen2": { "Package": "roxygen2", "Version": "7.2.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "da1f278262e563c835345872f2fef537", "Requirements": [ + "R", "R6", "brew", "cli", @@ -1015,73 +1155,81 @@ "desc", "digest", "knitr", + "methods", "pkgload", "purrr", "rlang", "stringi", "stringr", + "utils", "withr", "xml2" - ] + ], + "Hash": "da1f278262e563c835345872f2fef537" }, "rprojroot": { "Package": "rprojroot", "Version": "2.0.3", "Source": "Repository", "Repository": "RSPM", - "Hash": "1de7ab598047a87bba48434ba35d497d", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "1de7ab598047a87bba48434ba35d497d" }, "rstudioapi": { "Package": "rstudioapi", "Version": "0.14", "Source": "Repository", "Repository": "RSPM", - "Hash": "690bd2acc42a9166ce34845884459320", - "Requirements": [] + "Hash": "690bd2acc42a9166ce34845884459320" }, "rversions": { "Package": "rversions", "Version": "2.1.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "a9881dfed103e83f9de151dc17002cd1", "Requirements": [ "curl", + "utils", "xml2" - ] + ], + "Hash": "a9881dfed103e83f9de151dc17002cd1" }, "sass": { "Package": "sass", "Version": "0.4.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "1b191143d7d3444d504277843f3a95fe", "Requirements": [ "R6", "fs", "htmltools", "rappdirs", "rlang" - ] + ], + "Hash": "1b191143d7d3444d504277843f3a95fe" }, "sessioninfo": { "Package": "sessioninfo", "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", "Requirements": [ - "cli" - ] + "R", + "cli", + "tools", + "utils" + ], + "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f" }, "shiny": { "Package": "shiny", "Version": "1.7.3", "Source": "Repository", "Repository": "RSPM", - "Hash": "fe12df67fdb3b1142325cc54f100cc06", "Requirements": [ + "R", "R6", "bslib", "cachem", @@ -1091,39 +1239,46 @@ "fastmap", "fontawesome", "glue", + "grDevices", "htmltools", "httpuv", "jsonlite", "later", "lifecycle", + "methods", "mime", "promises", "rlang", "sourcetools", + "tools", + "utils", "withr", "xtable" - ] + ], + "Hash": "fe12df67fdb3b1142325cc54f100cc06" }, "sourcetools": { "Package": "sourcetools", "Version": "0.1.7", "Source": "Repository", "Repository": "RSPM", - "Hash": "947e4e02a79effa5d512473e10f41797", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "947e4e02a79effa5d512473e10f41797" }, "spelling": { "Package": "spelling", "Version": "2.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "b8c899a5c83f0d897286550481c91798", "Requirements": [ "commonmark", "hunspell", "knitr", "xml2" - ] + ], + "Hash": "b8c899a5c83f0d897286550481c91798" }, "staged.dependencies": { "Package": "staged.dependencies", @@ -1135,7 +1290,6 @@ "RemoteRepo": "staged.dependencies", "RemoteRef": "main", "RemoteSha": "ce7c112ba3d75cf48e4dd6310b3140ab0ec3b486", - "Hash": "89f2e1d1009601f58f64b7092abcc0d7", "Requirements": [ "desc", "devtools", @@ -1146,76 +1300,88 @@ "glue", "httr", "jsonlite", + "methods", "rcmdcheck", "remotes", "rlang", + "stats", "tidyr", + "utils", "withr", "yaml" - ] + ], + "Hash": "89f2e1d1009601f58f64b7092abcc0d7" }, "stringi": { "Package": "stringi", "Version": "1.7.8", "Source": "Repository", "Repository": "RSPM", - "Hash": "a68b980681bcbc84c7a67003fa796bfb", - "Requirements": [] + "Requirements": [ + "R", + "stats", + "tools", + "utils" + ], + "Hash": "a68b980681bcbc84c7a67003fa796bfb" }, "stringr": { "Package": "stringr", "Version": "1.4.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "a66ad12140cd34d4f9dfcc19e84fc2a5", "Requirements": [ + "R", "glue", "magrittr", "stringi" - ] + ], + "Hash": "a66ad12140cd34d4f9dfcc19e84fc2a5" }, "styler": { "Package": "styler", "Version": "1.8.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "c855e70eb69b3dd8883660b7110e0c44", "Requirements": [ + "R", "R.cache", "cli", "magrittr", "purrr", "rlang", "rprojroot", + "tools", "vctrs", "withr" - ] + ], + "Hash": "c855e70eb69b3dd8883660b7110e0c44" }, "sys": { "Package": "sys", "Version": "3.4.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "34c16f1ef796057bfa06d3f4ff818a5d", - "Requirements": [] + "Hash": "34c16f1ef796057bfa06d3f4ff818a5d" }, "systemfonts": { "Package": "systemfonts", "Version": "1.0.4", "Source": "Repository", "Repository": "RSPM", - "Hash": "90b28393209827327de889f49935140a", "Requirements": [ + "R", "cpp11" - ] + ], + "Hash": "90b28393209827327de889f49935140a" }, "testthat": { "Package": "testthat", - "Version": "3.1.5", + "Version": "3.1.7", "Source": "Repository", - "Repository": "RSPM", - "Hash": "6e3c4843f1ed0d3d90f35498671a001c", + "Repository": "CRAN", "Requirements": [ + "R", "R6", "brio", "callr", @@ -1227,49 +1393,56 @@ "jsonlite", "lifecycle", "magrittr", + "methods", "pkgload", "praise", "processx", "ps", "rlang", + "utils", "waldo", "withr" - ] + ], + "Hash": "7eb5fd202a61d2fb78af5869b6c08998" }, "textshaping": { "Package": "textshaping", "Version": "0.3.6", "Source": "Repository", "Repository": "RSPM", - "Hash": "1ab6223d3670fac7143202cb6a2d43d5", "Requirements": [ + "R", "cpp11", "systemfonts" - ] + ], + "Hash": "1ab6223d3670fac7143202cb6a2d43d5" }, "tibble": { "Package": "tibble", "Version": "3.1.8", "Source": "Repository", "Repository": "RSPM", - "Hash": "56b6934ef0f8c68225949a8672fe1a8f", "Requirements": [ + "R", "fansi", "lifecycle", "magrittr", + "methods", "pillar", "pkgconfig", "rlang", + "utils", "vctrs" - ] + ], + "Hash": "56b6934ef0f8c68225949a8672fe1a8f" }, "tidyr": { "Package": "tidyr", "Version": "1.2.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "cdb403db0de33ccd1b6f53b83736efa8", "Requirements": [ + "R", "cpp11", "dplyr", "ellipsis", @@ -1280,53 +1453,58 @@ "rlang", "tibble", "tidyselect", + "utils", "vctrs" - ] + ], + "Hash": "cdb403db0de33ccd1b6f53b83736efa8" }, "tidyselect": { "Package": "tidyselect", "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "79540e5fcd9e0435af547d885f184fd5", "Requirements": [ + "R", "cli", "glue", "lifecycle", "rlang", "vctrs", "withr" - ] + ], + "Hash": "79540e5fcd9e0435af547d885f184fd5" }, "tinytex": { "Package": "tinytex", "Version": "0.42", "Source": "Repository", "Repository": "RSPM", - "Hash": "7629c6c1540835d5248e6e7df265fa74", "Requirements": [ "xfun" - ] + ], + "Hash": "7629c6c1540835d5248e6e7df265fa74" }, "urlchecker": { "Package": "urlchecker", "Version": "1.0.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "409328b8e1253c8d729a7836fe7f7a16", "Requirements": [ + "R", "cli", "curl", + "tools", "xml2" - ] + ], + "Hash": "409328b8e1253c8d729a7836fe7f7a16" }, "usethis": { "Package": "usethis", "Version": "2.1.6", "Source": "Repository", "Repository": "RSPM", - "Hash": "a67a22c201832b12c036cc059f1d137d", "Requirements": [ + "R", "cli", "clipr", "crayon", @@ -1343,121 +1521,143 @@ "rlang", "rprojroot", "rstudioapi", + "stats", + "utils", "whisker", "withr", "yaml" - ] + ], + "Hash": "a67a22c201832b12c036cc059f1d137d" }, "utf8": { "Package": "utf8", "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "c9c462b759a5cc844ae25b5942654d13", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "c9c462b759a5cc844ae25b5942654d13" }, "vctrs": { "Package": "vctrs", "Version": "0.5.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "001fd6a5ebfff8316baf9fb2b5516dc9", "Requirements": [ + "R", "cli", "glue", "lifecycle", "rlang" - ] + ], + "Hash": "001fd6a5ebfff8316baf9fb2b5516dc9" }, "waldo": { "Package": "waldo", "Version": "0.4.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "035fba89d0c86e2113120f93301b98ad", "Requirements": [ "cli", "diffobj", "fansi", "glue", + "methods", "rematch2", "rlang", "tibble" - ] + ], + "Hash": "035fba89d0c86e2113120f93301b98ad" }, "whisker": { "Package": "whisker", "Version": "0.4", "Source": "Repository", "Repository": "RSPM", - "Hash": "ca970b96d894e90397ed20637a0c1bbe", - "Requirements": [] + "Hash": "ca970b96d894e90397ed20637a0c1bbe" }, "withr": { "Package": "withr", "Version": "2.5.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "c0e49a9760983e81e55cdd9be92e7182", - "Requirements": [] + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats" + ], + "Hash": "c0e49a9760983e81e55cdd9be92e7182" }, "xfun": { "Package": "xfun", "Version": "0.34", "Source": "Repository", "Repository": "RSPM", - "Hash": "9eba2411b0b1f879797141bd24df7407", - "Requirements": [] + "Requirements": [ + "stats", + "tools" + ], + "Hash": "9eba2411b0b1f879797141bd24df7407" }, "xml2": { "Package": "xml2", "Version": "1.3.3", "Source": "Repository", "Repository": "RSPM", - "Hash": "40682ed6a969ea5abfd351eb67833adc", - "Requirements": [] + "Requirements": [ + "R", + "methods" + ], + "Hash": "40682ed6a969ea5abfd351eb67833adc" }, "xmlparsedata": { "Package": "xmlparsedata", "Version": "1.0.5", "Source": "Repository", "Repository": "RSPM", - "Hash": "45e4bf3c46476896e821fc0a408fb4fc", - "Requirements": [] + "Requirements": [ + "R" + ], + "Hash": "45e4bf3c46476896e821fc0a408fb4fc" }, "xopen": { "Package": "xopen", "Version": "1.0.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "6c85f015dee9cc7710ddd20f86881f58", "Requirements": [ + "R", "processx" - ] + ], + "Hash": "6c85f015dee9cc7710ddd20f86881f58" }, "xtable": { "Package": "xtable", "Version": "1.8-4", "Source": "Repository", "Repository": "RSPM", - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", - "Requirements": [] + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" }, "yaml": { "Package": "yaml", "Version": "2.3.6", "Source": "Repository", "Repository": "RSPM", - "Hash": "9b570515751dcbae610f29885e025b41", - "Requirements": [] + "Hash": "9b570515751dcbae610f29885e025b41" }, "zip": { "Package": "zip", "Version": "2.2.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88", - "Requirements": [] + "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88" } } } From 32fd219163340531d84fe19dd5ecc19c7b015ff2 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Thu, 16 Mar 2023 18:02:07 +0100 Subject: [PATCH 026/100] 241_allow_expressions: add assert_named() and assert_expr_list() --- NAMESPACE | 2 + NEWS.md | 9 + R/assertions.R | 216 ++++++++++++++++----- docs/pkgdown.yml | 8 +- man/assert_atomic_vector.Rd | 4 +- man/assert_character_scalar.Rd | 6 +- man/assert_character_vector.Rd | 4 +- man/assert_data_frame.Rd | 4 +- man/assert_date_vector.Rd | 4 +- man/assert_expr.Rd | 4 +- man/assert_expr_list.Rd | 72 +++++++ man/assert_filter_cond.Rd | 4 +- man/assert_function.Rd | 12 +- man/assert_function_param.Rd | 4 +- man/assert_has_variables.Rd | 2 + man/assert_integer_scalar.Rd | 4 +- man/assert_list_element.Rd | 2 + man/assert_list_of.Rd | 4 +- man/assert_logical_scalar.Rd | 4 +- man/assert_named.Rd | 52 +++++ man/assert_named_exprs.Rd | 4 +- man/assert_numeric_vector.Rd | 4 +- man/assert_one_to_one.Rd | 2 + man/assert_order_vars.Rd | 4 +- man/assert_param_does_not_exist.Rd | 2 + man/assert_s3_class.Rd | 4 +- man/assert_same_type.Rd | 2 + man/assert_symbol.Rd | 4 +- man/assert_unit.Rd | 2 + man/assert_vars.Rd | 4 +- man/assert_varval_list.Rd | 8 +- tests/testthat/test-assertions.R | 301 ++++++++++++++++++----------- tests/testthat/test-get.R | 2 +- 33 files changed, 581 insertions(+), 183 deletions(-) create mode 100644 man/assert_expr_list.Rd create mode 100644 man/assert_named.Rd diff --git a/NAMESPACE b/NAMESPACE index 3c7f396c..4b57dd79 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -12,6 +12,7 @@ export(assert_data_frame) export(assert_date_var) export(assert_date_vector) export(assert_expr) +export(assert_expr_list) export(assert_filter_cond) export(assert_function) export(assert_function_param) @@ -20,6 +21,7 @@ export(assert_integer_scalar) export(assert_list_element) export(assert_list_of) export(assert_logical_scalar) +export(assert_named) export(assert_named_exprs) export(assert_numeric_vector) export(assert_one_to_one) diff --git a/NEWS.md b/NEWS.md index 1c0a9c95..03ac16e4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,12 @@ +# admiraldev 0.4.0 + +## New Features + +- New function `assert_named()` to check if all elements of an argument are +named (#241) +- New function `assert_expr_list()` to check if an argument is a list of +expressions (#241) + # admiraldev 0.3.0 ## New Features diff --git a/R/assertions.R b/R/assertions.R index f8a3fa16..90486645 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -6,7 +6,7 @@ #' @param arg A function argument to be checked #' @param required_vars A list of variables created using `exprs()` #' @param check_is_grouped Throw an error is `dataset` is grouped? Defaults to `TRUE`. -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -92,7 +92,7 @@ assert_data_frame <- function(arg, #' @param case_sensitive Should the argument be handled case-sensitive? #' If set to `FALSE`, the argument is converted to lower case for checking the #' permitted values and returning the argument. -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -116,7 +116,7 @@ assert_data_frame <- function(arg, #' #' try(example_fun(TRUE)) #' -#' # handling parameters case-insensitive +#' # handling arguments case-insensitive #' example_fun2 <- function(msg_type) { #' msg_type <- assert_character_scalar( #' msg_type, @@ -202,7 +202,7 @@ assert_character_scalar <- function(arg, #' @param values A `character` vector of valid values for `arg` #' @param named If set to `TRUE`, an error is issued if not all elements of the #' vector are named. -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -260,20 +260,8 @@ assert_character_vector <- function(arg, values = NULL, named = FALSE, optional } } - if (named && length(arg) > 0) { - if (is.null(names(arg))) { - abort(paste0( - "All elements of ", arg_name(substitute(arg)), " must be named.\n", - "No element is named." - )) - } - unnamed <- which(names(arg) == "") - if (length(unnamed) > 0) { - abort(paste0( - "All elements of ", arg_name(substitute(arg)), " must be named.\n", - "The following elements are not named: ", enumerate(unnamed, quote_fun = NULL) - )) - } + if (named) { + assert_named(arg) } } @@ -283,7 +271,7 @@ assert_character_vector <- function(arg, values = NULL, named = FALSE, optional #' #' @param arg A function argument to be checked #' -#' @param optional Is the checked parameter optional? +#' @param optional Is the checked argument optional? #' #' If set to `FALSE` and `arg` is `NULL` then an error is thrown. Otherwise, #' `NULL` is considered as valid value. @@ -331,7 +319,7 @@ assert_logical_scalar <- function(arg, optional = FALSE) { #' Checks if an argument is a symbol #' #' @param arg A function argument to be checked. Must be a `symbol`. See examples. -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -442,7 +430,7 @@ assert_expr <- function(arg, optional = FALSE) { #' library(rlang) #' data(admiral_dm) #' -#' # typical usage in a function as a parameter check +#' # typical usage in a function as an argument check #' example_fun <- function(dat, x) { #' x <- assert_filter_cond(enquo(x)) #' filter(dat, !!x) @@ -480,7 +468,7 @@ assert_filter_cond <- function(arg, optional = FALSE) { #' @param expect_names If the argument is set to `TRUE`, it is checked if all #' variables are named, e.g., `exprs(APERSDT = APxxSDT, APEREDT = APxxEDT)`. #' -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -537,7 +525,7 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) { #' using `exprs()` #' #' @param arg A function argument to be checked -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -586,8 +574,18 @@ assert_order_vars <- function(arg, optional = FALSE) { abort(default_err_msg) } - if (isTRUE(is_call(arg))) { - abort(default_err_msg) + is_valid <- map_lgl(arg, ~ is.call(.x) || is_expression(.x)) + if (!all(is_valid)) { + info_msg <- paste( + sprintf("\u2716 Element %s is %s", which(!is_valid), map_chr(arg[!is_valid], what_is_it)), + collapse = "\n" + ) + err_msg <- sprintf( + "Each element of `%s` must be an expression but the following are not:\n%s", + arg_name(substitute(arg)), + info_msg + ) + abort(err_msg) } invisible(arg) @@ -600,7 +598,7 @@ assert_order_vars <- function(arg, optional = FALSE) { #' @param arg A function argument to be checked #' @param subset A subset of integers that `arg` should be part of. Should be one #' of `"none"` (the default), `"positive"`, `"non-negative"` or `"negative"`. -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -657,7 +655,7 @@ assert_integer_scalar <- function(arg, subset = "none", optional = FALSE) { #' Checks if an argument is a numeric vector #' #' @param arg A function argument to be checked -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -699,7 +697,7 @@ assert_numeric_vector <- function(arg, optional = FALSE) { #' Checks if an argument is an atomic vector #' #' @param arg A function argument to be checked -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -741,7 +739,7 @@ assert_atomic_vector <- function(arg, optional = FALSE) { #' Checks if an argument is an object inheriting from the S3 class specified. #' @param arg A function argument to be checked #' @param class The S3 class to check for -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -792,7 +790,7 @@ assert_s3_class <- function(arg, class, optional = FALSE) { #' @param class The S3 class or type to check for #' @param named If set to `TRUE`, an error is issued if not all elements of the #' list are named. -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown #' #' @@ -865,6 +863,42 @@ assert_list_of <- function(arg, class, named = FALSE, optional = TRUE) { invisible(arg) } +#' Assert Argument is a Named List or Vector +#' +#' Assert that all elements of the argument are named. +#' +#' @inheritParams assert_data_frame +#' +#' @keywords assertion +#' @family assertion +#' +#' @return +#' The function throws an error if `arg` is not a named list or vector or +#' returns the input invisibly otherwise +#' +#' @export +assert_named <- function(arg, optional = FALSE) { + if (optional && is.null(arg)) { + return(invisible(arg)) + } + + if (length(arg) > 0) { + if (is.null(names(arg))) { + abort(paste0( + "All elements of `", arg_name(substitute(arg)), "` must be named.\n", + "No element is named." + )) + } + unnamed <- which(names(arg) == "") + if (length(unnamed) > 0) { + abort(paste0( + "All elements of `", arg_name(substitute(arg)), "` must be named.\n", + "The following elements are not named: ", enumerate(unnamed, quote_fun = NULL) + )) + } + } +} + #' Assert Argument is a Named List of Expressions #' #' @inheritParams assert_data_frame @@ -940,14 +974,14 @@ assert_has_variables <- function(dataset, required_vars) { #' Is Argument a Function? #' -#' Checks if the argument is a function and if all expected parameters are +#' Checks if the argument is a function and if all expected arguments are #' provided by the function. #' #' @param arg A function argument to be checked #' -#' @param params A character vector of expected parameter names +#' @param params A character vector of expected argument names #' -#' @param optional Is the checked parameter optional? +#' @param optional Is the checked argument optional? #' #' If set to `FALSE` and `arg` is `NULL` then an error is thrown. #' @@ -956,8 +990,8 @@ assert_has_variables <- function(dataset, required_vars) { #' #' - if the argument is not a function or #' -#' - if the function does not provide all parameters as specified for the -#' `params` parameter. +#' - if the function does not provide all arguments as specified for the +#' `params` argument. #' #' @export #' @@ -1001,9 +1035,9 @@ assert_function <- function(arg, params = NULL, optional = FALSE) { is_param <- params %in% names(formals(arg)) if (!all(is_param)) { txt <- if (sum(!is_param) == 1L) { - "%s is not a parameter of the function specified for `%s`" + "%s is not an argument of the function specified for `%s`" } else { - "%s are not parameters of the function specified for `%s`" + "%s are not arguments of the function specified for `%s`" } err_msg <- sprintf(txt, enumerate(params[!is_param]), arg_name(substitute(arg))) abort(err_msg) @@ -1021,7 +1055,7 @@ assert_function <- function(arg, params = NULL, optional = FALSE) { #' @family assertion #' #' @return -#' The function throws an error if any elements of `params` is not a parameter of +#' The function throws an error if any elements of `params` is not an argument of #' the function given by `arg` #' #' @export @@ -1042,9 +1076,9 @@ assert_function_param <- function(arg, params) { is_param <- params %in% names(formals(fun)) if (!all(is_param)) { txt <- if (sum(!is_param) == 1L) { - "%s is not a parameter of `%s()`" + "%s is not an argument of `%s()`" } else { - "%s are not parameters of `%s()`" + "%s are not arguments of `%s()`" } err_msg <- sprintf(txt, enumerate(params[!is_param]), arg) abort(err_msg) @@ -1170,15 +1204,15 @@ assert_param_does_not_exist <- function(dataset, param) { #' Is an Argument a Variable-Value List? #' #' Checks if the argument is a list of expressions where the expressions are -#' variable-value pairs. The value can be a symbol, a string, a numeric, or -#' `NA`. More general expression are not allowed. +#' variable-value pairs. The value can be a symbol, a string, a numeric, an +#' expression, or `NA`. #' #' @param arg A function argument to be checked #' @param required_elements A `character` vector of names that must be present in `arg` #' @param accept_expr Should expressions on the right hand side be accepted? #' @param accept_var Should unnamed variable names (e.g. `exprs(USUBJID)`) on the #' right hand side be accepted? -#' @param optional Is the checked parameter optional? If set to `FALSE` and `arg` +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` #' is `NULL` then an error is thrown. #' #' @@ -1303,6 +1337,100 @@ assert_varval_list <- function(arg, # nolint invisible(arg) } +#' Is an Argument a List of Expressions? +#' +#' Checks if the argument is a list of expressions. +#' +#' @param arg A function argument to be checked +#' @param required_elements A `character` vector of names that must be present in `arg` +#' @param named If set to `TRUE`, an error is issued if not all elements of the +#' list are named. +#' @param optional Is the checked argument optional? If set to `FALSE` and `arg` +#' is `NULL` then an error is thrown. +#' +#' @return +#' The function throws an error if `arg` is not a list of expressions. +#' Otherwise, the input it returned invisibly. +#' +#' @keywords assertion +#' @family assertion +#' @export +#' +#' @examples +#' library(rlang) +#' +#' example_fun <- function(vars) { +#' assert_expr_list(vars) +#' } +#' example_fun(exprs(DTHDOM = "AE", DTHSEQ = AESEQ)) +#' +#' try(example_fun(exprs("AE", DTSEQ = AESEQ, !!mean))) +assert_expr_list <- function(arg, # nolint + required_elements = NULL, + named = FALSE, + optional = FALSE) { + assert_logical_scalar(named) + assert_logical_scalar(optional) + assert_character_vector(required_elements, optional = TRUE) + + if (optional && is.null(arg)) { + return(invisible(arg)) + } + + if (!inherits(arg, "list")) { + err_msg <- sprintf( + paste0( + "`%s` must be a named list of expressions but it is %s\n", + "\u2139 To create a list of expressions use `exprs()`" + ), + arg_name(substitute(arg)), + what_is_it(arg) + ) + abort(err_msg) + } + + if (named) { + assert_named(arg) + } + + if (!is.null(required_elements)) { + missing_elements <- setdiff(required_elements, names(arg)) + if (length(missing_elements) >= 1L) { + err_msg <- sprintf( + "The following required elements are missing in `%s`: %s", + arg_name(substitute(arg)), + enumerate(missing_elements, quote_fun = squote) + ) + abort(err_msg) + } + } + + invalids <- arg[!map_lgl( + arg, + ~ is_call(.x) || is_expression(.x) + )] + + if (length(invalids) > 0) { + abort( + paste0( + "The elements of the list ", + arg_name(substitute(arg)), + " must be expressions.\n", + paste( + names(invalids), + "=", + map_chr(invalids, expr_label), + "is of type", + map_chr(invalids, typeof), + collapse = "\n" + ) + ) + ) + } + + invisible(arg) +} + #' Is an Element of a List of Lists/Classes Fulfilling a Condition? #' #' Checks if the elements of a list of named lists/classes fulfill a certain @@ -1526,7 +1654,7 @@ assert_date_var <- function(dataset, var, dataset_name = NULL, var_name = NULL) #' #' @param arg The function argument to be checked #' -#' @param optional Is the checked parameter optional? If set to `FALSE` +#' @param optional Is the checked argument optional? If set to `FALSE` #' and `arg` is `NULL` then the function `assert_date_vector` exits early and throw and error. #' #' @return diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e1010f62..13d33dcd 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.17.1.1 +pandoc: 2.11.4 pkgdown: 2.0.6 pkgdown_sha: ~ articles: @@ -10,8 +10,8 @@ articles: release_strategy: release_strategy.html unit_test_guidance: unit_test_guidance.html writing_vignettes: writing_vignettes.html -last_built: 2023-01-19T10:49Z +last_built: 2023-03-06T13:34Z urls: - reference: https://pharmaverse.github.io/admiraldev/devel/reference - article: https://pharmaverse.github.io/admiraldev/devel/articles + reference: https://pharmaverse.github.io/admiraldev/reference + article: https://pharmaverse.github.io/admiraldev/articles diff --git a/man/assert_atomic_vector.Rd b/man/assert_atomic_vector.Rd index aa5c2549..8ce5cbc0 100644 --- a/man/assert_atomic_vector.Rd +++ b/man/assert_atomic_vector.Rd @@ -9,7 +9,7 @@ assert_atomic_vector(arg, optional = FALSE) \arguments{ \item{arg}{A function argument to be checked} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -34,6 +34,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -44,6 +45,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_character_scalar.Rd b/man/assert_character_scalar.Rd index b66ce00a..53c9a11c 100644 --- a/man/assert_character_scalar.Rd +++ b/man/assert_character_scalar.Rd @@ -21,7 +21,7 @@ Values is converted to a lower case vector if case_sensitive = FALSE is used.} If set to \code{FALSE}, the argument is converted to lower case for checking the permitted values and returning the argument.} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -44,7 +44,7 @@ try(example_fun("message")) try(example_fun(TRUE)) -# handling parameters case-insensitive +# handling arguments case-insensitive example_fun2 <- function(msg_type) { msg_type <- assert_character_scalar( msg_type, @@ -64,6 +64,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -74,6 +75,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_character_vector.Rd b/man/assert_character_vector.Rd index ec9a33c6..faedadc3 100644 --- a/man/assert_character_vector.Rd +++ b/man/assert_character_vector.Rd @@ -14,7 +14,7 @@ assert_character_vector(arg, values = NULL, named = FALSE, optional = FALSE) \item{named}{If set to \code{TRUE}, an error is issued if not all elements of the vector are named.} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -46,6 +46,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_scalar}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -56,6 +57,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_data_frame.Rd b/man/assert_data_frame.Rd index cae983bc..8ac0a722 100644 --- a/man/assert_data_frame.Rd +++ b/man/assert_data_frame.Rd @@ -18,7 +18,7 @@ assert_data_frame( \item{check_is_grouped}{Throw an error is \code{dataset} is grouped? Defaults to \code{TRUE}.} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -52,6 +52,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_scalar}()}, \code{\link{assert_character_vector}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -62,6 +63,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_date_vector.Rd b/man/assert_date_vector.Rd index bdf9de22..68874182 100644 --- a/man/assert_date_vector.Rd +++ b/man/assert_date_vector.Rd @@ -9,7 +9,7 @@ assert_date_vector(arg, optional = FALSE) \arguments{ \item{arg}{The function argument to be checked} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then the function \code{assert_date_vector} exits early and throw and error.} } \value{ @@ -35,6 +35,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_scalar}()}, \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -45,6 +46,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_expr.Rd b/man/assert_expr.Rd index 5dba5c09..91899736 100644 --- a/man/assert_expr.Rd +++ b/man/assert_expr.Rd @@ -9,7 +9,7 @@ assert_expr(arg, optional = FALSE) \arguments{ \item{arg}{A function argument to be checked} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -26,6 +26,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, \code{\link{assert_function}()}, @@ -35,6 +36,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_expr_list.Rd b/man/assert_expr_list.Rd new file mode 100644 index 00000000..641030ae --- /dev/null +++ b/man/assert_expr_list.Rd @@ -0,0 +1,72 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/assertions.R +\name{assert_expr_list} +\alias{assert_expr_list} +\title{Is an Argument a List of Expressions?} +\usage{ +assert_expr_list( + arg, + required_elements = NULL, + named = FALSE, + optional = FALSE +) +} +\arguments{ +\item{arg}{A function argument to be checked} + +\item{required_elements}{A \code{character} vector of names that must be present in \code{arg}} + +\item{named}{If set to \code{TRUE}, an error is issued if not all elements of the +list are named.} + +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} +is \code{NULL} then an error is thrown.} +} +\value{ +The function throws an error if \code{arg} is not a list of expressions. +Otherwise, the input it returned invisibly. +} +\description{ +Checks if the argument is a list of expressions. +} +\examples{ +library(rlang) + +example_fun <- function(vars) { + assert_expr_list(vars) +} +example_fun(exprs(DTHDOM = "AE", DTHSEQ = AESEQ)) + +try(example_fun(exprs("AE", DTSEQ = AESEQ, !!mean))) +} +\seealso{ +Checks for valid input and returns warning or errors messages: +\code{\link{assert_atomic_vector}()}, +\code{\link{assert_character_scalar}()}, +\code{\link{assert_character_vector}()}, +\code{\link{assert_data_frame}()}, +\code{\link{assert_date_vector}()}, +\code{\link{assert_expr}()}, +\code{\link{assert_filter_cond}()}, +\code{\link{assert_function_param}()}, +\code{\link{assert_function}()}, +\code{\link{assert_has_variables}()}, +\code{\link{assert_integer_scalar}()}, +\code{\link{assert_list_element}()}, +\code{\link{assert_list_of}()}, +\code{\link{assert_logical_scalar}()}, +\code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, +\code{\link{assert_numeric_vector}()}, +\code{\link{assert_one_to_one}()}, +\code{\link{assert_order_vars}()}, +\code{\link{assert_param_does_not_exist}()}, +\code{\link{assert_s3_class}()}, +\code{\link{assert_same_type}()}, +\code{\link{assert_symbol}()}, +\code{\link{assert_unit}()}, +\code{\link{assert_vars}()}, +\code{\link{assert_varval_list}()} +} +\concept{assertion} +\keyword{assertion} diff --git a/man/assert_filter_cond.Rd b/man/assert_filter_cond.Rd index 69ac111b..3944ddda 100644 --- a/man/assert_filter_cond.Rd +++ b/man/assert_filter_cond.Rd @@ -28,7 +28,7 @@ library(dplyr, warn.conflicts = FALSE) library(rlang) data(admiral_dm) -# typical usage in a function as a parameter check +# typical usage in a function as an argument check example_fun <- function(dat, x) { x <- assert_filter_cond(enquo(x)) filter(dat, !!x) @@ -45,6 +45,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_function_param}()}, \code{\link{assert_function}()}, @@ -54,6 +55,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_function.Rd b/man/assert_function.Rd index 34fac421..4df27014 100644 --- a/man/assert_function.Rd +++ b/man/assert_function.Rd @@ -9,9 +9,9 @@ assert_function(arg, params = NULL, optional = FALSE) \arguments{ \item{arg}{A function argument to be checked} -\item{params}{A character vector of expected parameter names} +\item{params}{A character vector of expected argument names} -\item{optional}{Is the checked parameter optional? +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown.} } @@ -19,12 +19,12 @@ If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown.} The function throws an error \itemize{ \item if the argument is not a function or -\item if the function does not provide all parameters as specified for the -\code{params} parameter. +\item if the function does not provide all arguments as specified for the +\code{params} argument. } } \description{ -Checks if the argument is a function and if all expected parameters are +Checks if the argument is a function and if all expected arguments are provided by the function. } \examples{ @@ -45,6 +45,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -54,6 +55,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_function_param.Rd b/man/assert_function_param.Rd index 8c7fcf2b..8ada48da 100644 --- a/man/assert_function_param.Rd +++ b/man/assert_function_param.Rd @@ -12,7 +12,7 @@ assert_function_param(arg, params) \item{params}{A character vector of function parameters} } \value{ -The function throws an error if any elements of \code{params} is not a parameter of +The function throws an error if any elements of \code{params} is not an argument of the function given by \code{arg} } \description{ @@ -34,6 +34,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function}()}, @@ -43,6 +44,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_has_variables.Rd b/man/assert_has_variables.Rd index 73b09b6e..684a8817 100644 --- a/man/assert_has_variables.Rd +++ b/man/assert_has_variables.Rd @@ -33,6 +33,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -42,6 +43,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_integer_scalar.Rd b/man/assert_integer_scalar.Rd index 1157d866..caec862d 100644 --- a/man/assert_integer_scalar.Rd +++ b/man/assert_integer_scalar.Rd @@ -12,7 +12,7 @@ assert_integer_scalar(arg, subset = "none", optional = FALSE) \item{subset}{A subset of integers that \code{arg} should be part of. Should be one of \code{"none"} (the default), \code{"positive"}, \code{"non-negative"} or \code{"negative"}.} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -43,6 +43,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -52,6 +53,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_list_element.Rd b/man/assert_list_element.Rd index 40018e9d..5ba4d776 100644 --- a/man/assert_list_element.Rd +++ b/man/assert_list_element.Rd @@ -46,6 +46,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -55,6 +56,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_list_of.Rd b/man/assert_list_of.Rd index 9b481c2c..7f341fc5 100644 --- a/man/assert_list_of.Rd +++ b/man/assert_list_of.Rd @@ -14,7 +14,7 @@ assert_list_of(arg, class, named = FALSE, optional = TRUE) \item{named}{If set to \code{TRUE}, an error is issued if not all elements of the list are named.} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -48,6 +48,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -57,6 +58,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_element}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_logical_scalar.Rd b/man/assert_logical_scalar.Rd index 1bab8367..c6882658 100644 --- a/man/assert_logical_scalar.Rd +++ b/man/assert_logical_scalar.Rd @@ -9,7 +9,7 @@ assert_logical_scalar(arg, optional = FALSE) \arguments{ \item{arg}{A function argument to be checked} -\item{optional}{Is the checked parameter optional? +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown. Otherwise, \code{NULL} is considered as valid value.} @@ -41,6 +41,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -50,6 +51,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_element}()}, \code{\link{assert_list_of}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_named.Rd b/man/assert_named.Rd new file mode 100644 index 00000000..1a7b7790 --- /dev/null +++ b/man/assert_named.Rd @@ -0,0 +1,52 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/assertions.R +\name{assert_named} +\alias{assert_named} +\title{Assert Argument is a Named List or Vector} +\usage{ +assert_named(arg, optional = FALSE) +} +\arguments{ +\item{arg}{A function argument to be checked} + +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} +is \code{NULL} then an error is thrown} +} +\value{ +The function throws an error if \code{arg} is not a named list or vector or +returns the input invisibly otherwise +} +\description{ +Assert that all elements of the argument are named. +} +\seealso{ +Checks for valid input and returns warning or errors messages: +\code{\link{assert_atomic_vector}()}, +\code{\link{assert_character_scalar}()}, +\code{\link{assert_character_vector}()}, +\code{\link{assert_data_frame}()}, +\code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, +\code{\link{assert_expr}()}, +\code{\link{assert_filter_cond}()}, +\code{\link{assert_function_param}()}, +\code{\link{assert_function}()}, +\code{\link{assert_has_variables}()}, +\code{\link{assert_integer_scalar}()}, +\code{\link{assert_list_element}()}, +\code{\link{assert_list_of}()}, +\code{\link{assert_logical_scalar}()}, +\code{\link{assert_named_exprs}()}, +\code{\link{assert_numeric_vector}()}, +\code{\link{assert_one_to_one}()}, +\code{\link{assert_order_vars}()}, +\code{\link{assert_param_does_not_exist}()}, +\code{\link{assert_s3_class}()}, +\code{\link{assert_same_type}()}, +\code{\link{assert_symbol}()}, +\code{\link{assert_unit}()}, +\code{\link{assert_vars}()}, +\code{\link{assert_varval_list}()} +} +\concept{assertion} +\keyword{assertion} diff --git a/man/assert_named_exprs.Rd b/man/assert_named_exprs.Rd index 45b2a907..93b860bd 100644 --- a/man/assert_named_exprs.Rd +++ b/man/assert_named_exprs.Rd @@ -9,7 +9,7 @@ assert_named_exprs(arg, optional = FALSE) \arguments{ \item{arg}{A function argument to be checked} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -26,6 +26,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -35,6 +36,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_element}()}, \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_numeric_vector.Rd b/man/assert_numeric_vector.Rd index ed6f7ffa..531fc0c3 100644 --- a/man/assert_numeric_vector.Rd +++ b/man/assert_numeric_vector.Rd @@ -9,7 +9,7 @@ assert_numeric_vector(arg, optional = FALSE) \arguments{ \item{arg}{A function argument to be checked} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -35,6 +35,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -45,6 +46,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, diff --git a/man/assert_one_to_one.Rd b/man/assert_one_to_one.Rd index bdf6aa6f..39c81bce 100644 --- a/man/assert_one_to_one.Rd +++ b/man/assert_one_to_one.Rd @@ -28,6 +28,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -38,6 +39,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, diff --git a/man/assert_order_vars.Rd b/man/assert_order_vars.Rd index 551b8f24..12245766 100644 --- a/man/assert_order_vars.Rd +++ b/man/assert_order_vars.Rd @@ -9,7 +9,7 @@ assert_order_vars(arg, optional = FALSE) \arguments{ \item{arg}{A function argument to be checked} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -44,6 +44,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -54,6 +55,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_param_does_not_exist}()}, diff --git a/man/assert_param_does_not_exist.Rd b/man/assert_param_does_not_exist.Rd index 9ce0c1f2..ab5d439b 100644 --- a/man/assert_param_does_not_exist.Rd +++ b/man/assert_param_does_not_exist.Rd @@ -35,6 +35,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -45,6 +46,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_s3_class.Rd b/man/assert_s3_class.Rd index 3243e551..f73c399c 100644 --- a/man/assert_s3_class.Rd +++ b/man/assert_s3_class.Rd @@ -11,7 +11,7 @@ assert_s3_class(arg, class, optional = FALSE) \item{class}{The S3 class to check for} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -39,6 +39,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -49,6 +50,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_same_type.Rd b/man/assert_same_type.Rd index 639e5033..850eaa55 100644 --- a/man/assert_same_type.Rd +++ b/man/assert_same_type.Rd @@ -39,6 +39,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -49,6 +50,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_symbol.Rd b/man/assert_symbol.Rd index c92dd72b..2078a609 100644 --- a/man/assert_symbol.Rd +++ b/man/assert_symbol.Rd @@ -9,7 +9,7 @@ assert_symbol(arg, optional = FALSE) \arguments{ \item{arg}{A function argument to be checked. Must be a \code{symbol}. See examples.} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -45,6 +45,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -55,6 +56,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_unit.Rd b/man/assert_unit.Rd index 7034fcec..0842ffd5 100644 --- a/man/assert_unit.Rd +++ b/man/assert_unit.Rd @@ -41,6 +41,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -51,6 +52,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_vars.Rd b/man/assert_vars.Rd index c7c77cf4..af4a992d 100644 --- a/man/assert_vars.Rd +++ b/man/assert_vars.Rd @@ -12,7 +12,7 @@ assert_vars(arg, expect_names = FALSE, optional = FALSE) \item{expect_names}{If the argument is set to \code{TRUE}, it is checked if all variables are named, e.g., \code{exprs(APERSDT = APxxSDT, APEREDT = APxxEDT)}.} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown} } \value{ @@ -53,6 +53,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -63,6 +64,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/man/assert_varval_list.Rd b/man/assert_varval_list.Rd index ba08f7d6..f99d5864 100644 --- a/man/assert_varval_list.Rd +++ b/man/assert_varval_list.Rd @@ -22,7 +22,7 @@ assert_varval_list( \item{accept_var}{Should unnamed variable names (e.g. \code{exprs(USUBJID)}) on the right hand side be accepted?} -\item{optional}{Is the checked parameter optional? If set to \code{FALSE} and \code{arg} +\item{optional}{Is the checked argument optional? If set to \code{FALSE} and \code{arg} is \code{NULL} then an error is thrown.} } \value{ @@ -31,8 +31,8 @@ Otherwise, the input it returned invisibly. } \description{ Checks if the argument is a list of expressions where the expressions are -variable-value pairs. The value can be a symbol, a string, a numeric, or -\code{NA}. More general expression are not allowed. +variable-value pairs. The value can be a symbol, a string, a numeric, an +expression, or \code{NA}. } \examples{ library(dplyr, warn.conflicts = FALSE) @@ -52,6 +52,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_character_vector}()}, \code{\link{assert_data_frame}()}, \code{\link{assert_date_vector}()}, +\code{\link{assert_expr_list}()}, \code{\link{assert_expr}()}, \code{\link{assert_filter_cond}()}, \code{\link{assert_function_param}()}, @@ -62,6 +63,7 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_list_of}()}, \code{\link{assert_logical_scalar}()}, \code{\link{assert_named_exprs}()}, +\code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, \code{\link{assert_order_vars}()}, diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index ad234530..e18cd7a3 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -523,8 +523,8 @@ test_that("assert_vars Test 31: error if some elements of `arg` are not unquoted }) # assert_order_vars ---- -## Test 32: error if `arg` is not a list variable names or `desc()` ---- -test_that("assert_order_vars Test 32: error if `arg` is not a list variable names or `desc()`", { +## Test 32: error if `arg` is not a list ---- +test_that("assert_order_vars Test 32: error if `arg` is not a list", { expect_error( assert_order_vars(arg <- TRUE), regexp = @@ -545,23 +545,32 @@ test_that("assert_order_vars Test 32: error if `arg` is not a list variable name ) }) -## Test 33: no error if valid argument ---- -test_that("assert_order_vars Test 33: no error if valid argument", { +## Test 33: error if invalid elements ---- +test_that("assert_order_vars Test 33: error if invalid elements", { + expect_error( + assert_order_vars(arg <- exprs(USUBJID, !!mean)), + regexp = "Each element of `arg` must be an expression but the following are not:", + fixed = TRUE + ) +}) + +## Test 34: no error if valid argument ---- +test_that("assert_order_vars Test 34: no error if valid argument", { expect_invisible( assert_order_vars(arg <- exprs(USUBJID, desc(PARAMCD), -abs(AVAL))) ) }) -## Test 34: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_order_vars Test 34: no error if `arg` is NULL and optional is TRUE", { +## Test 35: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_order_vars Test 35: no error if `arg` is NULL and optional is TRUE", { expect_invisible( assert_order_vars(arg <- NULL, optional = TRUE) ) }) # assert_integer_scalar ---- -## Test 35: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_integer_scalar Test 35: no error if `arg` is NULL and optional is TRUE", { +## Test 36: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_integer_scalar Test 36: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_integer_scalar(arg, optional = TRUE) } @@ -571,8 +580,8 @@ test_that("assert_integer_scalar Test 35: no error if `arg` is NULL and optional ) }) -## Test 36: error if chosen subset not in subsets ---- -test_that("assert_integer_scalar Test 36: error if chosen subset not in subsets", { +## Test 37: error if chosen subset not in subsets ---- +test_that("assert_integer_scalar Test 37: error if chosen subset not in subsets", { example_fun <- function(arg) { assert_integer_scalar(arg, subset = "infinity") } @@ -582,8 +591,8 @@ test_that("assert_integer_scalar Test 36: error if chosen subset not in subsets" ) }) -## Test 37: no error if `arg` is in selected subset ---- -test_that("assert_integer_scalar Test 37: no error if `arg` is in selected subset", { +## Test 38: no error if `arg` is in selected subset ---- +test_that("assert_integer_scalar Test 38: no error if `arg` is in selected subset", { example_fun <- function(arg) { assert_integer_scalar(arg, subset = "positive") } @@ -593,8 +602,8 @@ test_that("assert_integer_scalar Test 37: no error if `arg` is in selected subse ) }) -## Test 38: error if `arg` is not an integer scalar ---- -test_that("assert_integer_scalar Test 38: error if `arg` is not an integer scalar", { +## Test 39: error if `arg` is not an integer scalar ---- +test_that("assert_integer_scalar Test 39: error if `arg` is not an integer scalar", { example_fun <- function(arg) { assert_integer_scalar(arg) } @@ -608,8 +617,8 @@ test_that("assert_integer_scalar Test 38: error if `arg` is not an integer scala }) # assert_numeric_vector ---- -## Test 39: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_numeric_vector Test 39: no error if `arg` is NULL and optional is TRUE", { +## Test 40: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_numeric_vector Test 40: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_numeric_vector(arg, optional = TRUE) } @@ -620,8 +629,8 @@ test_that("assert_numeric_vector Test 39: no error if `arg` is NULL and optional }) # assert_integer_scalar ---- -## Test 40: error if `arg` is not an integer scalar ---- -test_that("assert_integer_scalar Test 40: error if `arg` is not an integer scalar", { +## Test 41: error if `arg` is not an integer scalar ---- +test_that("assert_integer_scalar Test 41: error if `arg` is not an integer scalar", { example_fun <- function(arg) { assert_numeric_vector(arg) } @@ -634,8 +643,8 @@ test_that("assert_integer_scalar Test 40: error if `arg` is not an integer scala }) # assert_s3_class ---- -## Test 41: error if `arg` is not an object of a specific class S3 ---- -test_that("assert_s3_class Test 41: error if `arg` is not an object of a specific class S3", { +## Test 42: error if `arg` is not an object of a specific class S3 ---- +test_that("assert_s3_class Test 42: error if `arg` is not an object of a specific class S3", { example_fun <- function(arg) { assert_s3_class(arg, "factor") } @@ -643,8 +652,8 @@ test_that("assert_s3_class Test 41: error if `arg` is not an object of a specifi expect_error(example_fun("test")) }) -## Test 42: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_s3_class Test 42: no error if `arg` is NULL and optional is TRUE", { +## Test 43: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_s3_class Test 43: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_s3_class(arg, class = "factor", optional = TRUE) } @@ -654,8 +663,8 @@ test_that("assert_s3_class Test 42: no error if `arg` is NULL and optional is TR ) }) -## Test 43: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_s3_class Test 43: error if `arg` is NULL and optional is FALSE", { +## Test 44: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_s3_class Test 44: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_s3_class(arg, class = "factor", optional = FALSE) } @@ -667,8 +676,8 @@ test_that("assert_s3_class Test 43: error if `arg` is NULL and optional is FALSE ) }) -## Test 44: no error if `arg` is an object of a specific class S3 ---- -test_that("assert_s3_class Test 44: no error if `arg` is an object of a specific class S3", { +## Test 45: no error if `arg` is an object of a specific class S3 ---- +test_that("assert_s3_class Test 45: no error if `arg` is an object of a specific class S3", { example_fun <- function(arg) { assert_s3_class(arg, "factor") } @@ -677,8 +686,8 @@ test_that("assert_s3_class Test 44: no error if `arg` is an object of a specific }) # assert_list_of ---- -## Test 45: error if `arg` is not a list of specific class S3 objects ---- -test_that("assert_list_of Test 45: error if `arg` is not a list of specific class S3 objects", { +## Test 46: error if `arg` is not a list of specific class S3 objects ---- +test_that("assert_list_of Test 46: error if `arg` is not a list of specific class S3 objects", { example_fun <- function(arg) { assert_list_of(arg, "factor") } @@ -686,8 +695,8 @@ test_that("assert_list_of Test 45: error if `arg` is not a list of specific clas expect_error(example_fun(list("test"))) }) -## Test 46: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_list_of Test 46: no error if `arg` is NULL and optional is TRUE", { +## Test 47: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_list_of Test 47: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_list_of(arg, class = "factor", optional = TRUE) } @@ -697,8 +706,8 @@ test_that("assert_list_of Test 46: no error if `arg` is NULL and optional is TRU ) }) -## Test 47: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_list_of Test 47: error if `arg` is NULL and optional is FALSE", { +## Test 48: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_list_of Test 48: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_list_of(arg, class = "factor", optional = FALSE) } @@ -710,8 +719,8 @@ test_that("assert_list_of Test 47: error if `arg` is NULL and optional is FALSE" ) }) -## Test 48: no error if `arg` is a list of specific class S3 objects ---- -test_that("assert_list_of Test 48: no error if `arg` is a list of specific class S3 objects", { +## Test 49: no error if `arg` is a list of specific class S3 objects ---- +test_that("assert_list_of Test 49: no error if `arg` is a list of specific class S3 objects", { example_fun <- function(arg) { assert_list_of(arg, "factor") } @@ -723,8 +732,8 @@ test_that("assert_list_of Test 48: no error if `arg` is a list of specific class ) }) -## Test 49: error if `arg` is not a named list (no elements named) ---- -test_that("assert_list_of Test 49: error if `arg` is not a named list (no elements named)", { +## Test 50: error if `arg` is not a named list (no elements named) ---- +test_that("assert_list_of Test 50: error if `arg` is not a named list (no elements named)", { expect_error( assert_list_of(mylist <- list(1, 2, 3), class = "numeric", named = TRUE), paste( @@ -735,8 +744,8 @@ test_that("assert_list_of Test 49: error if `arg` is not a named list (no elemen ) }) -## Test 50: error if `arg` is not a named list (some elements named) ---- -test_that("assert_list_of Test 50: error if `arg` is not a named list (some elements named)", { +## Test 51: error if `arg` is not a named list (some elements named) ---- +test_that("assert_list_of Test 51: error if `arg` is not a named list (some elements named)", { expect_error( assert_list_of(mylist <- list(1, 2, 3, d = 4), class = "numeric", named = TRUE), paste( @@ -747,16 +756,35 @@ test_that("assert_list_of Test 50: error if `arg` is not a named list (some elem ) }) -## Test 51: no error if `arg` is a named list ---- -test_that("assert_list_of Test 51: no error if `arg` is a named list", { +## Test 52: no error if `arg` is a named list ---- +test_that("assert_list_of Test 52: no error if `arg` is a named list", { expect_invisible( assert_list_of(mylist <- list(a = 1, b = 2, c = 3), class = "numeric", named = TRUE) ) }) +# assert_named ---- +## Test 53: no error if arg is NULL and optional = TRUE ---- +test_that("assert_named Test 53: no error if arg is NULL and optional = TRUE", { + expect_invisible(assert_named(arg <- NULL, optional = TRUE)) +}) + +## Test 54: error if no elements are named ---- +test_that("assert_named Test 54: error if no elements are named", { + expect_error( + assert_named(arg <- c(1, 2)), + regexp = paste( + "All elements of `arg` must be named.", + "No element is named.", + sep = "\n" + ), + fixed = TRUE + ) +}) + # assert_named_exprs ---- -## Test 52: error if `arg` is not a named list of expressions ---- -test_that("assert_named_exprs Test 52: error if `arg` is not a named list of expressions", { +## Test 55: error if `arg` is not a named list of expressions ---- +test_that("assert_named_exprs Test 55: error if `arg` is not a named list of expressions", { example_fun <- function(arg) { assert_named_exprs(arg) } @@ -770,8 +798,8 @@ test_that("assert_named_exprs Test 52: error if `arg` is not a named list of exp expect_error(example_fun(arg)) }) -## Test 53: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_named_exprs Test 53: no error if `arg` is NULL and optional is TRUE", { +## Test 56: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_named_exprs Test 56: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_named_exprs(arg, optional = TRUE) } @@ -781,8 +809,8 @@ test_that("assert_named_exprs Test 53: no error if `arg` is NULL and optional is ) }) -## Test 54: no error if `arg` is a named list of expressions ---- -test_that("assert_named_exprs Test 54: no error if `arg` is a named list of expressions", { +## Test 57: no error if `arg` is a named list of expressions ---- +test_that("assert_named_exprs Test 57: no error if `arg` is a named list of expressions", { example_fun <- function(arg) { assert_named_exprs(arg) } @@ -795,8 +823,8 @@ test_that("assert_named_exprs Test 54: no error if `arg` is a named list of expr }) # assert_function ---- -## Test 55: error if `arg` is not a function ---- -test_that("assert_function Test 55: error if `arg` is not a function", { +## Test 58: error if `arg` is not a function ---- +test_that("assert_function Test 58: error if `arg` is not a function", { example_fun <- function(arg) { assert_function(arg) } @@ -805,8 +833,8 @@ test_that("assert_function Test 55: error if `arg` is not a function", { expect_error(example_fun()) }) -## Test 56: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_function Test 56: no error if `arg` is NULL and optional is TRUE", { +## Test 59: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_function Test 59: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_function(arg, optional = TRUE) } @@ -816,8 +844,8 @@ test_that("assert_function Test 56: no error if `arg` is NULL and optional is TR ) }) -## Test 57: no error if `arg` is a function with all parameters defined ---- -test_that("assert_function Test 57: no error if `arg` is a function with all parameters defined", { +## Test 60: no error if `arg` is a function with all parameters defined ---- +test_that("assert_function Test 60: no error if `arg` is a function with all parameters defined", { example_fun <- function(arg) { assert_function(arg, params = c("x")) } @@ -825,8 +853,8 @@ test_that("assert_function Test 57: no error if `arg` is a function with all par expect_invisible(example_fun(mean)) }) -## Test 58: error if `params` is missing with no default ---- -test_that("assert_function Test 58: error if `params` is missing with no default", { +## Test 61: error if `params` is missing with no default ---- +test_that("assert_function Test 61: error if `params` is missing with no default", { example_fun <- function(arg) { assert_function(arg, params = c("x")) } @@ -842,8 +870,8 @@ test_that("assert_function Test 58: error if `params` is missing with no defau # assert_function_param ---- -## Test 59: no error if `arg` is a parameter of a function ---- -test_that("assert_function_param Test 59: no error if `arg` is a parameter of a function", { +## Test 62: no error if `arg` is a parameter of a function ---- +test_that("assert_function_param Test 62: no error if `arg` is a parameter of a function", { hello <- function(name) { print(sprintf("Hello %s", name)) } @@ -851,8 +879,8 @@ test_that("assert_function_param Test 59: no error if `arg` is a parameter of a expect_invisible(assert_function_param("hello", "name")) }) -## Test 60: error if expected function parameters are missing ---- -test_that("assert_function_param Test 60: error if expected function parameters are missing", { +## Test 63: error if expected function parameters are missing ---- +test_that("assert_function_param Test 63: error if expected function parameters are missing", { hello <- function(name) { print(sprintf("Hello %s", name)) } @@ -862,8 +890,8 @@ test_that("assert_function_param Test 60: error if expected function parameters }) # assert_unit ---- -## Test 61: no error if the parameter is provided in the expected unit ---- -test_that("assert_unit Test 61: no error if the parameter is provided in the expected unit", { +## Test 64: no error if the parameter is provided in the expected unit ---- +test_that("assert_unit Test 64: no error if the parameter is provided in the expected unit", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -875,8 +903,8 @@ test_that("assert_unit Test 61: no error if the parameter is provided in the exp ) }) -## Test 62: error if there are multiple units in the input dataset ---- -test_that("assert_unit Test 62: error if there are multiple units in the input dataset", { +## Test 65: error if there are multiple units in the input dataset ---- +test_that("assert_unit Test 65: error if there are multiple units in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -888,8 +916,8 @@ test_that("assert_unit Test 62: error if there are multiple units in the input d ) }) -## Test 63: error if unexpected unit in the input dataset ---- -test_that("assert_unit Test 63: error if unexpected unit in the input dataset", { +## Test 66: error if unexpected unit in the input dataset ---- +test_that("assert_unit Test 66: error if unexpected unit in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -902,8 +930,8 @@ test_that("assert_unit Test 63: error if unexpected unit in the input dataset", }) # assert_param_does_not_exist ---- -## Test 64: error if parameter exists in the input dataset ---- -test_that("assert_param_does_not_exist Test 64: error if parameter exists in the input dataset", { +## Test 67: error if parameter exists in the input dataset ---- +test_that("assert_param_does_not_exist Test 67: error if parameter exists in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -915,8 +943,8 @@ test_that("assert_param_does_not_exist Test 64: error if parameter exists in the ) }) -## Test 65: no error if the parameter exists in the dataset ---- -test_that("assert_param_does_not_exist Test 65: no error if the parameter exists in the dataset", { +## Test 68: no error if the parameter exists in the dataset ---- +test_that("assert_param_does_not_exist Test 68: no error if the parameter exists in the dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -929,8 +957,8 @@ test_that("assert_param_does_not_exist Test 65: no error if the parameter exists }) # assert_varval_list ---- -## Test 66: error if `arg` is not a list of var-value expressions ---- -test_that("assert_varval_list Test 66: error if `arg` is not a list of var-value expressions", { +## Test 69: error if `arg` is not a list of var-value expressions ---- +test_that("assert_varval_list Test 69: error if `arg` is not a list of var-value expressions", { example_fun <- function(arg) { assert_varval_list(arg, accept_var = FALSE) } @@ -940,8 +968,8 @@ test_that("assert_varval_list Test 66: error if `arg` is not a list of var-value ) }) -## Test 67: error if `arg` is not a list of var-value expressions ---- -test_that("assert_varval_list Test 67: error if `arg` is not a list of var-value expressions", { +## Test 70: error if `arg` is not a list of var-value expressions ---- +test_that("assert_varval_list Test 70: error if `arg` is not a list of var-value expressions", { example_fun <- function(arg) { assert_varval_list(arg, accept_var = TRUE) } @@ -951,8 +979,8 @@ test_that("assert_varval_list Test 67: error if `arg` is not a list of var-value ) }) -## Test 68: error if `required_elements` are missing from `arg` ---- -test_that("assert_varval_list Test 68: error if `required_elements` are missing from `arg`", { +## Test 71: error if `required_elements` are missing from `arg` ---- +test_that("assert_varval_list Test 71: error if `required_elements` are missing from `arg`", { example_fun <- function(arg) { assert_varval_list(arg, required_elements = "DTHDOM") } @@ -962,8 +990,8 @@ test_that("assert_varval_list Test 68: error if `required_elements` are missing ) }) -## Test 69: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_varval_list Test 69: no error if `arg` is NULL and optional is TRUE", { +## Test 72: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_varval_list Test 72: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_varval_list(arg, optional = TRUE) } @@ -973,8 +1001,8 @@ test_that("assert_varval_list Test 69: no error if `arg` is NULL and optional is ) }) -## Test 70: error if `accept_expr` is TRUE and value is invalid ---- -test_that("assert_varval_list Test 70: error if `accept_expr` is TRUE and value is invalid", { +## Test 73: error if `accept_expr` is TRUE and value is invalid ---- +test_that("assert_varval_list Test 73: error if `accept_expr` is TRUE and value is invalid", { example_fun <- function(arg) { assert_varval_list(arg, accept_expr = TRUE) } @@ -984,8 +1012,8 @@ test_that("assert_varval_list Test 70: error if `accept_expr` is TRUE and value ) }) -## Test 71: error if `accept_expr` is FALSE and value is invalid ---- -test_that("assert_varval_list Test 71: error if `accept_expr` is FALSE and value is invalid", { +## Test 74: error if `accept_expr` is FALSE and value is invalid ---- +test_that("assert_varval_list Test 74: error if `accept_expr` is FALSE and value is invalid", { example_fun <- function(arg) { assert_varval_list(arg, accept_expr = FALSE) } @@ -995,8 +1023,8 @@ test_that("assert_varval_list Test 71: error if `accept_expr` is FALSE and value ) }) -## Test 72: no error if an argument is a variable-value list ---- -test_that("assert_varval_list Test 72: no error if an argument is a variable-value list", { +## Test 75: no error if an argument is a variable-value list ---- +test_that("assert_varval_list Test 75: no error if an argument is a variable-value list", { example_fun <- function(arg) { assert_varval_list(arg) } @@ -1006,9 +1034,66 @@ test_that("assert_varval_list Test 72: no error if an argument is a variable-val ) }) +# assert_expr_list ---- +## Test 76: error if `arg` is not a list of expressions ---- +test_that("assert_expr_list Test 76: error if `arg` is not a list of expressions", { + expect_error( + assert_expr_list(arg <- c("USUBJID", "PARAMCD", "VISIT")), + regexp = "`arg` must be a named list of expressions but it is a", + fixed = TRUE + ) +}) + +## Test 77: error if `arg` is not a named list of expressions ---- +test_that("assert_expr_list Test 77: error if `arg` is not a named list of expressions", { + expect_error( + assert_expr_list(arg <- exprs(USUBJID, PARAMCD, NULL), named = TRUE), + regexp = "All elements of `arg` must be named.", + fixed = TRUE + ) +}) + +## Test 78: error if `required_elements` are missing from `arg` ---- +test_that("assert_expr_list Test 78: error if `required_elements` are missing from `arg`", { + expect_error( + assert_expr_list( + arg <- exprs(DTHSEQ = AESEQ), + required_elements = "DTHDOM"), + regexp = "The following required elements are missing in `arg`: 'DTHDOM'", + fixed = TRUE + ) +}) + +## Test 79: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_expr_list Test 79: no error if `arg` is NULL and optional is TRUE", { + expect_invisible( + assert_expr_list(NULL, optional = TRUE) + ) +}) + +## Test 80: error if element is invalid ---- +test_that("assert_expr_list Test 80: error if element is invalid", { + expect_error( + assert_expr_list(arg <- exprs(DTHSEQ = !!mean)), + regexp = "The elements of the list arg must be expressions.", + fixed = TRUE + ) +}) + +## Test 81: no error if argument is valid ---- +test_that("assert_expr_list Test 81: no error if argument is valid", { + expect_invisible( + assert_expr_list(arg <- exprs( + DTHDOM = "AE", + DTHSEQ = AESEQ, + DTHVAR = if_else(!is.na(AEDECOD), "AEDECOD", NA)) + ) + ) +}) + # assert_list_element ---- -## Test 73: no error if the elements fulfill a certain condition ---- -test_that("assert_list_element Test 73: no error if the elements fulfill a certain condition", { +## Test 82: no error if the elements fulfill a certain condition ---- +test_that("assert_list_element Test 82: no error if the elements fulfill a certain condition", { expect_invisible( assert_list_element( list( @@ -1022,8 +1107,8 @@ test_that("assert_list_element Test 73: no error if the elements fulfill a certa ) }) -## Test 74: error if the elements do not fulfill the condition ---- -test_that("assert_list_element Test 74: error if the elements do not fulfill the condition", { +## Test 83: error if the elements do not fulfill the condition ---- +test_that("assert_list_element Test 83: error if the elements do not fulfill the condition", { expect_error( assert_list_element( input <- list( @@ -1040,23 +1125,23 @@ test_that("assert_list_element Test 74: error if the elements do not fulfill the }) # assert_one_to_one ---- -## Test 75: error if there is a one to many mapping ---- -test_that("assert_one_to_one Test 75: error if there is a one to many mapping", { +## Test 84: error if there is a one to many mapping ---- +test_that("assert_one_to_one Test 84: error if there is a one to many mapping", { expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(DOMAIN), exprs(USUBJID)) ) }) -## Test 76: error if there is a many to one mapping ---- -test_that("assert_one_to_one Test 76: error if there is a many to one mapping", { +## Test 85: error if there is a many to one mapping ---- +test_that("assert_one_to_one Test 85: error if there is a many to one mapping", { expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(USUBJID), exprs(DOMAIN)) ) }) # assert_date_var ---- -## Test 77: error if variable is not a date or datetime variable ---- -test_that("assert_date_var Test 77: error if variable is not a date or datetime variable", { +## Test 86: error if variable is not a date or datetime variable ---- +test_that("assert_date_var Test 86: error if variable is not a date or datetime variable", { example_fun <- function(dataset, var) { var <- assert_symbol(enexpr(var)) assert_date_var(dataset = dataset, var = !!var) @@ -1077,18 +1162,18 @@ test_that("assert_date_var Test 77: error if variable is not a date or datetime }) # assert_date_vector ---- -## Test 78: returns error if input vector is not a date formatted ---- -test_that("assert_date_vector Test 78: returns error if input vector is not a date formatted", { +## Test 87: returns error if input vector is not a date formatted ---- +test_that("assert_date_vector Test 87: returns error if input vector is not a date formatted", { expect_error(assert_date_vector("2018-08-23")) }) -## Test 79: returns invisible if input is date formatted ---- -test_that("assert_date_vector Test 79: returns invisible if input is date formatted", { +## Test 88: returns invisible if input is date formatted ---- +test_that("assert_date_vector Test 88: returns invisible if input is date formatted", { expect_invisible(assert_date_vector(as.Date("2022-10-25"))) }) -## Test 80: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_date_vector Test 80: no error if `arg` is NULL and optional is TRUE", { +## Test 89: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_date_vector Test 89: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_date_vector(arg, optional = TRUE) } @@ -1098,8 +1183,8 @@ test_that("assert_date_vector Test 80: no error if `arg` is NULL and optional is ) }) -## Test 81: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_date_vector Test 81: error if `arg` is NULL and optional is FALSE", { +## Test 90: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_date_vector Test 90: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_date_vector(arg, optional = FALSE) } @@ -1113,22 +1198,22 @@ test_that("assert_date_vector Test 81: error if `arg` is NULL and optional is FA # assert_atomic_vector ---- -## Test 82: error if input is not atomic vector ---- -test_that("assert_atomic_vector Test 82: error if input is not atomic vector", { +## Test 91: error if input is not atomic vector ---- +test_that("assert_atomic_vector Test 91: error if input is not atomic vector", { x <- list("a", "a", "b", "c", "d", "d", 1, 1, 4) expect_error(assert_atomic_vector(x)) }) # assert_same_type ---- -## Test 83: no error if same type ---- -test_that("assert_same_type Test 83: no error if same type", { +## Test 92: no error if same type ---- +test_that("assert_same_type Test 92: no error if same type", { true_value <- "Y" false_value <- "N" expect_invisible(assert_same_type(true_value, false_value)) }) -## Test 84: error if different type ---- -test_that("assert_same_type Test 84: error if different type", { +## Test 93: error if different type ---- +test_that("assert_same_type Test 93: error if different type", { true_value <- "Y" false_value <- "N" missing_value <- 0 @@ -1147,8 +1232,8 @@ test_that("assert_same_type Test 84: error if different type", { ) }) -## Test 85: works as intended ---- -test_that("assert_same_type Test 85: works as intended", { +## Test 94: works as intended ---- +test_that("assert_same_type Test 94: works as intended", { expect_equal( valid_time_units(), c("years", "months", "days", "hours", "minutes", "seconds") diff --git a/tests/testthat/test-get.R b/tests/testthat/test-get.R index f2a88101..165497a0 100644 --- a/tests/testthat/test-get.R +++ b/tests/testthat/test-get.R @@ -57,7 +57,7 @@ test_that("get_source_vars Test 4: x is a list of expressions", { test_that("get_source_vars Test 5: NULL returns NULL", { expect_equal( get_source_vars(NULL), - expr_c(NULL) + NULL ) }) From 6b3a527ed06612e67190c6462132c9301e7075f8 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Tue, 21 Mar 2023 13:32:22 +0100 Subject: [PATCH 027/100] 241_allow_expressions: deprecate assert_order_vars() --- DESCRIPTION | 2 +- NEWS.md | 4 + R/assertions.R | 58 +----- R/quo.R | 2 +- _pkgdown.yml | 14 ++ man/assert_atomic_vector.Rd | 1 - man/assert_character_scalar.Rd | 1 - man/assert_character_vector.Rd | 1 - man/assert_data_frame.Rd | 1 - man/assert_date_vector.Rd | 1 - man/assert_expr.Rd | 1 - man/assert_expr_list.Rd | 1 - man/assert_filter_cond.Rd | 1 - man/assert_function.Rd | 1 - man/assert_function_param.Rd | 1 - man/assert_has_variables.Rd | 1 - man/assert_integer_scalar.Rd | 1 - man/assert_list_element.Rd | 1 - man/assert_list_of.Rd | 1 - man/assert_logical_scalar.Rd | 1 - man/assert_named.Rd | 1 - man/assert_named_exprs.Rd | 1 - man/assert_numeric_vector.Rd | 1 - man/assert_one_to_one.Rd | 1 - man/assert_order_vars.Rd | 53 +----- man/assert_param_does_not_exist.Rd | 1 - man/assert_s3_class.Rd | 1 - man/assert_same_type.Rd | 1 - man/assert_symbol.Rd | 1 - man/assert_unit.Rd | 1 - man/assert_vars.Rd | 1 - man/assert_varval_list.Rd | 1 - tests/testthat/test-assertions.R | 283 +++++++++++++---------------- 33 files changed, 158 insertions(+), 284 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 95900d32..e618446f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: admiraldev Type: Package Title: Utility Functions and Development Tools for the Admiral Package Family -Version: 0.3.0 +Version: 0.4.0 Authors@R: c( person("Ben", "Straub", email = "ben.x.straub@gsk.com", role = c("aut", "cre")), person("Stefan", "Bundfuss", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 03ac16e4..38accac0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -7,6 +7,10 @@ named (#241) - New function `assert_expr_list()` to check if an argument is a list of expressions (#241) +## Breaking Changes + +- `assert_order_vars()` was deprecated in favor of `assert_expr_list()`. (#241) + # admiraldev 0.3.0 ## New Features diff --git a/R/assertions.R b/R/assertions.R index 90486645..d27f8c1d 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -521,6 +521,11 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) { #' Is an Argument a List of Order Variables? #' +#' @description +#' `r lifecycle::badge("deprecated")` +#' +#' This function is *deprecated*, please use `assert_expr_list()` instead. +#' #' Checks if an argument is a valid list of order variables/expressions created #' using `exprs()` #' @@ -536,59 +541,14 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) { #' #' @export #' -#' @keywords assertion -#' @family assertion -#' @examples -#' library(dplyr, warn.conflicts = FALSE) -#' library(rlang) -#' -#' example_fun <- function(by_vars) { -#' assert_order_vars(by_vars) -#' } -#' -#' example_fun(exprs(USUBJID, PARAMCD, desc(AVISITN))) -#' -#' example_fun(exprs(USUBJID, if_else(AVALC == "Y", 1, 0))) -#' -#' try(example_fun(quos(USUBJID, PARAMCD))) -#' -#' try(example_fun(c("USUBJID", "PARAMCD", "VISIT"))) +#' @keywords deprecated +#' @family deprecated assert_order_vars <- function(arg, optional = FALSE) { assert_logical_scalar(optional) - default_err_msg <- paste( - backquote(arg_name(substitute(arg))), - "must be a list of unquoted variable names or expressions,", - "e.g. `exprs(USUBJID, desc(VISITNUM), -abs(AVAL))`" - ) - - if (isTRUE(tryCatch(force(arg), error = function(e) TRUE))) { - abort(default_err_msg) - } - - if (optional && is.null(arg)) { - return(invisible(arg)) - } - - if (!inherits(arg, "list")) { - abort(default_err_msg) - } - - is_valid <- map_lgl(arg, ~ is.call(.x) || is_expression(.x)) - if (!all(is_valid)) { - info_msg <- paste( - sprintf("\u2716 Element %s is %s", which(!is_valid), map_chr(arg[!is_valid], what_is_it)), - collapse = "\n" - ) - err_msg <- sprintf( - "Each element of `%s` must be an expression but the following are not:\n%s", - arg_name(substitute(arg)), - info_msg - ) - abort(err_msg) - } + deprecate_warn("0.11.0", "assert_order_vars()", "assert_expr_list()") - invisible(arg) + assert_expr_list(arg, optional = optional) } #' Is an Argument an Integer Scalar? diff --git a/R/quo.R b/R/quo.R index b5d5506e..47494782 100644 --- a/R/quo.R +++ b/R/quo.R @@ -234,7 +234,7 @@ replace_symbol_in_expr <- function(expression, add_suffix_to_vars <- function(order, vars, suffix) { - assert_order_vars(order) + assert_expr_list(order) assert_vars(vars) assert_character_scalar(suffix) for (i in seq_along(vars)) { diff --git a/_pkgdown.yml b/_pkgdown.yml index 1ed36a31..a4b68766 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -78,6 +78,20 @@ reference: contents: - has_keyword('dev_utility') +- title: Deprecated + desc: | + As `{admiral}` is still evolving, functions/parameters may need to be removed or replaced over time. In such cases, the function/parameter will enter the following 6-month deprecation cycle: + + * In the first release (0-3 months), there will be a warning issued if you use the function/parameter, but it will still be available to use. + * In the following release (3-6 months), an error will be produced if you use the function/parameter. + * Finally, from the 3rd release (6 months) onwards, the function/parameter will be removed from `{admiral}` and its documentation completely. + + *Note: Guidance on replacement functionality can be found in the warning/error message produced or in the function's documentation.* + + Below, you can find a list of functions in the process of being deprecated: + contents: + - has_keyword("deprecated") + navbar: components: reference: diff --git a/man/assert_atomic_vector.Rd b/man/assert_atomic_vector.Rd index 8ce5cbc0..5314c62e 100644 --- a/man/assert_atomic_vector.Rd +++ b/man/assert_atomic_vector.Rd @@ -48,7 +48,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_character_scalar.Rd b/man/assert_character_scalar.Rd index 53c9a11c..a4c8539f 100644 --- a/man/assert_character_scalar.Rd +++ b/man/assert_character_scalar.Rd @@ -78,7 +78,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_character_vector.Rd b/man/assert_character_vector.Rd index faedadc3..08e20d99 100644 --- a/man/assert_character_vector.Rd +++ b/man/assert_character_vector.Rd @@ -60,7 +60,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_data_frame.Rd b/man/assert_data_frame.Rd index 8ac0a722..0b2a8c7d 100644 --- a/man/assert_data_frame.Rd +++ b/man/assert_data_frame.Rd @@ -66,7 +66,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_date_vector.Rd b/man/assert_date_vector.Rd index 68874182..e9f1e2a9 100644 --- a/man/assert_date_vector.Rd +++ b/man/assert_date_vector.Rd @@ -49,7 +49,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_expr.Rd b/man/assert_expr.Rd index 91899736..aaa51970 100644 --- a/man/assert_expr.Rd +++ b/man/assert_expr.Rd @@ -39,7 +39,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_expr_list.Rd b/man/assert_expr_list.Rd index 641030ae..4c42c1c6 100644 --- a/man/assert_expr_list.Rd +++ b/man/assert_expr_list.Rd @@ -59,7 +59,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_filter_cond.Rd b/man/assert_filter_cond.Rd index 3944ddda..797cb61c 100644 --- a/man/assert_filter_cond.Rd +++ b/man/assert_filter_cond.Rd @@ -58,7 +58,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_function.Rd b/man/assert_function.Rd index 4df27014..728746ff 100644 --- a/man/assert_function.Rd +++ b/man/assert_function.Rd @@ -58,7 +58,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_function_param.Rd b/man/assert_function_param.Rd index 8ada48da..93a69636 100644 --- a/man/assert_function_param.Rd +++ b/man/assert_function_param.Rd @@ -47,7 +47,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_has_variables.Rd b/man/assert_has_variables.Rd index 684a8817..98fd5c4e 100644 --- a/man/assert_has_variables.Rd +++ b/man/assert_has_variables.Rd @@ -46,7 +46,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_integer_scalar.Rd b/man/assert_integer_scalar.Rd index caec862d..05d59895 100644 --- a/man/assert_integer_scalar.Rd +++ b/man/assert_integer_scalar.Rd @@ -56,7 +56,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_list_element.Rd b/man/assert_list_element.Rd index 5ba4d776..7167d04b 100644 --- a/man/assert_list_element.Rd +++ b/man/assert_list_element.Rd @@ -59,7 +59,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_list_of.Rd b/man/assert_list_of.Rd index 7f341fc5..6541616b 100644 --- a/man/assert_list_of.Rd +++ b/man/assert_list_of.Rd @@ -61,7 +61,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_logical_scalar.Rd b/man/assert_logical_scalar.Rd index c6882658..640fed0f 100644 --- a/man/assert_logical_scalar.Rd +++ b/man/assert_logical_scalar.Rd @@ -54,7 +54,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_named.Rd b/man/assert_named.Rd index 1a7b7790..d8f48e2f 100644 --- a/man/assert_named.Rd +++ b/man/assert_named.Rd @@ -39,7 +39,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named_exprs}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_named_exprs.Rd b/man/assert_named_exprs.Rd index 93b860bd..e81213a2 100644 --- a/man/assert_named_exprs.Rd +++ b/man/assert_named_exprs.Rd @@ -39,7 +39,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_numeric_vector.Rd b/man/assert_numeric_vector.Rd index 531fc0c3..a12da5ca 100644 --- a/man/assert_numeric_vector.Rd +++ b/man/assert_numeric_vector.Rd @@ -48,7 +48,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named_exprs}()}, \code{\link{assert_named}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_one_to_one.Rd b/man/assert_one_to_one.Rd index 39c81bce..09a71367 100644 --- a/man/assert_one_to_one.Rd +++ b/man/assert_one_to_one.Rd @@ -41,7 +41,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named_exprs}()}, \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_order_vars.Rd b/man/assert_order_vars.Rd index 12245766..9e662627 100644 --- a/man/assert_order_vars.Rd +++ b/man/assert_order_vars.Rd @@ -18,53 +18,12 @@ expressions created using \code{exprs()} and returns the input invisibly otherwise. } \description{ -Checks if an argument is a valid list of order variables/expressions created -using \code{exprs()} -} -\examples{ -library(dplyr, warn.conflicts = FALSE) -library(rlang) - -example_fun <- function(by_vars) { - assert_order_vars(by_vars) -} +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} -example_fun(exprs(USUBJID, PARAMCD, desc(AVISITN))) +This function is \emph{deprecated}, please use \code{assert_expr_list()} instead. -example_fun(exprs(USUBJID, if_else(AVALC == "Y", 1, 0))) - -try(example_fun(quos(USUBJID, PARAMCD))) - -try(example_fun(c("USUBJID", "PARAMCD", "VISIT"))) -} -\seealso{ -Checks for valid input and returns warning or errors messages: -\code{\link{assert_atomic_vector}()}, -\code{\link{assert_character_scalar}()}, -\code{\link{assert_character_vector}()}, -\code{\link{assert_data_frame}()}, -\code{\link{assert_date_vector}()}, -\code{\link{assert_expr_list}()}, -\code{\link{assert_expr}()}, -\code{\link{assert_filter_cond}()}, -\code{\link{assert_function_param}()}, -\code{\link{assert_function}()}, -\code{\link{assert_has_variables}()}, -\code{\link{assert_integer_scalar}()}, -\code{\link{assert_list_element}()}, -\code{\link{assert_list_of}()}, -\code{\link{assert_logical_scalar}()}, -\code{\link{assert_named_exprs}()}, -\code{\link{assert_named}()}, -\code{\link{assert_numeric_vector}()}, -\code{\link{assert_one_to_one}()}, -\code{\link{assert_param_does_not_exist}()}, -\code{\link{assert_s3_class}()}, -\code{\link{assert_same_type}()}, -\code{\link{assert_symbol}()}, -\code{\link{assert_unit}()}, -\code{\link{assert_vars}()}, -\code{\link{assert_varval_list}()} +Checks if an argument is a valid list of order variables/expressions created +using \code{exprs()} } -\concept{assertion} -\keyword{assertion} +\concept{deprecated} +\keyword{deprecated} diff --git a/man/assert_param_does_not_exist.Rd b/man/assert_param_does_not_exist.Rd index ab5d439b..c51ec8df 100644 --- a/man/assert_param_does_not_exist.Rd +++ b/man/assert_param_does_not_exist.Rd @@ -49,7 +49,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, \code{\link{assert_symbol}()}, diff --git a/man/assert_s3_class.Rd b/man/assert_s3_class.Rd index f73c399c..1726392b 100644 --- a/man/assert_s3_class.Rd +++ b/man/assert_s3_class.Rd @@ -53,7 +53,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_same_type}()}, \code{\link{assert_symbol}()}, diff --git a/man/assert_same_type.Rd b/man/assert_same_type.Rd index 850eaa55..c12d7c6c 100644 --- a/man/assert_same_type.Rd +++ b/man/assert_same_type.Rd @@ -53,7 +53,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_symbol}()}, diff --git a/man/assert_symbol.Rd b/man/assert_symbol.Rd index 2078a609..52819dfb 100644 --- a/man/assert_symbol.Rd +++ b/man/assert_symbol.Rd @@ -59,7 +59,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_unit.Rd b/man/assert_unit.Rd index 0842ffd5..52820720 100644 --- a/man/assert_unit.Rd +++ b/man/assert_unit.Rd @@ -55,7 +55,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_vars.Rd b/man/assert_vars.Rd index af4a992d..596f418a 100644 --- a/man/assert_vars.Rd +++ b/man/assert_vars.Rd @@ -67,7 +67,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/man/assert_varval_list.Rd b/man/assert_varval_list.Rd index f99d5864..343fe57c 100644 --- a/man/assert_varval_list.Rd +++ b/man/assert_varval_list.Rd @@ -66,7 +66,6 @@ Checks for valid input and returns warning or errors messages: \code{\link{assert_named}()}, \code{\link{assert_numeric_vector}()}, \code{\link{assert_one_to_one}()}, -\code{\link{assert_order_vars}()}, \code{\link{assert_param_does_not_exist}()}, \code{\link{assert_s3_class}()}, \code{\link{assert_same_type}()}, diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index e18cd7a3..701815f6 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -523,54 +523,17 @@ test_that("assert_vars Test 31: error if some elements of `arg` are not unquoted }) # assert_order_vars ---- -## Test 32: error if `arg` is not a list ---- -test_that("assert_order_vars Test 32: error if `arg` is not a list", { - expect_error( - assert_order_vars(arg <- TRUE), - regexp = - paste( - "`arg` must be a list of unquoted variable names or expressions,", - "e.g. `exprs(USUBJID, desc(VISITNUM), -abs(AVAL))`" - ), - fixed = TRUE - ) - expect_error( - assert_order_vars(arg <- 1), - regexp = - paste( - "`arg` must be a list of unquoted variable names or expressions,", - "e.g. `exprs(USUBJID, desc(VISITNUM), -abs(AVAL))`" - ), - fixed = TRUE - ) -}) - -## Test 33: error if invalid elements ---- -test_that("assert_order_vars Test 33: error if invalid elements", { - expect_error( - assert_order_vars(arg <- exprs(USUBJID, !!mean)), - regexp = "Each element of `arg` must be an expression but the following are not:", - fixed = TRUE - ) -}) - -## Test 34: no error if valid argument ---- -test_that("assert_order_vars Test 34: no error if valid argument", { - expect_invisible( - assert_order_vars(arg <- exprs(USUBJID, desc(PARAMCD), -abs(AVAL))) - ) -}) - -## Test 35: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_order_vars Test 35: no error if `arg` is NULL and optional is TRUE", { - expect_invisible( - assert_order_vars(arg <- NULL, optional = TRUE) +## Test 32: warn if assert_order_vars() is called ---- +test_that("assert_order_vars Test 32: warn if assert_order_vars() is called", { + expect_warning( + assert_order_vars(arg <- exprs(USUBJID)), + class = "lifecycle_warning_deprecated" ) }) # assert_integer_scalar ---- -## Test 36: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_integer_scalar Test 36: no error if `arg` is NULL and optional is TRUE", { +## Test 33: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_integer_scalar Test 33: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_integer_scalar(arg, optional = TRUE) } @@ -580,8 +543,8 @@ test_that("assert_integer_scalar Test 36: no error if `arg` is NULL and optional ) }) -## Test 37: error if chosen subset not in subsets ---- -test_that("assert_integer_scalar Test 37: error if chosen subset not in subsets", { +## Test 34: error if chosen subset not in subsets ---- +test_that("assert_integer_scalar Test 34: error if chosen subset not in subsets", { example_fun <- function(arg) { assert_integer_scalar(arg, subset = "infinity") } @@ -591,8 +554,8 @@ test_that("assert_integer_scalar Test 37: error if chosen subset not in subsets" ) }) -## Test 38: no error if `arg` is in selected subset ---- -test_that("assert_integer_scalar Test 38: no error if `arg` is in selected subset", { +## Test 35: no error if `arg` is in selected subset ---- +test_that("assert_integer_scalar Test 35: no error if `arg` is in selected subset", { example_fun <- function(arg) { assert_integer_scalar(arg, subset = "positive") } @@ -602,8 +565,8 @@ test_that("assert_integer_scalar Test 38: no error if `arg` is in selected subse ) }) -## Test 39: error if `arg` is not an integer scalar ---- -test_that("assert_integer_scalar Test 39: error if `arg` is not an integer scalar", { +## Test 36: error if `arg` is not an integer scalar ---- +test_that("assert_integer_scalar Test 36: error if `arg` is not an integer scalar", { example_fun <- function(arg) { assert_integer_scalar(arg) } @@ -617,8 +580,8 @@ test_that("assert_integer_scalar Test 39: error if `arg` is not an integer scala }) # assert_numeric_vector ---- -## Test 40: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_numeric_vector Test 40: no error if `arg` is NULL and optional is TRUE", { +## Test 37: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_numeric_vector Test 37: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_numeric_vector(arg, optional = TRUE) } @@ -629,8 +592,8 @@ test_that("assert_numeric_vector Test 40: no error if `arg` is NULL and optional }) # assert_integer_scalar ---- -## Test 41: error if `arg` is not an integer scalar ---- -test_that("assert_integer_scalar Test 41: error if `arg` is not an integer scalar", { +## Test 38: error if `arg` is not an integer scalar ---- +test_that("assert_integer_scalar Test 38: error if `arg` is not an integer scalar", { example_fun <- function(arg) { assert_numeric_vector(arg) } @@ -643,8 +606,8 @@ test_that("assert_integer_scalar Test 41: error if `arg` is not an integer scala }) # assert_s3_class ---- -## Test 42: error if `arg` is not an object of a specific class S3 ---- -test_that("assert_s3_class Test 42: error if `arg` is not an object of a specific class S3", { +## Test 39: error if `arg` is not an object of a specific class S3 ---- +test_that("assert_s3_class Test 39: error if `arg` is not an object of a specific class S3", { example_fun <- function(arg) { assert_s3_class(arg, "factor") } @@ -652,8 +615,8 @@ test_that("assert_s3_class Test 42: error if `arg` is not an object of a specifi expect_error(example_fun("test")) }) -## Test 43: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_s3_class Test 43: no error if `arg` is NULL and optional is TRUE", { +## Test 40: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_s3_class Test 40: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_s3_class(arg, class = "factor", optional = TRUE) } @@ -663,8 +626,8 @@ test_that("assert_s3_class Test 43: no error if `arg` is NULL and optional is TR ) }) -## Test 44: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_s3_class Test 44: error if `arg` is NULL and optional is FALSE", { +## Test 41: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_s3_class Test 41: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_s3_class(arg, class = "factor", optional = FALSE) } @@ -676,8 +639,8 @@ test_that("assert_s3_class Test 44: error if `arg` is NULL and optional is FALSE ) }) -## Test 45: no error if `arg` is an object of a specific class S3 ---- -test_that("assert_s3_class Test 45: no error if `arg` is an object of a specific class S3", { +## Test 42: no error if `arg` is an object of a specific class S3 ---- +test_that("assert_s3_class Test 42: no error if `arg` is an object of a specific class S3", { example_fun <- function(arg) { assert_s3_class(arg, "factor") } @@ -686,8 +649,8 @@ test_that("assert_s3_class Test 45: no error if `arg` is an object of a specific }) # assert_list_of ---- -## Test 46: error if `arg` is not a list of specific class S3 objects ---- -test_that("assert_list_of Test 46: error if `arg` is not a list of specific class S3 objects", { +## Test 43: error if `arg` is not a list of specific class S3 objects ---- +test_that("assert_list_of Test 43: error if `arg` is not a list of specific class S3 objects", { example_fun <- function(arg) { assert_list_of(arg, "factor") } @@ -695,8 +658,8 @@ test_that("assert_list_of Test 46: error if `arg` is not a list of specific clas expect_error(example_fun(list("test"))) }) -## Test 47: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_list_of Test 47: no error if `arg` is NULL and optional is TRUE", { +## Test 44: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_list_of Test 44: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_list_of(arg, class = "factor", optional = TRUE) } @@ -706,8 +669,8 @@ test_that("assert_list_of Test 47: no error if `arg` is NULL and optional is TRU ) }) -## Test 48: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_list_of Test 48: error if `arg` is NULL and optional is FALSE", { +## Test 45: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_list_of Test 45: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_list_of(arg, class = "factor", optional = FALSE) } @@ -719,8 +682,8 @@ test_that("assert_list_of Test 48: error if `arg` is NULL and optional is FALSE" ) }) -## Test 49: no error if `arg` is a list of specific class S3 objects ---- -test_that("assert_list_of Test 49: no error if `arg` is a list of specific class S3 objects", { +## Test 46: no error if `arg` is a list of specific class S3 objects ---- +test_that("assert_list_of Test 46: no error if `arg` is a list of specific class S3 objects", { example_fun <- function(arg) { assert_list_of(arg, "factor") } @@ -732,8 +695,8 @@ test_that("assert_list_of Test 49: no error if `arg` is a list of specific class ) }) -## Test 50: error if `arg` is not a named list (no elements named) ---- -test_that("assert_list_of Test 50: error if `arg` is not a named list (no elements named)", { +## Test 47: error if `arg` is not a named list (no elements named) ---- +test_that("assert_list_of Test 47: error if `arg` is not a named list (no elements named)", { expect_error( assert_list_of(mylist <- list(1, 2, 3), class = "numeric", named = TRUE), paste( @@ -744,8 +707,8 @@ test_that("assert_list_of Test 50: error if `arg` is not a named list (no elemen ) }) -## Test 51: error if `arg` is not a named list (some elements named) ---- -test_that("assert_list_of Test 51: error if `arg` is not a named list (some elements named)", { +## Test 48: error if `arg` is not a named list (some elements named) ---- +test_that("assert_list_of Test 48: error if `arg` is not a named list (some elements named)", { expect_error( assert_list_of(mylist <- list(1, 2, 3, d = 4), class = "numeric", named = TRUE), paste( @@ -756,21 +719,21 @@ test_that("assert_list_of Test 51: error if `arg` is not a named list (some elem ) }) -## Test 52: no error if `arg` is a named list ---- -test_that("assert_list_of Test 52: no error if `arg` is a named list", { +## Test 49: no error if `arg` is a named list ---- +test_that("assert_list_of Test 49: no error if `arg` is a named list", { expect_invisible( assert_list_of(mylist <- list(a = 1, b = 2, c = 3), class = "numeric", named = TRUE) ) }) # assert_named ---- -## Test 53: no error if arg is NULL and optional = TRUE ---- -test_that("assert_named Test 53: no error if arg is NULL and optional = TRUE", { +## Test 50: no error if arg is NULL and optional = TRUE ---- +test_that("assert_named Test 50: no error if arg is NULL and optional = TRUE", { expect_invisible(assert_named(arg <- NULL, optional = TRUE)) }) -## Test 54: error if no elements are named ---- -test_that("assert_named Test 54: error if no elements are named", { +## Test 51: error if no elements are named ---- +test_that("assert_named Test 51: error if no elements are named", { expect_error( assert_named(arg <- c(1, 2)), regexp = paste( @@ -783,8 +746,8 @@ test_that("assert_named Test 54: error if no elements are named", { }) # assert_named_exprs ---- -## Test 55: error if `arg` is not a named list of expressions ---- -test_that("assert_named_exprs Test 55: error if `arg` is not a named list of expressions", { +## Test 52: error if `arg` is not a named list of expressions ---- +test_that("assert_named_exprs Test 52: error if `arg` is not a named list of expressions", { example_fun <- function(arg) { assert_named_exprs(arg) } @@ -798,8 +761,8 @@ test_that("assert_named_exprs Test 55: error if `arg` is not a named list of exp expect_error(example_fun(arg)) }) -## Test 56: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_named_exprs Test 56: no error if `arg` is NULL and optional is TRUE", { +## Test 53: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_named_exprs Test 53: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_named_exprs(arg, optional = TRUE) } @@ -809,8 +772,8 @@ test_that("assert_named_exprs Test 56: no error if `arg` is NULL and optional is ) }) -## Test 57: no error if `arg` is a named list of expressions ---- -test_that("assert_named_exprs Test 57: no error if `arg` is a named list of expressions", { +## Test 54: no error if `arg` is a named list of expressions ---- +test_that("assert_named_exprs Test 54: no error if `arg` is a named list of expressions", { example_fun <- function(arg) { assert_named_exprs(arg) } @@ -823,8 +786,8 @@ test_that("assert_named_exprs Test 57: no error if `arg` is a named list of expr }) # assert_function ---- -## Test 58: error if `arg` is not a function ---- -test_that("assert_function Test 58: error if `arg` is not a function", { +## Test 55: error if `arg` is not a function ---- +test_that("assert_function Test 55: error if `arg` is not a function", { example_fun <- function(arg) { assert_function(arg) } @@ -833,8 +796,8 @@ test_that("assert_function Test 58: error if `arg` is not a function", { expect_error(example_fun()) }) -## Test 59: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_function Test 59: no error if `arg` is NULL and optional is TRUE", { +## Test 56: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_function Test 56: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_function(arg, optional = TRUE) } @@ -844,8 +807,8 @@ test_that("assert_function Test 59: no error if `arg` is NULL and optional is TR ) }) -## Test 60: no error if `arg` is a function with all parameters defined ---- -test_that("assert_function Test 60: no error if `arg` is a function with all parameters defined", { +## Test 57: no error if `arg` is a function with all parameters defined ---- +test_that("assert_function Test 57: no error if `arg` is a function with all parameters defined", { example_fun <- function(arg) { assert_function(arg, params = c("x")) } @@ -853,8 +816,8 @@ test_that("assert_function Test 60: no error if `arg` is a function with all par expect_invisible(example_fun(mean)) }) -## Test 61: error if `params` is missing with no default ---- -test_that("assert_function Test 61: error if `params` is missing with no default", { +## Test 58: error if `params` is missing with no default ---- +test_that("assert_function Test 58: error if `params` is missing with no default", { example_fun <- function(arg) { assert_function(arg, params = c("x")) } @@ -870,8 +833,8 @@ test_that("assert_function Test 61: error if `params` is missing with no defau # assert_function_param ---- -## Test 62: no error if `arg` is a parameter of a function ---- -test_that("assert_function_param Test 62: no error if `arg` is a parameter of a function", { +## Test 59: no error if `arg` is a parameter of a function ---- +test_that("assert_function_param Test 59: no error if `arg` is a parameter of a function", { hello <- function(name) { print(sprintf("Hello %s", name)) } @@ -879,8 +842,8 @@ test_that("assert_function_param Test 62: no error if `arg` is a parameter of a expect_invisible(assert_function_param("hello", "name")) }) -## Test 63: error if expected function parameters are missing ---- -test_that("assert_function_param Test 63: error if expected function parameters are missing", { +## Test 60: error if expected function parameters are missing ---- +test_that("assert_function_param Test 60: error if expected function parameters are missing", { hello <- function(name) { print(sprintf("Hello %s", name)) } @@ -890,8 +853,8 @@ test_that("assert_function_param Test 63: error if expected function parameters }) # assert_unit ---- -## Test 64: no error if the parameter is provided in the expected unit ---- -test_that("assert_unit Test 64: no error if the parameter is provided in the expected unit", { +## Test 61: no error if the parameter is provided in the expected unit ---- +test_that("assert_unit Test 61: no error if the parameter is provided in the expected unit", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -903,8 +866,8 @@ test_that("assert_unit Test 64: no error if the parameter is provided in the exp ) }) -## Test 65: error if there are multiple units in the input dataset ---- -test_that("assert_unit Test 65: error if there are multiple units in the input dataset", { +## Test 62: error if there are multiple units in the input dataset ---- +test_that("assert_unit Test 62: error if there are multiple units in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -916,8 +879,8 @@ test_that("assert_unit Test 65: error if there are multiple units in the input d ) }) -## Test 66: error if unexpected unit in the input dataset ---- -test_that("assert_unit Test 66: error if unexpected unit in the input dataset", { +## Test 63: error if unexpected unit in the input dataset ---- +test_that("assert_unit Test 63: error if unexpected unit in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -930,8 +893,8 @@ test_that("assert_unit Test 66: error if unexpected unit in the input dataset", }) # assert_param_does_not_exist ---- -## Test 67: error if parameter exists in the input dataset ---- -test_that("assert_param_does_not_exist Test 67: error if parameter exists in the input dataset", { +## Test 64: error if parameter exists in the input dataset ---- +test_that("assert_param_does_not_exist Test 64: error if parameter exists in the input dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -943,8 +906,8 @@ test_that("assert_param_does_not_exist Test 67: error if parameter exists in the ) }) -## Test 68: no error if the parameter exists in the dataset ---- -test_that("assert_param_does_not_exist Test 68: no error if the parameter exists in the dataset", { +## Test 65: no error if the parameter exists in the dataset ---- +test_that("assert_param_does_not_exist Test 65: no error if the parameter exists in the dataset", { advs <- tibble::tribble( ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL, "P01", "WEIGHT", 80.1, "kg", "WEIGHT", 80.1, @@ -957,8 +920,8 @@ test_that("assert_param_does_not_exist Test 68: no error if the parameter exists }) # assert_varval_list ---- -## Test 69: error if `arg` is not a list of var-value expressions ---- -test_that("assert_varval_list Test 69: error if `arg` is not a list of var-value expressions", { +## Test 66: error if `arg` is not a list of var-value expressions ---- +test_that("assert_varval_list Test 66: error if `arg` is not a list of var-value expressions", { example_fun <- function(arg) { assert_varval_list(arg, accept_var = FALSE) } @@ -968,8 +931,8 @@ test_that("assert_varval_list Test 69: error if `arg` is not a list of var-value ) }) -## Test 70: error if `arg` is not a list of var-value expressions ---- -test_that("assert_varval_list Test 70: error if `arg` is not a list of var-value expressions", { +## Test 67: error if `arg` is not a list of var-value expressions ---- +test_that("assert_varval_list Test 67: error if `arg` is not a list of var-value expressions", { example_fun <- function(arg) { assert_varval_list(arg, accept_var = TRUE) } @@ -979,8 +942,8 @@ test_that("assert_varval_list Test 70: error if `arg` is not a list of var-value ) }) -## Test 71: error if `required_elements` are missing from `arg` ---- -test_that("assert_varval_list Test 71: error if `required_elements` are missing from `arg`", { +## Test 68: error if `required_elements` are missing from `arg` ---- +test_that("assert_varval_list Test 68: error if `required_elements` are missing from `arg`", { example_fun <- function(arg) { assert_varval_list(arg, required_elements = "DTHDOM") } @@ -990,8 +953,8 @@ test_that("assert_varval_list Test 71: error if `required_elements` are missing ) }) -## Test 72: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_varval_list Test 72: no error if `arg` is NULL and optional is TRUE", { +## Test 69: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_varval_list Test 69: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_varval_list(arg, optional = TRUE) } @@ -1001,8 +964,8 @@ test_that("assert_varval_list Test 72: no error if `arg` is NULL and optional is ) }) -## Test 73: error if `accept_expr` is TRUE and value is invalid ---- -test_that("assert_varval_list Test 73: error if `accept_expr` is TRUE and value is invalid", { +## Test 70: error if `accept_expr` is TRUE and value is invalid ---- +test_that("assert_varval_list Test 70: error if `accept_expr` is TRUE and value is invalid", { example_fun <- function(arg) { assert_varval_list(arg, accept_expr = TRUE) } @@ -1012,8 +975,8 @@ test_that("assert_varval_list Test 73: error if `accept_expr` is TRUE and value ) }) -## Test 74: error if `accept_expr` is FALSE and value is invalid ---- -test_that("assert_varval_list Test 74: error if `accept_expr` is FALSE and value is invalid", { +## Test 71: error if `accept_expr` is FALSE and value is invalid ---- +test_that("assert_varval_list Test 71: error if `accept_expr` is FALSE and value is invalid", { example_fun <- function(arg) { assert_varval_list(arg, accept_expr = FALSE) } @@ -1023,8 +986,8 @@ test_that("assert_varval_list Test 74: error if `accept_expr` is FALSE and value ) }) -## Test 75: no error if an argument is a variable-value list ---- -test_that("assert_varval_list Test 75: no error if an argument is a variable-value list", { +## Test 72: no error if an argument is a variable-value list ---- +test_that("assert_varval_list Test 72: no error if an argument is a variable-value list", { example_fun <- function(arg) { assert_varval_list(arg) } @@ -1035,8 +998,8 @@ test_that("assert_varval_list Test 75: no error if an argument is a variable-val }) # assert_expr_list ---- -## Test 76: error if `arg` is not a list of expressions ---- -test_that("assert_expr_list Test 76: error if `arg` is not a list of expressions", { +## Test 73: error if `arg` is not a list of expressions ---- +test_that("assert_expr_list Test 73: error if `arg` is not a list of expressions", { expect_error( assert_expr_list(arg <- c("USUBJID", "PARAMCD", "VISIT")), regexp = "`arg` must be a named list of expressions but it is a", @@ -1044,8 +1007,8 @@ test_that("assert_expr_list Test 76: error if `arg` is not a list of expressions ) }) -## Test 77: error if `arg` is not a named list of expressions ---- -test_that("assert_expr_list Test 77: error if `arg` is not a named list of expressions", { +## Test 74: error if `arg` is not a named list of expressions ---- +test_that("assert_expr_list Test 74: error if `arg` is not a named list of expressions", { expect_error( assert_expr_list(arg <- exprs(USUBJID, PARAMCD, NULL), named = TRUE), regexp = "All elements of `arg` must be named.", @@ -1053,8 +1016,8 @@ test_that("assert_expr_list Test 77: error if `arg` is not a named list of expre ) }) -## Test 78: error if `required_elements` are missing from `arg` ---- -test_that("assert_expr_list Test 78: error if `required_elements` are missing from `arg`", { +## Test 75: error if `required_elements` are missing from `arg` ---- +test_that("assert_expr_list Test 75: error if `required_elements` are missing from `arg`", { expect_error( assert_expr_list( arg <- exprs(DTHSEQ = AESEQ), @@ -1064,15 +1027,15 @@ test_that("assert_expr_list Test 78: error if `required_elements` are missing fr ) }) -## Test 79: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_expr_list Test 79: no error if `arg` is NULL and optional is TRUE", { +## Test 76: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_expr_list Test 76: no error if `arg` is NULL and optional is TRUE", { expect_invisible( assert_expr_list(NULL, optional = TRUE) ) }) -## Test 80: error if element is invalid ---- -test_that("assert_expr_list Test 80: error if element is invalid", { +## Test 77: error if element is invalid ---- +test_that("assert_expr_list Test 77: error if element is invalid", { expect_error( assert_expr_list(arg <- exprs(DTHSEQ = !!mean)), regexp = "The elements of the list arg must be expressions.", @@ -1080,8 +1043,8 @@ test_that("assert_expr_list Test 80: error if element is invalid", { ) }) -## Test 81: no error if argument is valid ---- -test_that("assert_expr_list Test 81: no error if argument is valid", { +## Test 78: no error if argument is valid ---- +test_that("assert_expr_list Test 78: no error if argument is valid", { expect_invisible( assert_expr_list(arg <- exprs( DTHDOM = "AE", @@ -1092,8 +1055,8 @@ test_that("assert_expr_list Test 81: no error if argument is valid", { }) # assert_list_element ---- -## Test 82: no error if the elements fulfill a certain condition ---- -test_that("assert_list_element Test 82: no error if the elements fulfill a certain condition", { +## Test 79: no error if the elements fulfill a certain condition ---- +test_that("assert_list_element Test 79: no error if the elements fulfill a certain condition", { expect_invisible( assert_list_element( list( @@ -1107,8 +1070,8 @@ test_that("assert_list_element Test 82: no error if the elements fulfill a certa ) }) -## Test 83: error if the elements do not fulfill the condition ---- -test_that("assert_list_element Test 83: error if the elements do not fulfill the condition", { +## Test 80: error if the elements do not fulfill the condition ---- +test_that("assert_list_element Test 80: error if the elements do not fulfill the condition", { expect_error( assert_list_element( input <- list( @@ -1125,23 +1088,23 @@ test_that("assert_list_element Test 83: error if the elements do not fulfill the }) # assert_one_to_one ---- -## Test 84: error if there is a one to many mapping ---- -test_that("assert_one_to_one Test 84: error if there is a one to many mapping", { +## Test 81: error if there is a one to many mapping ---- +test_that("assert_one_to_one Test 81: error if there is a one to many mapping", { expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(DOMAIN), exprs(USUBJID)) ) }) -## Test 85: error if there is a many to one mapping ---- -test_that("assert_one_to_one Test 85: error if there is a many to one mapping", { +## Test 82: error if there is a many to one mapping ---- +test_that("assert_one_to_one Test 82: error if there is a many to one mapping", { expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(USUBJID), exprs(DOMAIN)) ) }) # assert_date_var ---- -## Test 86: error if variable is not a date or datetime variable ---- -test_that("assert_date_var Test 86: error if variable is not a date or datetime variable", { +## Test 83: error if variable is not a date or datetime variable ---- +test_that("assert_date_var Test 83: error if variable is not a date or datetime variable", { example_fun <- function(dataset, var) { var <- assert_symbol(enexpr(var)) assert_date_var(dataset = dataset, var = !!var) @@ -1162,18 +1125,18 @@ test_that("assert_date_var Test 86: error if variable is not a date or datetime }) # assert_date_vector ---- -## Test 87: returns error if input vector is not a date formatted ---- -test_that("assert_date_vector Test 87: returns error if input vector is not a date formatted", { +## Test 84: returns error if input vector is not a date formatted ---- +test_that("assert_date_vector Test 84: returns error if input vector is not a date formatted", { expect_error(assert_date_vector("2018-08-23")) }) -## Test 88: returns invisible if input is date formatted ---- -test_that("assert_date_vector Test 88: returns invisible if input is date formatted", { +## Test 85: returns invisible if input is date formatted ---- +test_that("assert_date_vector Test 85: returns invisible if input is date formatted", { expect_invisible(assert_date_vector(as.Date("2022-10-25"))) }) -## Test 89: no error if `arg` is NULL and optional is TRUE ---- -test_that("assert_date_vector Test 89: no error if `arg` is NULL and optional is TRUE", { +## Test 86: no error if `arg` is NULL and optional is TRUE ---- +test_that("assert_date_vector Test 86: no error if `arg` is NULL and optional is TRUE", { example_fun <- function(arg) { assert_date_vector(arg, optional = TRUE) } @@ -1183,8 +1146,8 @@ test_that("assert_date_vector Test 89: no error if `arg` is NULL and optional is ) }) -## Test 90: error if `arg` is NULL and optional is FALSE ---- -test_that("assert_date_vector Test 90: error if `arg` is NULL and optional is FALSE", { +## Test 87: error if `arg` is NULL and optional is FALSE ---- +test_that("assert_date_vector Test 87: error if `arg` is NULL and optional is FALSE", { example_fun <- function(arg) { assert_date_vector(arg, optional = FALSE) } @@ -1198,22 +1161,22 @@ test_that("assert_date_vector Test 90: error if `arg` is NULL and optional is FA # assert_atomic_vector ---- -## Test 91: error if input is not atomic vector ---- -test_that("assert_atomic_vector Test 91: error if input is not atomic vector", { +## Test 88: error if input is not atomic vector ---- +test_that("assert_atomic_vector Test 88: error if input is not atomic vector", { x <- list("a", "a", "b", "c", "d", "d", 1, 1, 4) expect_error(assert_atomic_vector(x)) }) # assert_same_type ---- -## Test 92: no error if same type ---- -test_that("assert_same_type Test 92: no error if same type", { +## Test 89: no error if same type ---- +test_that("assert_same_type Test 89: no error if same type", { true_value <- "Y" false_value <- "N" expect_invisible(assert_same_type(true_value, false_value)) }) -## Test 93: error if different type ---- -test_that("assert_same_type Test 93: error if different type", { +## Test 90: error if different type ---- +test_that("assert_same_type Test 90: error if different type", { true_value <- "Y" false_value <- "N" missing_value <- 0 @@ -1232,8 +1195,8 @@ test_that("assert_same_type Test 93: error if different type", { ) }) -## Test 94: works as intended ---- -test_that("assert_same_type Test 94: works as intended", { +## Test 91: works as intended ---- +test_that("assert_same_type Test 91: works as intended", { expect_equal( valid_time_units(), c("years", "months", "days", "hours", "minutes", "seconds") From a2748e3d4c068c8f98981fcbf5b93e194b498586 Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 23 Mar 2023 09:28:52 +0000 Subject: [PATCH 028/100] renv update from pharmaverse/admiralci --- renv/profiles/4.2/renv.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 7a184f4b..ef168c98 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.2.2", + "Version": "4.2.3", "Repositories": [ { "Name": "CRAN", @@ -223,13 +223,13 @@ }, "codetools": { "Package": "codetools", - "Version": "0.2-18", + "Version": "0.2-19", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "019388fc48e48b3da0d3a76ff94608a8" + "Hash": "c089a619a7fae175d149d89164f8c7d8" }, "commonmark": { "Package": "commonmark", From 11b2a9c1b7d42fafea170d3d94d50e125e014595 Mon Sep 17 00:00:00 2001 From: galachad Date: Thu, 23 Mar 2023 10:03:50 +0000 Subject: [PATCH 029/100] renv update from pharmaverse/admiralci --- renv.lock | 4 ++-- renv/profiles/4.0/renv.lock | 4 ++-- renv/profiles/4.1/renv.lock | 4 ++-- renv/profiles/4.2/renv.lock | 6 +++--- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/renv.lock b/renv.lock index 628cf197..a4df9cbb 100644 --- a/renv.lock +++ b/renv.lock @@ -1310,7 +1310,7 @@ }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1325,7 +1325,7 @@ "vctrs", "withr" ], - "Hash": "c855e70eb69b3dd8883660b7110e0c44" + "Hash": "ed8c90822b7da46beee603f263a85fe0" }, "sys": { "Package": "sys", diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index 628cf197..a4df9cbb 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -1310,7 +1310,7 @@ }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1325,7 +1325,7 @@ "vctrs", "withr" ], - "Hash": "c855e70eb69b3dd8883660b7110e0c44" + "Hash": "ed8c90822b7da46beee603f263a85fe0" }, "sys": { "Package": "sys", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index d13b1d96..2a2b73f8 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -1316,7 +1316,7 @@ }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1331,7 +1331,7 @@ "vctrs", "withr" ], - "Hash": "c855e70eb69b3dd8883660b7110e0c44" + "Hash": "ed8c90822b7da46beee603f263a85fe0" }, "sys": { "Package": "sys", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index ef168c98..db0b84f9 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -1340,9 +1340,9 @@ }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R.cache", @@ -1355,7 +1355,7 @@ "vctrs", "withr" ], - "Hash": "c855e70eb69b3dd8883660b7110e0c44" + "Hash": "ed8c90822b7da46beee603f263a85fe0" }, "sys": { "Package": "sys", From 80ffbad2f1d1acebc7252a488c29cf07bbb4a381 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Fri, 24 Mar 2023 11:55:09 +0100 Subject: [PATCH 030/100] 247_update_deprecation: update programming strategy --- NEWS.md | 7 + vignettes/programming_strategy.Rmd | 199 ++++++++++++++++------------- 2 files changed, 118 insertions(+), 88 deletions(-) diff --git a/NEWS.md b/NEWS.md index 1c0a9c95..a7d6f8f3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# admiraldev 0.4.0 + +## Documentation + +- The deprecation strategy was updated regarding unit tests for deprecated +functions/arguments in phase 1. (#247) + # admiraldev 0.3.0 ## New Features diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index 211723f7..92c00887 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -82,19 +82,19 @@ For example: * The source variables or newly created variables and conditions for selecting observations should not be hard-coded. - * It is useful if a parameter triggers optional steps, e.g. if the filter parameter is specified, the input dataset + * It is useful if an argument triggers optional steps, e.g. if the `filter` argument is specified, the input dataset is restricted, otherwise this step is skipped. - * However, parameters should not trigger completely different algorithms. For example `BNRIND` could be derived based + * However, arguments should not trigger completely different algorithms. For example `BNRIND` could be derived based on `BASE` or based on `ANRIND`. It should not be implemented within one function as the algorithms are completely different. If `BASE` is used, the values are categorized while if `ANRIND` is used, the values are merged from the baseline observation. ## Input, Output, and Side-effects * The behavior of the function is only determined by its input, not by any global object, -i.e. all input like datasets, variable names, options, … must be provided to the function by parameters. +i.e. all input like datasets, variable names, options, … must be provided to the function by arguments. * It is expected that the input datasets are not grouped. If any are grouped, the function must issue an error. -* If a function requires grouping, the function must provide the `by_vars` parameter. +* If a function requires grouping, the function must provide the `by_vars` argument. * The output dataset must be ungrouped. * The functions should not sort (arrange) the output dataset at the end. * If the function needs to create temporary variables in an input dataset, names @@ -150,25 +150,25 @@ documentation of `set_admiral_options()`. -Please note that the appropriate *var*/*vars* prefix should be used for all cases in which the function creates any variable(s), regardless of the presence of a `new_var` parameter in the function call. +Please note that the appropriate *var*/*vars* prefix should be used for all cases in which the function creates any variable(s), regardless of the presence of a `new_var` argument in the function call. -## Function Parameters +## Function Arguments -The default value of optional parameters should be `NULL`. +The default value of optional arguments should be `NULL`. -There is a recommended parameter order that all contributors are asked to adhere to +There is a recommended argument order that all contributors are asked to adhere to (in order to keep consistency across functions): 1. `dataset` (and any additional datasets denoted by `dataset_*`) 1. `by_vars` 1. `order` -1. `new_var` (and any related `new_var_*` parameters) +1. `new_var` (and any related `new_var_*` arguments) 1. `filter` (and any additional filters denoted by `filter_*`) 1. all additional arguments: * Make sure to always mention `start_date` before `end_date` (or related). Names of variables inside a dataset should be passed as symbols rather than strings, i.e. `AVAL` rather than `"AVAL"`. -If a parameter accepts one or more variables as input, the variables should be wrapped inside `exprs()`. +If an argument accepts one or more variables as input, the variables should be wrapped inside `exprs()`. For example: @@ -177,8 +177,8 @@ For example: * `filter = PARAMCD == "TEMP"` * `order = exprs(AVISIT, desc(AESEV))` -Parameter must not accept expressions for assigning the value of the new -variable. Instead separate parameters need to be provided for defining the +Argument must not accept expressions for assigning the value of the new +variable. Instead separate arguments need to be provided for defining the value. For example, if a function derives a variable which may be imputed, the following is **not acceptable**. @@ -190,7 +190,7 @@ following is **not acceptable**. ... ``` -Separate parameters for the imputation must be provided, e.g.: +Separate arguments for the imputation must be provided, e.g.: ``` ... new_var = mydtm, @@ -200,7 +200,7 @@ Separate parameters for the imputation must be provided, e.g.: ... ``` -Each function parameter needs to be tested with `assert_` type of function. +Each function argument needs to be tested with `assert_` type of function. Each expression needs to be tested for the following (there are many utility functions in `{admiral}` available to the contributor): @@ -210,31 +210,34 @@ Each expression needs to be tested for the following The only exception to this is `derive_var_basetype()` where we allowed the use of `rlang::exprs()`. The reason is that in this case the user needs to have the flexibility to provide not just symbols but -usually more complicated filtering conditions (that may be based on multiple input parameters). +usually more complicated filtering conditions (that may be based on multiple input arguments). -## Common Function Parameters Naming Convention +## Common Function Arguments Naming Convention -The first parameter of `derive_` functions should be the input dataset and it should be named `dataset`. -If more than one input dataset is required, the other input dataset should start with `dataset_`, e.g., `dataset_ex.` +The first argument of `derive_` functions should be the input dataset and it +should be named `dataset`. If more than one input dataset is required, the other +input dataset should start with `dataset_`, e.g., `dataset_ex.` -Parameters for specifying items to add should start with `new_`. -If a variable is added, the second part of the parameter name should be var, if a parameter is added, it should be `param.` -For example: `new_var`, `new_var_unit`, `new_param`. +Arguments for specifying items to add should start with `new_`. If a variable is +added, the second part of the argument name should be var, if a parameter is +added, it should be `param.` For example: `new_var`, `new_var_unit`, +`new_param`. -Parameters which expect a boolean or boolean vector must start with a verb, e.g., `is_imputed` or `impute_date`. +Arguments which expect a boolean or boolean vector must start with a verb, e.g., +`is_imputed` or `impute_date`. -## List of Common Parameters +## List of Common Arguments -| Parameter Name | Description | +| Argument Name | Description | |------------------|--------------------------------------------------------------------------------------------------------------------| | `dataset` | The input dataset. Expects a data.frame or a tibble. | | `by_vars` | Variables to group by. | | `order` | List of expressions for sorting a dataset, e.g., `exprs(PARAMCD, AVISITN, desc(AVAL))`. | | `new_var` | Name of a single variable to be added to the dataset. | | `new_vars` | List of variables to be added to the dataset. | -| `new_var_unit` | Name of the unit variable to be added. It should be the unit of the variable specified for the new_var parameter. | +| `new_var_unit` | Name of the unit variable to be added. It should be the unit of the variable specified for the `new_var` argument. | | `filter` | Expression to filter a dataset, e.g., `PARAMCD == "TEMP"`. | | `start_date` | The start date of an event/interval. Expects a date object. | | `end_date` | The end date of an event/interval. Expects a date object. | @@ -321,16 +324,16 @@ here only a warning should be displayed and the function should continue executi Inputs should be checked using custom assertion functions defined in [`R/assertions.R`](https://github.com/pharmaverse/admiraldev/blob/main/R/assertions.R). These custom assertion functions should either return an error in case of an invalid input or return nothing. -For the most common types of input parameters like a single variable, a list of +For the most common types of input arguments like a single variable, a list of variables, a dataset, ... functions for checking are available (see [assertions](../reference/index.html#section-assertions)). -Parameters which expect keywords should handle them in a case-insensitive manner, e.g., both -`date_imputation = "FIRST"` and `date_imputation = "first"` should be accepted. -The `assert_character_scalar()` function helps with handling parameters in a -case-insensitive manner. +Arguments which expect keywords should handle them in a case-insensitive manner, +e.g., both `date_imputation = "FIRST"` and `date_imputation = "first"` should be +accepted. The `assert_character_scalar()` function helps with handling arguments +in a case-insensitive manner. -A parameter should not be checked in an outer function if the parameter name is the same as in the inner function. +A argument should not be checked in an outer function if the argument name is the same as in the inner function. This rule is applicable only if both functions are part of `{admiral}`. @@ -339,7 +342,7 @@ This rule is applicable only if both functions are part of `{admiral}`. Every function that is exported from the package must have an accompanying header that should be formatted according to the [roxygen2](https://roxygen2.r-lib.org/) convention. -In addition to the roxygen2 parameters, `@keywords` is also used. +In addition to the roxygen2 tags, `@keywords` is also used. The keywords are used to categorize the function. Please see section "Categorization of functions". @@ -354,7 +357,7 @@ An example is given below: #' @param dataset Input dataset #' #' The columns specified by the `reference_date` and the `source_vars` -#' parameter are expected. +#' argument are expected. #' #' @param reference_date The start date column, e.g., date of first treatment #' @@ -410,8 +413,8 @@ An example is given below: The following fields are mandatory: -* `@param`: One entry per function parameter. -The following attributes should be described: expected data type (e.g. `data.frame`, `logical`, `numeric` etc.), default value (if any), permitted values (if applicable), optionality (i.e. is this a required parameter). +* `@param`: One entry per function argument. +The following attributes should be described: expected data type (e.g. `data.frame`, `logical`, `numeric` etc.), default value (if any), permitted values (if applicable), optionality (i.e. is this a required argument). If the expected input is a dataset then the required variables should be clearly stated. * `@details`: A natural-language description of the derivation used inside the function. * `@keyword`: One applicable tag to the function - identical to family. @@ -426,22 +429,22 @@ If other functions are called in the example, please specify `library(pkg_name)` Make sure to align columns as this ensures quick code readability. Copying descriptions should be avoided as it makes the documentation hard to -maintain. For example if the same parameter with the same description is used by -more than one function, the parameter should be described for one function and +maintain. For example if the same argument with the same description is used by +more than one function, the argument should be described for one function and the other functions should use `@inheritParams `. +argument is described>`. Please note that if `@inheritParams func_first` is used in the header of the -`func_second()` function, those parameter descriptions of `func_first()` are +`func_second()` function, those argument descriptions of `func_first()` are included in the documentation of `func_second()` for which -- the parameter is offered by `func_second()` and -- no `@param` tag for the parameter is included in the header of +- the argument is offered by `func_second()` and +- no `@param` tag for the argument is included in the header of `func_second()`. The order of the `@param` tags should be the same as in the function definition. The `@inheritParams` tags should be after the `@param`. This does not affect the -order of the parameter description in the rendered documentation but makes it +order of the argument description in the rendered documentation but makes it easier to maintain the headers. Variable names, expressions, functions, and any other code must be enclosed @@ -569,30 +572,37 @@ See [Writing Unit Tests in {admiral}](unit_test_guidance.html#writing-unit-tests # Deprecation -As `{admiral}` is still evolving, functions or parameters may need to be removed or replaced with more -efficient options from one release to another. In such cases, the relevant function or parameter -must be marked as deprecated. This deprecation is done in three phases over our release cycles. +As `{admiral}` is still evolving, functions or arguments may need to be removed +or replaced with more efficient options from one release to another. In such +cases, the relevant function or argument must be marked as deprecated. This +deprecation is done in three phases over our release cycles. -- **Phase 1:** In the release where the identified function or parameter is to be deprecated there will be a warning issued when using the function or parameter using `deprecate_warn()` +- **Phase 1:** In the release where the identified function or argument is to +be deprecated there will be a warning issued when using the function or argument +using `deprecate_warn()`. -- **Phase 2:** In the next release an error will be thrown using `deprecate_stop()` +- **Phase 2:** In the next release an error will be thrown using +`deprecate_stop()`. -- **Phase 3:** Finally in the 3rd release thereafter the function will be removed from the package altogether +- **Phase 3:** Finally in the 3rd release thereafter the function will be +removed from the package altogether. Information about deprecation timelines must be added to the warning/error message. -Note that the deprecation cycle time for a function or parameter based on our current release schedule is 6 months. +Note that the deprecation cycle time for a function or argument based on our +current release schedule is 6 months. ## Documentation -If a function or parameter is removed, the documentation must be updated to indicate the function -or the parameter is now deprecated and which new function/parameter should be used instead. +If a function or argument is removed, the documentation must be updated to +indicate the function or the argument is now deprecated and which new +function/argument should be used instead. The documentation will be updated at: + the description level for a function, + the keywords will be replaced with `deprecated` -+ the @family roxygen tag will become `deprecated` ++ the `@family` roxygen tag will become `deprecated` ```{r, eval=FALSE} #' Title of the function @@ -610,25 +620,27 @@ The documentation will be updated at: + the `@examples` section should be removed. -+ the `@param` level for a parameter. ++ the `@param` level for a argument. ``` @param old_param *Deprecated*, please use `new_param` instead. ``` -## Handling of warning and error +## Handling of Warning and Error -When a function or parameter is deprecated, the function must be updated to issue a -warning or error using `deprecate_warn()` and `deprecate_stop()`, respectively, as -described above. +When a function or argument is deprecated, the function must be updated to issue +a warning or error using `deprecate_warn()` and `deprecate_stop()`, +respectively, as described above. -There should be a test case added in `tests/testthat/test-deprecation.R` that checks whether this warning/error is issued as appropriate when using the deprecated function or parameter. +There should be a test case added in the test file of the function that checks +whether this warning/error is issued as appropriate when using the deprecated +function or argument. ### Function -In the initial release in which a function is deprecated the original function body -must be replaced with a call to `deprecate_warn()` and subsequently all arguments -should be passed on to the new function. +In the initial release in which a function is deprecated the original function +body must be replaced with a call to `deprecate_warn()` and subsequently all +arguments should be passed on to the new function. ```r fun_xxx <- function(dataset, some_param, other_param) { @@ -652,9 +664,9 @@ fun_xxx <- function(dataset, some_param, other_param) { Finally, in the next release the function should be removed from the package. -### Parameter +### Argument -If a parameter is removed and is not replaced, an **error** must be generated: +If an argument is removed and is not replaced, an **error** must be generated: ``` ### BEGIN DEPRECATION @@ -664,9 +676,9 @@ If a parameter is removed and is not replaced, an **error** must be generated: ### END DEPRECATION ``` -If the parameter is renamed or replaced, a **warning** must be issued and the -new parameter takes the value of the old parameter until the next release. Note: -parameters which are not passed as `exprs()` argument (e.g. `new_var = VAR1` or +If the argument is renamed or replaced, a **warning** must be issued and the +new argument takes the value of the old argument until the next release. Note: +arguments which are not passed as `exprs()` argument (e.g. `new_var = VAR1` or `filter = AVAL >10`) will need to be quoted. ``` @@ -683,50 +695,61 @@ parameters which are not passed as `exprs()` argument (e.g. `new_var = VAR1` or ## Unit Testing -Unit tests for deprecated functions and parameters must be added to -`tests/testthat/test-deprecation.R` to ensure that a warning or error is issued. +Unit tests for deprecated functions and arguments must be added to the test +file of the function to ensure that a warning or error is issued. -When writing the unit test, check that the error or warning has the right class, i.e. "lifecycle_error_deprecated" or "lifecycle_warning_deprecated", respectively. The unit-test should follow the corresponding format, per the [unit test guidance](unit_test_guidance.html#writing-unit-tests-in-admiral-): +When writing the unit test, check that the error or warning has the right class, +i.e. `"lifecycle_error_deprecated"` or `"lifecycle_warning_deprecated"`, +respectively. The unit-test should follow the corresponding format, per the +[unit test guidance](unit_test_guidance.html#writing-unit-tests-in-admiral-). -``` -# For deprecated functions that issues error +### For Deprecated Functions that Issues a Warning (Phase 1) -## Test #: An error is thrown if `derive_var_example()` is called ---- -test_that("deprecation Test #: derive_var_example() An error is thrown if - `derive_var_example()` is called", { - expect_error( +A unit test like the following must be added. +``` +## Test #: deprecation warning if function is called ---- +test_that("derive_var_example() Test #: deprecation warning if function is called", { + expect_warning( derive_var_example(), - class = "lifecycle_error_deprecated" + class = "lifecycle_warning_deprecated" ) }) ``` +In the existing unit tests the call of the deprecated function need to be enclosed by `suppress_warning()`. For example, ``` -# For deprecated functions that issues warning - -## Test #: A warning is thrown if `derive_var_example()` is called ---- -test_that("deprecation Test #: derive_var_example() A warning is thrown if - `derive_var_example()` is called", { - expect_warning( + actual <- suppress_warning( derive_var_example(), - class = "lifecycle_warning_deprecated" + regexpr = "was deprecated" ) -}) ``` +The `regexpr` argument must be specified to ensure that only the deprecation +warning is suppressed. +### For Deprecated Functions that Issues an Error (Phase 2) -Other unit tests of deprecated functions must be removed. +A unit test like the following must be added. +``` +## Test #: error if function is called ---- +test_that("derive_var_example() Test #: deprecation error if function is called", { + expect_error( + derive_var_example(), + class = "lifecycle_error_deprecated" + ) +}) +``` +Other unit tests of the deprecated function must be removed. # Best Practices and Hints Please take the following list as recommendation and try to adhere to its rules if possible. -* Parameters in function calls should be named except for the first parameter +* Arguments in function calls should be named except for the first parameter (e.g. `assert_data_frame(dataset, required_vars = exprs(var1, var2), optional = TRUE)`). * `dplyr::if_else()` should be used when there are only two conditions. -Try to always set the `missing` parameter whenever appropriate. +Try to always set the `missing` argument whenever appropriate. -# R and package versions for development +# R and Package Versions for Development * The choice of R Version is not set in stone. However, a common development environment is important to establish when working across multiple companies and multiple developers. We currently work in the earliest of the three latest R Versions. This need for a common development environment also carries over for our choice of package versions. * GitHub allows us through the Actions/Workflows to test `{admiral}` under several versions of R as well as several versions of dependent R packages needed for `{admiral}`. Currently we test `{admiral}` against the three latest R Versions and the closest snapshots of packages to those R versions. You can view this workflow and others on our [admiralci GitHub Repository](https://github.com/pharmaverse/admiralci). From 3868cf45898a12066b0699b27f8ef2a58f96678d Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Fri, 24 Mar 2023 15:51:57 +0100 Subject: [PATCH 031/100] 247_update_deprecation: fix link and add test file name --- vignettes/programming_strategy.Rmd | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index 92c00887..b653bb42 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -695,13 +695,16 @@ arguments which are not passed as `exprs()` argument (e.g. `new_var = VAR1` or ## Unit Testing -Unit tests for deprecated functions and arguments must be added to the test -file of the function to ensure that a warning or error is issued. +Unit tests for deprecated functions and arguments must be added to the test file [^1] of the function to ensure that a warning or error is issued. + +[^1]: For example, if `derive_var_example()` is going to be deprecated and +it is defined in `examples.R`, the unit tests are in +`tests/testthat/test-examples.R`. When writing the unit test, check that the error or warning has the right class, -i.e. `"lifecycle_error_deprecated"` or `"lifecycle_warning_deprecated"`, +i.e., `"lifecycle_error_deprecated"` or `"lifecycle_warning_deprecated"`, respectively. The unit-test should follow the corresponding format, per the -[unit test guidance](unit_test_guidance.html#writing-unit-tests-in-admiral-). +[unit test guidance](unit_test_guidance.html#writing-unit-tests-in-admiral). ### For Deprecated Functions that Issues a Warning (Phase 1) From 12c1cc50d39ccefb624f7c37a40fe97ca1766636 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Fri, 24 Mar 2023 16:12:44 +0100 Subject: [PATCH 032/100] 247_update_deprecation: trigger workflows From 8e3a3195dbb1a9f9484ea7bb0a1ad4ebe6c215e9 Mon Sep 17 00:00:00 2001 From: esimms999-gsk Date: Fri, 24 Mar 2023 19:16:07 +0000 Subject: [PATCH 033/100] Use styler 1.9.1 and fix any changes needed due to this. --- R/addin_format_testthat.R | 1 - renv.lock | 2 +- vignettes/programming_strategy.Rmd | 14 +++++++------- 3 files changed, 8 insertions(+), 9 deletions(-) diff --git a/R/addin_format_testthat.R b/R/addin_format_testthat.R index 2aae2443..df6c5b0a 100644 --- a/R/addin_format_testthat.R +++ b/R/addin_format_testthat.R @@ -1,4 +1,3 @@ - # Returns the call for updating a given test_that test file # by adding a function name, a test number, and a section. # Call the function either by using RStudio Addin "format_test_that_file" or diff --git a/renv.lock b/renv.lock index 628cf197..c589e2d4 100644 --- a/renv.lock +++ b/renv.lock @@ -1310,7 +1310,7 @@ }, "styler": { "Package": "styler", - "Version": "1.8.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index b653bb42..0bcbc983 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -394,14 +394,14 @@ An example is given below: #' library(tibble) #' #' datain <- tribble( -#' ~TRTSDTM, ~ASTDTM, ~AENDT, -#' "2014-01-17T23:59:59", "2014-01-18T13:09:O9", "2014-01-20" +#' ~TRTSDTM, ~ASTDTM, ~AENDT, +#' "2014-01-17T23:59:59", "2014-01-18T13:09:O9", "2014-01-20" #' ) %>% -#' mutate( -#' TRTSDTM = as_datetime(TRTSDTM), -#' ASTDTM = as_datetime(ASTDTM), -#' AENDT = ymd(AENDT) -#' ) +#' mutate( +#' TRTSDTM = as_datetime(TRTSDTM), +#' ASTDTM = as_datetime(ASTDTM), +#' AENDT = ymd(AENDT) +#' ) #' #' derive_vars_dy( #' datain, From 76fcf2bc2017ee04583fd6a2a427af3b5936c698 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Mon, 27 Mar 2023 14:09:22 +0200 Subject: [PATCH 034/100] 241_allow_expressions: fix replace_values_by_names() --- R/quo.R | 6 +++++ man/replace_values_by_names.Rd | 3 +++ tests/testthat/test-quo.R | 43 +++++++++++++++++++++------------- 3 files changed, 36 insertions(+), 16 deletions(-) diff --git a/R/quo.R b/R/quo.R index 47494782..a833cf83 100644 --- a/R/quo.R +++ b/R/quo.R @@ -102,6 +102,9 @@ quo_not_missing <- function(x) { #' #' @return A list of expressions #' @export +#' +#' @examples +#' replace_values_by_names(exprs(AVAL, ADT = convert_dtc_to_dt(EXSTDTC))) replace_values_by_names <- function(expressions, quosures) { if (!missing(quosures)) { deprecate_warn( @@ -111,6 +114,9 @@ replace_values_by_names <- function(expressions, quosures) { ) expressions <- map(quosures, rlang::quo_get_expr) } + if (is.null(names(expressions))) { + return(expressions) + } map2(expressions, names(expressions), function(e, n) { if (n == "") { return(e) diff --git a/man/replace_values_by_names.Rd b/man/replace_values_by_names.Rd index 821d85cf..92e51ff7 100644 --- a/man/replace_values_by_names.Rd +++ b/man/replace_values_by_names.Rd @@ -17,6 +17,9 @@ A list of expressions \description{ Replace Expression Value with Name } +\examples{ +replace_values_by_names(exprs(AVAL, ADT = convert_dtc_to_dt(EXSTDTC))) +} \seealso{ Helpers for working with Quosures: \code{\link{add_suffix_to_vars}()}, diff --git a/tests/testthat/test-quo.R b/tests/testthat/test-quo.R index 56ca99bc..68741d2f 100644 --- a/tests/testthat/test-quo.R +++ b/tests/testthat/test-quo.R @@ -94,8 +94,8 @@ test_that("quo_not_missing Test 9: `quo_not_missing` throws an Error if missing }) # replace_values_by_names ---- -## Test 10: names of quosures replace value ---- -test_that("replace_values_by_names Test 10: names of quosures replace value", { +## Test 10: names of expressions replace value ---- +test_that("replace_values_by_names Test 10: names of expressions replace value", { z <- exprs(USUBJID, STUDYID) z_noname <- replace_values_by_names(z) @@ -122,8 +122,19 @@ test_that("replace_values_by_names Test 10: names of quosures replace value", { ) }) -## Test 11: warning if quosures argument is used ---- -test_that("replace_values_by_names Test 11: warning if quosures argument is used", { +## Test 11: names of argument is NULL ---- +test_that("replace_values_by_names Test 11: names of argument is NULL", { + z <- exprs(USUBJID, STUDYID) + names(z) <- NULL + + expect_equal( + expected = z, + object = replace_values_by_names(z) + ) +}) + +## Test 12: warning if quosures argument is used ---- +test_that("replace_values_by_names Test 12: warning if quosures argument is used", { expect_warning( replace_values_by_names(quosures = rlang::quos(STUDYID, USUBJID)), class = "lifecycle_warning_deprecated" @@ -131,8 +142,8 @@ test_that("replace_values_by_names Test 11: warning if quosures argument is used }) # replace_symbol_in_quo ---- -## Test 12: error if called ---- -test_that("replace_symbol_in_quo Test 12: error if called", { +## Test 13: error if called ---- +test_that("replace_symbol_in_quo Test 13: error if called", { expect_error( replace_symbol_in_quo(), class = "lifecycle_error_deprecated" @@ -140,8 +151,8 @@ test_that("replace_symbol_in_quo Test 12: error if called", { }) # replace_symbol_in_expr ---- -## Test 13: symbol is replaced ---- -test_that("replace_symbol_in_expr Test 13: symbol is replaced", { +## Test 14: symbol is replaced ---- +test_that("replace_symbol_in_expr Test 14: symbol is replaced", { expect_equal( expected = expr(AVAL.join), object = replace_symbol_in_expr( @@ -152,8 +163,8 @@ test_that("replace_symbol_in_expr Test 13: symbol is replaced", { ) }) -## Test 14: partial match is not replaced ---- -test_that("replace_symbol_in_expr Test 14: partial match is not replaced", { +## Test 15: partial match is not replaced ---- +test_that("replace_symbol_in_expr Test 15: partial match is not replaced", { expect_equal( expected = expr(AVALC), object = replace_symbol_in_expr( @@ -164,8 +175,8 @@ test_that("replace_symbol_in_expr Test 14: partial match is not replaced", { ) }) -## Test 15: symbol in expression is replaced ---- -test_that("replace_symbol_in_expr Test 15: symbol in expression is replaced", { +## Test 16: symbol in expression is replaced ---- +test_that("replace_symbol_in_expr Test 16: symbol in expression is replaced", { expect_equal( expected = expr(desc(AVAL.join)), object = replace_symbol_in_expr( @@ -177,8 +188,8 @@ test_that("replace_symbol_in_expr Test 15: symbol in expression is replaced", { }) # add_suffix_to_vars ---- -## Test 16: with single variable ---- -test_that("add_suffix_to_vars Test 16: with single variable", { +## Test 17: with single variable ---- +test_that("add_suffix_to_vars Test 17: with single variable", { expect_equal( expected = exprs(ADT, desc(AVAL.join), AVALC), object = add_suffix_to_vars( @@ -189,8 +200,8 @@ test_that("add_suffix_to_vars Test 16: with single variable", { ) }) -## Test 17: with more than one variable ---- -test_that("add_suffix_to_vars Test 17: with more than one variable", { +## Test 18: with more than one variable ---- +test_that("add_suffix_to_vars Test 18: with more than one variable", { expect_equal( expected = exprs(ADT, desc(AVAL.join), AVALC.join), object = add_suffix_to_vars( From caaede6a0a45d3bcbca45b70e80baae9242fb768 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Tue, 28 Mar 2023 18:22:13 +0200 Subject: [PATCH 035/100] 241_allow_expressions: update programming strategy --- vignettes/programming_strategy.Rmd | 31 ++---------------------------- 1 file changed, 2 insertions(+), 29 deletions(-) diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index b653bb42..312809cd 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -168,7 +168,7 @@ There is a recommended argument order that all contributors are asked to adhere * Make sure to always mention `start_date` before `end_date` (or related). Names of variables inside a dataset should be passed as symbols rather than strings, i.e. `AVAL` rather than `"AVAL"`. -If an argument accepts one or more variables as input, the variables should be wrapped inside `exprs()`. +If an argument accepts one or more variables or expressions as input, the variables should be wrapped inside `exprs()`. For example: @@ -176,29 +176,7 @@ For example: * `by_vars = exprs(PARAMCD, AVISIT)` * `filter = PARAMCD == "TEMP"` * `order = exprs(AVISIT, desc(AESEV))` - -Argument must not accept expressions for assigning the value of the new -variable. Instead separate arguments need to be provided for defining the -value. For example, if a function derives a variable which may be imputed, the -following is **not acceptable**. - -``` - ... - new_var = exprs(mydtm = convert_dtc_to_dtm(impute_dtc(cmstdtc, - date_imputation = "last", - time_imputation = "last"))), - ... -``` - -Separate arguments for the imputation must be provided, e.g.: -``` - ... - new_var = mydtm, - source_var = cmstdtc, - date_imputation = "last", - time_imputation = "last", - ... -``` +* `new_vars = exprs(LDOSE = EXDOSE, LDOSEDT = convert_dtc_to_dt(EXSTDTC))` Each function argument needs to be tested with `assert_` type of function. @@ -208,11 +186,6 @@ Each expression needs to be tested for the following * whether it is an expression (or a list of expressions, depending on the function) * whether it is a valid expression (i.e. whether it evaluates without error) -The only exception to this is `derive_var_basetype()` where we allowed the use of `rlang::exprs()`. -The reason is that in this case the user needs to have the flexibility to provide not just symbols but -usually more complicated filtering conditions (that may be based on multiple input arguments). - - ## Common Function Arguments Naming Convention The first argument of `derive_` functions should be the input dataset and it From 04343cadc585a838b36c1ba158b6589e07326b0e Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 29 Mar 2023 08:30:31 +0000 Subject: [PATCH 036/100] renv update from pharmaverse/admiralci --- renv.lock | 6 +- renv/profiles/4.0/renv.lock | 6 +- renv/profiles/4.0_legacy/renv.lock | 1630 ++++++++++++++++++++ renv/profiles/4.0_legacy/renv/.gitignore | 7 + renv/profiles/4.0_legacy/renv/settings.dcf | 10 + renv/profiles/4.1/renv.lock | 6 +- renv/settings.dcf | 8 +- 7 files changed, 1662 insertions(+), 11 deletions(-) create mode 100644 renv/profiles/4.0_legacy/renv.lock create mode 100644 renv/profiles/4.0_legacy/renv/.gitignore create mode 100644 renv/profiles/4.0_legacy/renv/settings.dcf diff --git a/renv.lock b/renv.lock index a4df9cbb..dd399932 100644 --- a/renv.lock +++ b/renv.lock @@ -264,10 +264,10 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.2.7", + "Version": "0.4.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "730eebcc741a5c36761f7d4d0f5e37b8" + "Repository": "CRAN", + "Hash": "ed588261931ee3be2c700d22e94a29ab" }, "crayon": { "Package": "crayon", diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index a4df9cbb..dd399932 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -264,10 +264,10 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.2.7", + "Version": "0.4.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "730eebcc741a5c36761f7d4d0f5e37b8" + "Repository": "CRAN", + "Hash": "ed588261931ee3be2c700d22e94a29ab" }, "crayon": { "Package": "crayon", diff --git a/renv/profiles/4.0_legacy/renv.lock b/renv/profiles/4.0_legacy/renv.lock new file mode 100644 index 00000000..dc085f1d --- /dev/null +++ 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+local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/profiles/4.0_legacy/renv/settings.dcf b/renv/profiles/4.0_legacy/renv/settings.dcf new file mode 100644 index 00000000..c4ab61bd --- /dev/null +++ b/renv/profiles/4.0_legacy/renv/settings.dcf @@ -0,0 +1,10 @@ +bioconductor.version: +external.libraries: +ignored.packages: admiral, admiraldev, admiral.test, admiralci +package.dependency.fields: Imports, Depends, LinkingTo +r.version: +snapshot.type: custom +use.cache: TRUE +vcs.ignore.cellar: TRUE +vcs.ignore.library: TRUE +vcs.ignore.local: TRUE diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 2a2b73f8..f78ab97a 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -258,10 +258,10 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.4.2", + "Version": "0.4.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "fa53ce256cd280f468c080a58ea5ba8c" + "Repository": "CRAN", + "Hash": "ed588261931ee3be2c700d22e94a29ab" }, "crayon": { "Package": "crayon", diff --git a/renv/settings.dcf b/renv/settings.dcf index 0c5119c7..c4ab61bd 100644 --- a/renv/settings.dcf +++ b/renv/settings.dcf @@ -1,6 +1,10 @@ -ignored.packages: +bioconductor.version: +external.libraries: +ignored.packages: admiral, admiraldev, admiral.test, admiralci package.dependency.fields: Imports, Depends, LinkingTo r.version: -snapshot.type: implicit +snapshot.type: custom use.cache: TRUE +vcs.ignore.cellar: TRUE vcs.ignore.library: TRUE +vcs.ignore.local: TRUE From 00fadaa5063770da425fdd1074ffadf663a5a382 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Thu, 30 Mar 2023 11:02:44 +0200 Subject: [PATCH 037/100] 241_allow_expressions: update assert_expr() --- R/assertions.R | 5 ++-- tests/testthat/test-assertions.R | 50 +++++--------------------------- 2 files changed, 10 insertions(+), 45 deletions(-) diff --git a/R/assertions.R b/R/assertions.R index d27f8c1d..6e24411d 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -393,11 +393,10 @@ assert_expr <- function(arg, optional = FALSE) { } if (is_missing(arg)) { - err_msg <- sprintf("Argument `%s` missing, with no default", arg_name(substitute(arg))) - abort(err_msg) + abort("Argument `arg` missing, with no default") } - if (!is_symbolic(arg)) { + if (!(is_call(arg) || is_expression(arg))) { err_msg <- sprintf( "`%s` must be an expression but is %s", arg_name(substitute(arg)), diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index 701815f6..bd917120 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -432,67 +432,33 @@ test_that("assert_symbol Test 25: `assert_symbol` does not throw an error if `ar # assert_expr ---- ## Test 26: `assert_expr` does not throw an error if `arg` is an expression ---- test_that("assert_expr Test 26: `assert_expr` does not throw an error if `arg` is an expression", { - f <- function(var) { - v <- enexpr(var) - } - - example_fun <- function(arg) { - assert_expr(arg) - } - expect_invisible( - example_fun( - f(admiral.test::admiral_dm) - ) + assert_expr(var <- expr(admiral.test::admiral_dm)) ) }) ## Test 27: no error if optional is TRUE and `arg` is NULL ---- test_that("assert_expr Test 27: no error if optional is TRUE and `arg` is NULL", { - f <- function(var) { - v <- enexpr(var) - } - - example_fun <- function(arg) { - assert_expr(arg, optional = TRUE) - } - expect_invisible( - example_fun( - f(NULL) - ) + assert_expr(var <- NULL, optional = TRUE) ) }) ## Test 28: `assert_expr` throws an error if `arg` is missing ---- test_that("assert_expr Test 28: `assert_expr` throws an error if `arg` is missing", { - f <- function(var) { - v <- enexpr(var) - } - - example_fun <- function(arg) { - assert_expr(arg) - } - expect_error( - example_fun(f()) + assert_expr(), + regexp = "Argument `arg` missing, with no default", + fixed = TRUE ) }) ## Test 29: `assert_expr` throws an error if `arg` is not an expression ---- test_that("assert_expr Test 29: `assert_expr` throws an error if `arg` is not an expression", { - f <- function(var) { - v <- enexpr(var) - } - - example_fun <- function(arg) { - assert_expr(arg) - } - expect_error( - example_fun( - f(NULL) - ) + assert_expr(var <- c(1, 2)), + regexp = "`var` must be an expression but is a double vector", + fixed = TRUE ) }) From 2681e54d97e7c87675e13531e580aa5ac1a6bc3b Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 30 Mar 2023 15:20:33 +0000 Subject: [PATCH 038/100] Release to github snippet --- vignettes/release_strategy.Rmd | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/vignettes/release_strategy.Rmd b/vignettes/release_strategy.Rmd index 5e042f51..39cdc09b 100644 --- a/vignettes/release_strategy.Rmd +++ b/vignettes/release_strategy.Rmd @@ -70,6 +70,17 @@ Occasionally we will need to release a hot fix to address a package breaking bug **Hot Fix Release**: `patch >> pre-release >> main >> devel` +# Releasing to Github +Under the [Releases](https://github.com/pharmaverse/admiral/releases) section in the main repo, select `Draft a New Release`. Proceed by creating the appropriate release tag and header, denoted as "vX.X.X" and "admiral X.X.X" respectively, for the release: + +![](https://user-images.githubusercontent.com/43018762/228875673-5b6daa64-1909-47c9-bd61-69b810c2f742.png) + +Copy the contents of the `NEWS.md` section for the release, paste it into the release notes section: + +![](https://user-images.githubusercontent.com/43018762/228875743-d17729fe-9b38-432a-9bb0-5fdc157ec231.png) + +Then in the upload box where it says, "Attach binaries by dropping them here or selecting them" upload the appropriate "admiral_X.X.X.tar.gz" file available for download at the [CRAN website](https://cran.r-project.org/web/packages/admiral/index.html). Click `Publish Release` and you're all done! + # Communications After the release, we raise awareness via our Slack channel and LinkedIn. From 671e093ee51ac42be4a64e37aebf7e6d87fac5ac Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 30 Mar 2023 15:35:22 +0000 Subject: [PATCH 039/100] get around spellcheck without adding to wordlist --- vignettes/release_strategy.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vignettes/release_strategy.Rmd b/vignettes/release_strategy.Rmd index 39cdc09b..e84cd0fd 100644 --- a/vignettes/release_strategy.Rmd +++ b/vignettes/release_strategy.Rmd @@ -71,7 +71,7 @@ Occasionally we will need to release a hot fix to address a package breaking bug **Hot Fix Release**: `patch >> pre-release >> main >> devel` # Releasing to Github -Under the [Releases](https://github.com/pharmaverse/admiral/releases) section in the main repo, select `Draft a New Release`. Proceed by creating the appropriate release tag and header, denoted as "vX.X.X" and "admiral X.X.X" respectively, for the release: +Under the [Releases](https://github.com/pharmaverse/admiral/releases) section in the main repo, select `Draft a New Release`. Proceed by creating the appropriate release tag and header, denoted as `vX.X.X` and `admiral X.X.X` respectively, for the release: ![](https://user-images.githubusercontent.com/43018762/228875673-5b6daa64-1909-47c9-bd61-69b810c2f742.png) @@ -79,7 +79,7 @@ Copy the contents of the `NEWS.md` section for the release, paste it into the re ![](https://user-images.githubusercontent.com/43018762/228875743-d17729fe-9b38-432a-9bb0-5fdc157ec231.png) -Then in the upload box where it says, "Attach binaries by dropping them here or selecting them" upload the appropriate "admiral_X.X.X.tar.gz" file available for download at the [CRAN website](https://cran.r-project.org/web/packages/admiral/index.html). Click `Publish Release` and you're all done! +Then in the upload box where it says, "Attach binaries by dropping them here or selecting them" upload the appropriate `admiral_X.X.X.tar.gz` file available for download at the [CRAN website](https://cran.r-project.org/web/packages/admiral/index.html). Click `Publish Release` and you're all done! # Communications From 095384f2e45224a5bc9936a9cbf7cb729fc72bb1 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 30 Mar 2023 19:10:11 +0000 Subject: [PATCH 040/100] remove mention of pre-release branch --- vignettes/release_strategy.Rmd | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/vignettes/release_strategy.Rmd b/vignettes/release_strategy.Rmd index e84cd0fd..2d4fabed 100644 --- a/vignettes/release_strategy.Rmd +++ b/vignettes/release_strategy.Rmd @@ -43,17 +43,17 @@ updates via the community meetings, especially any anticipated breaking changes. A package release is done in five parts: -1) Create a Pull Request from `devel` into the `pre-release` branch. Issues identified in this Pull Request should have work done in separate branches and merged into the `pre-release` branch and **NOT** `devel`. -1) Verify that all CI/CD checks are passing for the `devel` into the `pre-release` Pull Request, merge and then bundle up and send off to CRAN. -1) Once the package is available on CRAN, another Pull Request is created for merging the `pre-release` branch into the `main` branch. This will trigger the GitHub action to rebuild the `{admiral}` website with all the updates for this release. -1) Use the release button on GitHub to "release" the package onto GitHub. This release onto Github archives the version of code within the `main` branch, attaches the News/Changelog file, bundles the code into a `tar.gz` file and makes a validation report via the GitHub action `validation` from [insightsengineering/validatoR](https://github.com/insightsengineering/thevalidatoR). Please see past [admiral releases](https://github.com/pharmaverse/admiral/releases) for reference. -1) Any issues fixed in the `pre-release/main` branches should be merged back into `devel`. +1) Create a Pull Request from `devel` into the `main` branch. Issues identified in this Pull Request should have work done in separate branches and merged once again into `devel`. +1) Verify that all CI/CD checks are passing for the `devel` into the `main` Pull Request, merge and then bundle up and send off to CRAN. +1) If CRAN asks for modifications, repeat steps 1-2 as necessary. +1) Once the package is accepted and available on CRAN, a GitHub action is set up to rebuild the `{admiral}` website with all the updates for this release. +1) Use the release button on GitHub to "release" the package onto GitHub. This release onto Github archives the version of code within the `main` branch, attaches the News/Changelog file, bundles the code into a `tar.gz` file and makes a validation report via the GitHub action `validation` from [insightsengineering/validatoR](https://github.com/insightsengineering/thevalidatoR). Please see past [admiral releases](https://github.com/pharmaverse/admiral/releases) for reference and the [Releasing to Github](release_strategy.html#releasing-to-github) section for more details. +1) Any issues fixed in the `main` branches should be merged back into `devel`. 1) Once a release is completed the `main` branch should be merged into `patch` to be ready for hotfixes. **Quarterly Release:** -* `devel >> pre-release >> main` -* `pre-release >> main >> devel` (Fixes done after a CRAN rejection) +* `devel >> main` * `main >> patch` (To be prepared in case of a needed hotfix) ## Hot Fix Release @@ -63,12 +63,12 @@ Occasionally we will need to release a hot fix to address a package breaking bug 1) Identify all the bugs that need to be fixed for this hot fix release and label with hot fix label. 1) Branches addressing the bugs should have Pull Requests merged into the `patch` branch **NOT** the `devel` branch. 1) When naming the branch follow the [naming conventions](git_usage.html#implementing-an-issue) guide but use the `@main` suffix -1) Create a Pull Request from `patch` into the `pre-release` branch. Verify that all CI/CD checks are passing, merge and bundle up and send off to CRAN. -1) Once package is approved and available on CRAN, another Pull Request is created for merging the `pre-release` branch into the `main` branch. This will trigger the action to rebuild the `{admiral}` website with all the updates for this hot fix release. -1) Use the release button on GitHub to "release" the package onto GitHub. This release onto Github archives the version of code within the `main` branch, attaches the News/Changelog file, bundles the code into a `tar.gz` file and makes a validation report via the GitHub action `validation` from [insightsengineering/validatoR](https://github.com/insightsengineering/thevalidatoR). Please see past [admiral releases](https://github.com/pharmaverse/admiral/releases) for reference. +1) Create a Pull Request from `patch` into the `main` branch. Verify that all CI/CD checks are passing, merge and bundle up and send off to CRAN. +1) If CRAN asks for modifications, repeat steps 1-4 as necessary. +1) Use the release button on GitHub to "release" the package onto GitHub. This release onto Github archives the version of code within the `main` branch, attaches the News/Changelog file, bundles the code into a `tar.gz` file and makes a validation report via the GitHub action `validation` from [insightsengineering/validatoR](https://github.com/insightsengineering/thevalidatoR). Please see past [admiral releases](https://github.com/pharmaverse/admiral/releases) for reference and the [Releasing to Github](release_strategy.html#releasing-to-github) section for more details. 1) These hot fixes should then be merged into the `devel` branch through an additional Pull Request. -**Hot Fix Release**: `patch >> pre-release >> main >> devel` +**Hot Fix Release**: `patch >> main >> devel` # Releasing to Github Under the [Releases](https://github.com/pharmaverse/admiral/releases) section in the main repo, select `Draft a New Release`. Proceed by creating the appropriate release tag and header, denoted as `vX.X.X` and `admiral X.X.X` respectively, for the release: From fc54ed59ec5d387a04677433561579fc885d5556 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Fri, 31 Mar 2023 15:26:18 +0200 Subject: [PATCH 041/100] 241_allow_expressions: fix example --- R/quo.R | 1 + man/replace_values_by_names.Rd | 1 + 2 files changed, 2 insertions(+) diff --git a/R/quo.R b/R/quo.R index a833cf83..c611e312 100644 --- a/R/quo.R +++ b/R/quo.R @@ -104,6 +104,7 @@ quo_not_missing <- function(x) { #' @export #' #' @examples +#' library(rlang) #' replace_values_by_names(exprs(AVAL, ADT = convert_dtc_to_dt(EXSTDTC))) replace_values_by_names <- function(expressions, quosures) { if (!missing(quosures)) { diff --git a/man/replace_values_by_names.Rd b/man/replace_values_by_names.Rd index 92e51ff7..b407b5c9 100644 --- a/man/replace_values_by_names.Rd +++ b/man/replace_values_by_names.Rd @@ -18,6 +18,7 @@ A list of expressions Replace Expression Value with Name } \examples{ +library(rlang) replace_values_by_names(exprs(AVAL, ADT = convert_dtc_to_dt(EXSTDTC))) } \seealso{ From d16eec11b1951812be180a09a937b0dfbc76cbf4 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Fri, 31 Mar 2023 13:27:11 +0000 Subject: [PATCH 042/100] Address feedback and comments --- vignettes/release_strategy.Rmd | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/vignettes/release_strategy.Rmd b/vignettes/release_strategy.Rmd index 2d4fabed..347515e2 100644 --- a/vignettes/release_strategy.Rmd +++ b/vignettes/release_strategy.Rmd @@ -44,9 +44,9 @@ updates via the community meetings, especially any anticipated breaking changes. A package release is done in five parts: 1) Create a Pull Request from `devel` into the `main` branch. Issues identified in this Pull Request should have work done in separate branches and merged once again into `devel`. -1) Verify that all CI/CD checks are passing for the `devel` into the `main` Pull Request, merge and then bundle up and send off to CRAN. +1) Verify that all CI/CD checks are passing for the `devel` into the `main` Pull Request, merge and then bundle up and send off to CRAN. See the [chapter](https://r-pkgs.org/release.html#decide-the-release-type) in R Packages for more details. 1) If CRAN asks for modifications, repeat steps 1-2 as necessary. -1) Once the package is accepted and available on CRAN, a GitHub action is set up to rebuild the `{admiral}` website with all the updates for this release. +1) Once the package is accepted and available on CRAN, a [GitHub action](https://github.com/pharmaverse/admiral/actions/workflows/pages/pages-build-deployment) is set up to rebuild the `{admiral}` website with all the updates for this release. 1) Use the release button on GitHub to "release" the package onto GitHub. This release onto Github archives the version of code within the `main` branch, attaches the News/Changelog file, bundles the code into a `tar.gz` file and makes a validation report via the GitHub action `validation` from [insightsengineering/validatoR](https://github.com/insightsengineering/thevalidatoR). Please see past [admiral releases](https://github.com/pharmaverse/admiral/releases) for reference and the [Releasing to Github](release_strategy.html#releasing-to-github) section for more details. 1) Any issues fixed in the `main` branches should be merged back into `devel`. 1) Once a release is completed the `main` branch should be merged into `patch` to be ready for hotfixes. @@ -56,6 +56,8 @@ A package release is done in five parts: * `devel >> main` * `main >> patch` (To be prepared in case of a needed hotfix) +Be on the look out for an automated check PR whenever `devel` goes into `main` as a future upcoming feature. + ## Hot Fix Release Occasionally we will need to release a hot fix to address a package breaking bug. A hot fix release is done in 6 parts: @@ -63,8 +65,9 @@ Occasionally we will need to release a hot fix to address a package breaking bug 1) Identify all the bugs that need to be fixed for this hot fix release and label with hot fix label. 1) Branches addressing the bugs should have Pull Requests merged into the `patch` branch **NOT** the `devel` branch. 1) When naming the branch follow the [naming conventions](git_usage.html#implementing-an-issue) guide but use the `@main` suffix -1) Create a Pull Request from `patch` into the `main` branch. Verify that all CI/CD checks are passing, merge and bundle up and send off to CRAN. +1) Create a Pull Request from `patch` into the `main` branch. Verify that all CI/CD checks are passing, merge and them bundle up and send off to CRAN. See the [chapter](https://r-pkgs.org/release.html#decide-the-release-type) in R Packages for more details. 1) If CRAN asks for modifications, repeat steps 1-4 as necessary. +1) Once the package is accepted and available on CRAN, a [GitHub action](https://github.com/pharmaverse/admiral/actions/workflows/pages/pages-build-deployment) is set up to rebuild the `{admiral}` website with all the updates for this release. 1) Use the release button on GitHub to "release" the package onto GitHub. This release onto Github archives the version of code within the `main` branch, attaches the News/Changelog file, bundles the code into a `tar.gz` file and makes a validation report via the GitHub action `validation` from [insightsengineering/validatoR](https://github.com/insightsengineering/thevalidatoR). Please see past [admiral releases](https://github.com/pharmaverse/admiral/releases) for reference and the [Releasing to Github](release_strategy.html#releasing-to-github) section for more details. 1) These hot fixes should then be merged into the `devel` branch through an additional Pull Request. From 51b7d659469047d53d4868fa40362d1dfb85b8a6 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Fri, 31 Mar 2023 15:31:09 +0200 Subject: [PATCH 043/100] 241_allow_expressions: style files --- R/assertions.R | 6 +++--- R/quo.R | 5 +++-- tests/testthat/test-assertions.R | 7 ++++--- tests/testthat/test-quo.R | 3 +-- 4 files changed, 11 insertions(+), 10 deletions(-) diff --git a/R/assertions.R b/R/assertions.R index 6e24411d..432f1e58 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -1365,9 +1365,9 @@ assert_expr_list <- function(arg, # nolint } invalids <- arg[!map_lgl( - arg, - ~ is_call(.x) || is_expression(.x) - )] + arg, + ~ is_call(.x) || is_expression(.x) + )] if (length(invalids) > 0) { abort( diff --git a/R/quo.R b/R/quo.R index c611e312..8fcbc23e 100644 --- a/R/quo.R +++ b/R/quo.R @@ -43,13 +43,14 @@ expr_c <- function(...) { # transform single expression into list of expression inputs <- map( list(...), - function(x) + function(x) { if (typeof(x) != "list") { list(x) } else { x } - ) + } + ) inputs <- purrr::flatten(inputs) stopifnot(all(map_lgl(inputs, is_expression))) is_null <- map_lgl(inputs, is.null) diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index bd917120..79932356 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -987,7 +987,8 @@ test_that("assert_expr_list Test 75: error if `required_elements` are missing fr expect_error( assert_expr_list( arg <- exprs(DTHSEQ = AESEQ), - required_elements = "DTHDOM"), + required_elements = "DTHDOM" + ), regexp = "The following required elements are missing in `arg`: 'DTHDOM'", fixed = TRUE ) @@ -1015,8 +1016,8 @@ test_that("assert_expr_list Test 78: no error if argument is valid", { assert_expr_list(arg <- exprs( DTHDOM = "AE", DTHSEQ = AESEQ, - DTHVAR = if_else(!is.na(AEDECOD), "AEDECOD", NA)) - ) + DTHVAR = if_else(!is.na(AEDECOD), "AEDECOD", NA) + )) ) }) diff --git a/tests/testthat/test-quo.R b/tests/testthat/test-quo.R index 68741d2f..e0644054 100644 --- a/tests/testthat/test-quo.R +++ b/tests/testthat/test-quo.R @@ -53,8 +53,7 @@ test_that("expr_c Test 5: concatenating named list of expressions", { expected = exprs(PARAMCD = "DOSE", PARAMN = 1), object = expr_c(exprs(PARAMCD = "DOSE", PARAMN = 1, NULL)) ) -} -) +}) ## Test 6: concatenating list and single expression ---- test_that("expr_c Test 6: concatenating list and single expression", { From ff2f1741978af8800fb3c9485e22b60fd0cf644a Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Fri, 31 Mar 2023 16:01:03 +0200 Subject: [PATCH 044/100] 241_allow_expressions: try to fix R-CMD check 4.2 in admiral --- R/warnings.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/warnings.R b/R/warnings.R index 13a905e5..8f6f3799 100644 --- a/R/warnings.R +++ b/R/warnings.R @@ -201,7 +201,7 @@ suppress_warning <- function(expr, regexpr) { withCallingHandlers( expr, warning = function(w) { - if (grepl(regexpr, w$message)) { + if (any(grepl(regexpr, w$message))) { invokeRestart("muffleWarning") } } From 7b2757142d1200e1166e0f2f95f39820ab76b9d0 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Fri, 31 Mar 2023 16:18:44 +0200 Subject: [PATCH 045/100] 241_allow_expressions: fix links? --- _pkgdown.yml | 2 +- docs/pkgdown.yml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index a4b68766..96ba8d27 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://pharmaverse.github.io/admiraldev +url: https://pharmaverse.github.io/admiraldev/main template: bootstrap: 5 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 13d33dcd..91fdefe5 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 2.11.4 -pkgdown: 2.0.6 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: admiraldev: admiraldev.html @@ -10,8 +10,8 @@ articles: release_strategy: release_strategy.html unit_test_guidance: unit_test_guidance.html writing_vignettes: writing_vignettes.html -last_built: 2023-03-06T13:34Z +last_built: 2023-03-31T14:13Z urls: - reference: https://pharmaverse.github.io/admiraldev/reference - article: https://pharmaverse.github.io/admiraldev/articles + reference: https://pharmaverse.github.io/admiraldev/main/reference + article: https://pharmaverse.github.io/admiraldev/main/articles From 835fb55b0a0937d1ae690217308b75298b874cd6 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 12 Apr 2023 11:56:32 +0000 Subject: [PATCH 046/100] renv update from pharmaverse/admiralci --- renv/profiles/4.0_legacy/renv.lock | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/renv/profiles/4.0_legacy/renv.lock b/renv/profiles/4.0_legacy/renv.lock index dc085f1d..3ce610f5 100644 --- a/renv/profiles/4.0_legacy/renv.lock +++ b/renv/profiles/4.0_legacy/renv.lock @@ -1078,6 +1078,16 @@ ], "Hash": "430a0908aee75b1fcba0e62857cab0ce" }, + "renv": { + "Package": "renv", + "Version": "0.17.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "ce3065fc1a0b64a859f55ac3998d6927" + }, "rex": { "Package": "rex", "Version": "1.2.0", From da115d016b12d3a9309705df3516a5d32ec37595 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 12 Apr 2023 12:32:52 +0000 Subject: [PATCH 047/100] renv update from pharmaverse/admiralci --- renv.lock | 28 +++++++++++++++++++--------- renv/profiles/4.0/renv.lock | 28 +++++++++++++++++++--------- renv/profiles/4.1/renv.lock | 10 ++++++++++ renv/profiles/4.2/renv.lock | 10 ++++++++++ 4 files changed, 58 insertions(+), 18 deletions(-) diff --git a/renv.lock b/renv.lock index dd399932..a99fa094 100644 --- a/renv.lock +++ b/renv.lock @@ -460,14 +460,14 @@ }, "ellipsis": { "Package": "ellipsis", - "Version": "0.3.1", + "Version": "0.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "rlang" ], - "Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a" + "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" }, "evaluate": { "Package": "evaluate", @@ -743,15 +743,15 @@ }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.0", + "Version": "1.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "glue", "rlang" ], - "Hash": "3471fb65971f1a7b2d4ae7848cf2db8d" + "Hash": "a6b6d352e3ed897373ab19d8395c98d0" }, "lintr": { "Package": "lintr", @@ -1054,9 +1054,9 @@ }, "remotes": { "Package": "remotes", - "Version": "2.2.0", + "Version": "2.4.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods", @@ -1064,7 +1064,17 @@ "tools", "utils" ], - "Hash": "430a0908aee75b1fcba0e62857cab0ce" + "Hash": "227045be9aee47e6dda9bb38ac870d67" + }, + "renv": { + "Package": "renv", + "Version": "0.17.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "ce3065fc1a0b64a859f55ac3998d6927" }, "rex": { "Package": "rex", diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index dd399932..a99fa094 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -460,14 +460,14 @@ }, "ellipsis": { "Package": "ellipsis", - "Version": "0.3.1", + "Version": "0.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "rlang" ], - "Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a" + "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" }, "evaluate": { "Package": "evaluate", @@ -743,15 +743,15 @@ }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.0", + "Version": "1.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "glue", "rlang" ], - "Hash": "3471fb65971f1a7b2d4ae7848cf2db8d" + "Hash": "a6b6d352e3ed897373ab19d8395c98d0" }, "lintr": { "Package": "lintr", @@ -1054,9 +1054,9 @@ }, "remotes": { "Package": "remotes", - "Version": "2.2.0", + "Version": "2.4.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods", @@ -1064,7 +1064,17 @@ "tools", "utils" ], - "Hash": "430a0908aee75b1fcba0e62857cab0ce" + "Hash": "227045be9aee47e6dda9bb38ac870d67" + }, + "renv": { + "Package": "renv", + "Version": "0.17.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "ce3065fc1a0b64a859f55ac3998d6927" }, "rex": { "Package": "rex", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index f78ab97a..c1c5e689 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -1072,6 +1072,16 @@ ], "Hash": "227045be9aee47e6dda9bb38ac870d67" }, + "renv": { + "Package": "renv", + "Version": "0.17.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "ce3065fc1a0b64a859f55ac3998d6927" + }, "rex": { "Package": "rex", "Version": "1.2.1", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index db0b84f9..38a0bfc5 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -1096,6 +1096,16 @@ ], "Hash": "227045be9aee47e6dda9bb38ac870d67" }, + "renv": { + "Package": "renv", + "Version": "0.17.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "ce3065fc1a0b64a859f55ac3998d6927" + }, "rex": { "Package": "rex", "Version": "1.2.1", From 09b7d39cfba1c5ab515e1c8a34b0b2b96475c91e Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Wed, 12 Apr 2023 17:24:22 +0200 Subject: [PATCH 048/100] 241_allow_expressions: improve documentation and messages --- R/assertions.R | 43 ++++++++++++++++++++---------- R/quo.R | 4 +-- _pkgdown.yml | 8 +++--- man/assert_expr_list.Rd | 2 +- man/assert_named.Rd | 11 ++++++++ tests/testthat/test-assertions.R | 2 +- vignettes/programming_strategy.Rmd | 6 +++-- 7 files changed, 52 insertions(+), 24 deletions(-) diff --git a/R/assertions.R b/R/assertions.R index 432f1e58..7154dbe6 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -545,7 +545,7 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) { assert_order_vars <- function(arg, optional = FALSE) { assert_logical_scalar(optional) - deprecate_warn("0.11.0", "assert_order_vars()", "assert_expr_list()") + deprecate_warn("0.4.0", "assert_order_vars()", "assert_expr_list()") assert_expr_list(arg, optional = optional) } @@ -836,6 +836,17 @@ assert_list_of <- function(arg, class, named = FALSE, optional = TRUE) { #' returns the input invisibly otherwise #' #' @export +#' +#' @examples +#' example_fun <- function(varval_list) { +#' assert_named(varval_list) +#' } +#' +#' example_fun(list(var1 = 1, var2 = "x")) +#' +#' try(example_fun(list(1, "x"))) +#' +#' try(example_fun(list(var = 1, "x"))) assert_named <- function(arg, optional = FALSE) { if (optional && is.null(arg)) { return(invisible(arg)) @@ -1323,7 +1334,7 @@ assert_varval_list <- function(arg, # nolint #' } #' example_fun(exprs(DTHDOM = "AE", DTHSEQ = AESEQ)) #' -#' try(example_fun(exprs("AE", DTSEQ = AESEQ, !!mean))) +#' try(example_fun(exprs("AE", DTSEQ = AESEQ, !!list("a")))) assert_expr_list <- function(arg, # nolint required_elements = NULL, named = FALSE, @@ -1364,23 +1375,27 @@ assert_expr_list <- function(arg, # nolint } } - invalids <- arg[!map_lgl( + invalids <- !map_lgl( arg, ~ is_call(.x) || is_expression(.x) - )] + ) + invalidargs <- arg[invalids] - if (length(invalids) > 0) { + if (any(invalids)) { + argname <- arg_name(substitute(arg)) abort( paste0( - "The elements of the list ", - arg_name(substitute(arg)), - " must be expressions.\n", - paste( - names(invalids), - "=", - map_chr(invalids, expr_label), - "is of type", - map_chr(invalids, typeof), + "All elements of `", + argname, + "` must be expressions.\n", + paste0( + argname, + "[[", + if_else(names(invalidargs) == "", as.character(which(invalids)), names(invalidargs)), + "]] = ", + map_chr(invalidargs, expr_label), + " is of type ", + map_chr(invalidargs, typeof), collapse = "\n" ) ) diff --git a/R/quo.R b/R/quo.R index 8fcbc23e..a0d7f938 100644 --- a/R/quo.R +++ b/R/quo.R @@ -40,7 +40,7 @@ quo_c <- function(...) { #' #' @export expr_c <- function(...) { - # transform single expression into list of expression + # Transform single expression into list of expression inputs <- map( list(...), function(x) { @@ -51,7 +51,7 @@ expr_c <- function(...) { } } ) - inputs <- purrr::flatten(inputs) + inputs <- flatten(inputs) stopifnot(all(map_lgl(inputs, is_expression))) is_null <- map_lgl(inputs, is.null) inputs[!is_null] diff --git a/_pkgdown.yml b/_pkgdown.yml index 96ba8d27..2415067a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -80,11 +80,11 @@ reference: - title: Deprecated desc: | - As `{admiral}` is still evolving, functions/parameters may need to be removed or replaced over time. In such cases, the function/parameter will enter the following 6-month deprecation cycle: + As `{admiral}` is still evolving, functions/arguments may need to be removed or replaced over time. In such cases, the function/argument will enter the following 6-month deprecation cycle: - * In the first release (0-3 months), there will be a warning issued if you use the function/parameter, but it will still be available to use. - * In the following release (3-6 months), an error will be produced if you use the function/parameter. - * Finally, from the 3rd release (6 months) onwards, the function/parameter will be removed from `{admiral}` and its documentation completely. + * In the first release (0-3 months), there will be a warning issued if you use the function/argument, but it will still be available to use. + * In the following release (3-6 months), an error will be produced if you use the function/argument. + * Finally, from the 3rd release (6 months) onwards, the function/argument will be removed from `{admiral}` and its documentation completely. *Note: Guidance on replacement functionality can be found in the warning/error message produced or in the function's documentation.* diff --git a/man/assert_expr_list.Rd b/man/assert_expr_list.Rd index 4c42c1c6..790f8ec6 100644 --- a/man/assert_expr_list.Rd +++ b/man/assert_expr_list.Rd @@ -37,7 +37,7 @@ example_fun <- function(vars) { } example_fun(exprs(DTHDOM = "AE", DTHSEQ = AESEQ)) -try(example_fun(exprs("AE", DTSEQ = AESEQ, !!mean))) +try(example_fun(exprs("AE", DTSEQ = AESEQ, !!list("a")))) } \seealso{ Checks for valid input and returns warning or errors messages: diff --git a/man/assert_named.Rd b/man/assert_named.Rd index d8f48e2f..24a486ee 100644 --- a/man/assert_named.Rd +++ b/man/assert_named.Rd @@ -19,6 +19,17 @@ returns the input invisibly otherwise \description{ Assert that all elements of the argument are named. } +\examples{ +example_fun <- function(varval_list) { + assert_named(varval_list) +} + +example_fun(list(var1 = 1, var2 = "x")) + +try(example_fun(list(1, "x"))) + +try(example_fun(list(var = 1, "x"))) +} \seealso{ Checks for valid input and returns warning or errors messages: \code{\link{assert_atomic_vector}()}, diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index 79932356..e397e122 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -1005,7 +1005,7 @@ test_that("assert_expr_list Test 76: no error if `arg` is NULL and optional is T test_that("assert_expr_list Test 77: error if element is invalid", { expect_error( assert_expr_list(arg <- exprs(DTHSEQ = !!mean)), - regexp = "The elements of the list arg must be expressions.", + regexp = "All elements of `arg` must be expressions.", fixed = TRUE ) }) diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index 312809cd..40ad1d2d 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -167,8 +167,10 @@ There is a recommended argument order that all contributors are asked to adhere 1. all additional arguments: * Make sure to always mention `start_date` before `end_date` (or related). -Names of variables inside a dataset should be passed as symbols rather than strings, i.e. `AVAL` rather than `"AVAL"`. -If an argument accepts one or more variables or expressions as input, the variables should be wrapped inside `exprs()`. +Names of variables inside a dataset should be passed as symbols rather than +strings, i.e. `AVAL` rather than `"AVAL"`. If an argument accepts one or more +variables or expressions as input then the variables and expressions should be +wrapped inside `exprs()`. For example: From 4fe51151764f890c976498d9512336851563783e Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Wed, 12 Apr 2023 17:29:39 +0200 Subject: [PATCH 049/100] 241_allow_expressions: improve wording of messages --- R/assertions.R | 2 +- tests/testthat/test-assertions.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/assertions.R b/R/assertions.R index 7154dbe6..eafa856b 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -1387,7 +1387,7 @@ assert_expr_list <- function(arg, # nolint paste0( "All elements of `", argname, - "` must be expressions.\n", + "` must be an expression.\n", paste0( argname, "[[", diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index e397e122..71d5a667 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -1005,7 +1005,7 @@ test_that("assert_expr_list Test 76: no error if `arg` is NULL and optional is T test_that("assert_expr_list Test 77: error if element is invalid", { expect_error( assert_expr_list(arg <- exprs(DTHSEQ = !!mean)), - regexp = "All elements of `arg` must be expressions.", + regexp = "All elements of `arg` must be an expression.", fixed = TRUE ) }) From 1dc4e109b7fd00e63ea1e9a74cf143f1f9d0e377 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Wed, 12 Apr 2023 18:33:24 +0200 Subject: [PATCH 050/100] 241_allow_expressions: fix styler check --- R/assertions.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/assertions.R b/R/assertions.R index eafa856b..9f83cc95 100644 --- a/R/assertions.R +++ b/R/assertions.R @@ -1391,7 +1391,7 @@ assert_expr_list <- function(arg, # nolint paste0( argname, "[[", - if_else(names(invalidargs) == "", as.character(which(invalids)), names(invalidargs)), + if_else(names(invalidargs) == "", as.character(which(invalids)), names(invalidargs)), "]] = ", map_chr(invalidargs, expr_label), " is of type ", From 96f55003b20f16f7756251491ef50e3c42c33a4c Mon Sep 17 00:00:00 2001 From: sadchla-codes Date: Wed, 12 Apr 2023 16:43:15 +0000 Subject: [PATCH 051/100] Closes #257: adding `Report a bug` link to the website --- DESCRIPTION | 1 + NEWS.md | 8 ++++++++ man/admiraldev-package.Rd | 1 + 3 files changed, 10 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 95900d32..d82db66d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -22,6 +22,7 @@ Description: Utility functions to check data, variables and conditions for funct 'admiral' and 'admiral' extension packages. Additional utility helper functions to assist developers with maintaining documentation, testing and general upkeep of 'admiral' and 'admiral' extension packages. License: Apache License (>= 2) +BugReports: https://github.com/pharmaverse/admiraldev/issues URL: https://pharmaverse.github.io/admiraldev/main/, https://github.com/pharmaverse/admiraldev/ Encoding: UTF-8 Language: en-US diff --git a/NEWS.md b/NEWS.md index a7d6f8f3..590e9669 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,13 @@ # admiraldev 0.4.0 +## New Features + +- Added a **Report a bug** link on `admiraldev` website (#257) + +## Updates of Existing Functions + +## Breaking Changes + ## Documentation - The deprecation strategy was updated regarding unit tests for deprecated diff --git a/man/admiraldev-package.Rd b/man/admiraldev-package.Rd index e8c6db91..912f544d 100644 --- a/man/admiraldev-package.Rd +++ b/man/admiraldev-package.Rd @@ -15,6 +15,7 @@ Useful links: \itemize{ \item \url{https://pharmaverse.github.io/admiraldev/main/} \item \url{https://github.com/pharmaverse/admiraldev/} + \item Report bugs at \url{https://github.com/pharmaverse/admiraldev/issues} } } From b52c7b9a716c06346d8df18310ef2f3ed5b4e43c Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Wed, 12 Apr 2023 18:47:58 +0200 Subject: [PATCH 052/100] 241_allow_expressions: fix links --- vignettes/development_process.Rmd | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/vignettes/development_process.Rmd b/vignettes/development_process.Rmd index c0617c5f..00cf5830 100644 --- a/vignettes/development_process.Rmd +++ b/vignettes/development_process.Rmd @@ -16,7 +16,7 @@ knitr::opts_chunk$set( ``` Once you’ve familiarized yourself with the `{admiral}` [contribution -model](https://pharmaverse.github.io/admiral/articles/contribution_model.html) and you’re ready to make your first code +model](https://pharmaverse.github.io/admiral/main/articles/contribution_model.html) and you’re ready to make your first code contribution, this development process step-by-step guide will help tie all the other detailed vignettes together to give you the simplest experience of helping to grow and enhance our codebase. @@ -32,7 +32,9 @@ strategy](programming_strategy.html), and then make the required code updates. a. Did you create/add appropriate [unit tests](unit_test_guidance.html#writing-unit-tests-in-admiral)? a. If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](programming_strategy.html#deprecation)? a. Did you update the [documentation](programming_strategy.html#function-header-documentation)? If so, remember to run `devtools::document()` and include the updated `NAMESPACE` and `.Rd` files in `man/` - a. Does your code update have any impact on the [ADaM template](https://pharmaverse.github.io/admiral/articles/admiral.html#starting-a-script) R scripts stored in `inst/templates`? + a. Does your code update have any impact on the [ADaM + template](https://pharmaverse.github.io/admiral/main/articles/admiral.html#starting-a-script) + R scripts stored in `inst/templates`? a. Does your code update have any impact on the vignettes stored in vignettes? a. Did you update the Changelog `NEWS.md`? a. Did you build `{admiral}` site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](../reference/index.html)" page? From 7176ffedc4fa4b59387c5f953714b3fb5dceaab0 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Wed, 12 Apr 2023 19:27:22 +0200 Subject: [PATCH 053/100] 241_allow_expressions: fix urls --- _pkgdown.yml | 2 +- docs/pkgdown.yml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 2415067a..e9425344 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://pharmaverse.github.io/admiraldev/main +url: https://pharmaverse.github.io/admiraldev/devel template: bootstrap: 5 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 91fdefe5..4e7f8407 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,8 +10,8 @@ articles: release_strategy: release_strategy.html unit_test_guidance: unit_test_guidance.html writing_vignettes: writing_vignettes.html -last_built: 2023-03-31T14:13Z +last_built: 2023-04-12T17:21Z urls: - reference: https://pharmaverse.github.io/admiraldev/main/reference - article: https://pharmaverse.github.io/admiraldev/main/articles + reference: https://pharmaverse.github.io/admiraldev/devel/reference + article: https://pharmaverse.github.io/admiraldev/devel/articles From 1e6e2e49a6c6a09a0adebe10c54d0e8ce63f1772 Mon Sep 17 00:00:00 2001 From: sadchla-codes Date: Thu, 13 Apr 2023 19:27:05 +0000 Subject: [PATCH 054/100] Closes #259 Fix broken links in development_process.Rmd --- docs/pkgdown.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e1010f62..e8426316 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.17.1.1 +pandoc: 2.19.2 pkgdown: 2.0.6 pkgdown_sha: ~ articles: @@ -10,8 +10,8 @@ articles: release_strategy: release_strategy.html unit_test_guidance: unit_test_guidance.html writing_vignettes: writing_vignettes.html -last_built: 2023-01-19T10:49Z +last_built: 2023-04-13T19:24Z urls: - reference: https://pharmaverse.github.io/admiraldev/devel/reference - article: https://pharmaverse.github.io/admiraldev/devel/articles + reference: https://pharmaverse.github.io/admiraldev/reference + article: https://pharmaverse.github.io/admiraldev/articles From 953eb82915e6e1caa7f960f0afc436f17d2eb707 Mon Sep 17 00:00:00 2001 From: sadchla-codes Date: Thu, 13 Apr 2023 19:39:31 +0000 Subject: [PATCH 055/100] Closes #259 fixed broken link --- vignettes/development_process.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vignettes/development_process.Rmd b/vignettes/development_process.Rmd index c0617c5f..f406320a 100644 --- a/vignettes/development_process.Rmd +++ b/vignettes/development_process.Rmd @@ -16,7 +16,7 @@ knitr::opts_chunk$set( ``` Once you’ve familiarized yourself with the `{admiral}` [contribution -model](https://pharmaverse.github.io/admiral/articles/contribution_model.html) and you’re ready to make your first code +model](https://pharmaverse.github.io/admiral/cran-release/articles/contribution_model.html) and you’re ready to make your first code contribution, this development process step-by-step guide will help tie all the other detailed vignettes together to give you the simplest experience of helping to grow and enhance our codebase. @@ -32,7 +32,7 @@ strategy](programming_strategy.html), and then make the required code updates. a. Did you create/add appropriate [unit tests](unit_test_guidance.html#writing-unit-tests-in-admiral)? a. If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](programming_strategy.html#deprecation)? a. Did you update the [documentation](programming_strategy.html#function-header-documentation)? If so, remember to run `devtools::document()` and include the updated `NAMESPACE` and `.Rd` files in `man/` - a. Does your code update have any impact on the [ADaM template](https://pharmaverse.github.io/admiral/articles/admiral.html#starting-a-script) R scripts stored in `inst/templates`? + a. Does your code update have any impact on the [ADaM template](https://pharmaverse.github.io/admiral/cran-release/articles/admiral.html#starting-a-script) R scripts stored in `inst/templates`? a. Does your code update have any impact on the vignettes stored in vignettes? a. Did you update the Changelog `NEWS.md`? a. Did you build `{admiral}` site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](../reference/index.html)" page? From 025ebd126fcd05c58195a9629086bf70c8692070 Mon Sep 17 00:00:00 2001 From: sadchla-codes Date: Thu, 13 Apr 2023 19:43:46 +0000 Subject: [PATCH 056/100] Updated pkgdown.yml --- docs/pkgdown.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e8426316..e1010f62 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.19.2 +pandoc: 2.17.1.1 pkgdown: 2.0.6 pkgdown_sha: ~ articles: @@ -10,8 +10,8 @@ articles: release_strategy: release_strategy.html unit_test_guidance: unit_test_guidance.html writing_vignettes: writing_vignettes.html -last_built: 2023-04-13T19:24Z +last_built: 2023-01-19T10:49Z urls: - reference: https://pharmaverse.github.io/admiraldev/reference - article: https://pharmaverse.github.io/admiraldev/articles + reference: https://pharmaverse.github.io/admiraldev/devel/reference + article: https://pharmaverse.github.io/admiraldev/devel/articles From f41bcec75dbf0b3652ffc87e0be3a4354bd15c82 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Mon, 17 Apr 2023 12:19:48 +0200 Subject: [PATCH 057/100] 241_allow_expressions: fix styling --- vignettes/programming_strategy.Rmd | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index 40ad1d2d..67dc2267 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -369,14 +369,14 @@ An example is given below: #' library(tibble) #' #' datain <- tribble( -#' ~TRTSDTM, ~ASTDTM, ~AENDT, -#' "2014-01-17T23:59:59", "2014-01-18T13:09:O9", "2014-01-20" +#' ~TRTSDTM, ~ASTDTM, ~AENDT, +#' "2014-01-17T23:59:59", "2014-01-18T13:09:O9", "2014-01-20" #' ) %>% -#' mutate( -#' TRTSDTM = as_datetime(TRTSDTM), -#' ASTDTM = as_datetime(ASTDTM), -#' AENDT = ymd(AENDT) -#' ) +#' mutate( +#' TRTSDTM = as_datetime(TRTSDTM), +#' ASTDTM = as_datetime(ASTDTM), +#' AENDT = ymd(AENDT) +#' ) #' #' derive_vars_dy( #' datain, From 6cce5ebe2aa47b2aab06d8bac7c412951db5bd11 Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Mon, 17 Apr 2023 12:51:10 +0200 Subject: [PATCH 058/100] 241_allow_expressions: add utils_print keyword --- vignettes/programming_strategy.Rmd | 1 + 1 file changed, 1 insertion(+) diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index 67dc2267..0212a3d3 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -474,6 +474,7 @@ add an issue in GitHub for discussion. | `utils_ds_chk` | Utilities for Dataset Checking | | `utils_fil` | Utilities for Filtering Observations | | `utils_fmt` | Utilities for Formatting Observations | +| `utils_print` | Utilities for Printing Objects in the Console | | `utils_help` | Utilities used within Derivation functions | | `utils_examples` | Utilities used for examples and template scripts | | `source_specifications` | Source Objects | From b247b8653b758727b156abafb7bf67d43b661bbd Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Tue, 18 Apr 2023 08:46:29 +0000 Subject: [PATCH 059/100] 241_allow_expressions: fix extract_vars() --- R/dev_utilities.R | 13 +++++++++---- man/extract_vars.Rd | 7 ++++++- tests/testthat/test-dev_utilities.R | 23 +++++++++++++++++++++++ 3 files changed, 38 insertions(+), 5 deletions(-) diff --git a/R/dev_utilities.R b/R/dev_utilities.R index 658851f4..d21d07fb 100644 --- a/R/dev_utilities.R +++ b/R/dev_utilities.R @@ -62,7 +62,7 @@ arg_name <- function(expr) { # nolint #' Extract All Symbols from a List of Expressions #' #' @param x An `R` object -#' @param side One of `"lhs"` (the default) or `"rhs"` +#' @param side One of `"lhs"` (the default) or `"rhs"` for formulas #' #' @return A list of expressions #' @@ -70,6 +70,11 @@ arg_name <- function(expr) { # nolint #' @keywords dev_utility #' @family dev_utility #' @export +#' +#' @examples +#' extract_vars(exprs(PARAMCD, (BASE - AVAL)/BASE + 100)) +#' extract_vars(AVAL ~ ARMCD + AGEGR1) +#' extract_vars(AVAL ~ ARMCD + AGEGR1, side = "rhs") extract_vars <- function(x, side = "lhs") { if (is.null(x)) { NULL @@ -80,9 +85,9 @@ extract_vars <- function(x, side = "lhs") { } else if (is_formula(x)) { funs <- list("lhs" = f_lhs, "rhs" = f_rhs) assert_character_scalar(side, values = names(funs)) - expr(!!funs[[side]](x)) - } else { - abort() + extract_vars(expr(!!funs[[side]](x))) + } else if (is_call(x)) { + extract_vars(as.list(x[-1])) } } diff --git a/man/extract_vars.Rd b/man/extract_vars.Rd index 540015c6..81bbd009 100644 --- a/man/extract_vars.Rd +++ b/man/extract_vars.Rd @@ -9,7 +9,7 @@ extract_vars(x, side = "lhs") \arguments{ \item{x}{An \code{R} object} -\item{side}{One of \code{"lhs"} (the default) or \code{"rhs"}} +\item{side}{One of \code{"lhs"} (the default) or \code{"rhs"} for formulas} } \value{ A list of expressions @@ -17,6 +17,11 @@ A list of expressions \description{ Extract All Symbols from a List of Expressions } +\examples{ +extract_vars(exprs(PARAMCD, (BASE - AVAL)/BASE + 100)) +extract_vars(AVAL ~ ARMCD + AGEGR1) +extract_vars(AVAL ~ ARMCD + AGEGR1, side = "rhs") +} \seealso{ Developer Utility Functions: \code{\link{\%notin\%}()}, diff --git a/tests/testthat/test-dev_utilities.R b/tests/testthat/test-dev_utilities.R index 0481d6c2..9677a1fd 100644 --- a/tests/testthat/test-dev_utilities.R +++ b/tests/testthat/test-dev_utilities.R @@ -84,3 +84,26 @@ test_that("vars2chr Test 9: warning if quosures argument is used", { class = "lifecycle_warning_deprecated" ) }) + +# extract_vars ---- +## Test 10: works with formulas (lhs) ---- +test_that("extract_vars Test 10: works with formulas (lhs)", { + expect_equal( + object = extract_vars(AVAL ~ ARMCD + AGEGR1), + expected = unname(exprs(AVAL))) +}) + +## Test 11: works with formulas (rhs) ---- +test_that("extract_vars Test 11: works with formulas (rhs)", { + expect_equal( + object = extract_vars(AVAL ~ ARMCD + AGEGR1, side = "rhs"), + expected = unname(exprs(ARMCD, AGEGR1))) +}) + +## Test 12: works with calls ---- +test_that("extract_vars Test 12: works with calls", { + fun <- mean + expect_equal( + object = extract_vars(expr({{fun}}((BASE - AVAL)/BASE * 100 , LLQ/2))), + expected = unname(exprs(BASE, AVAL, LLQ))) +}) From 8c6f6de008703f1b1c78554dc9deae9b1075e93d Mon Sep 17 00:00:00 2001 From: "Bundfuss, Stefan {MDBB~Basel}" Date: Tue, 18 Apr 2023 11:05:59 +0200 Subject: [PATCH 060/100] 241_allow_expressions: fix R-CMD check for 4.0 and 4.1 --- R/dev_utilities.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/dev_utilities.R b/R/dev_utilities.R index d21d07fb..8ff1f66d 100644 --- a/R/dev_utilities.R +++ b/R/dev_utilities.R @@ -80,7 +80,7 @@ extract_vars <- function(x, side = "lhs") { NULL } else if (is.list(x)) { do.call(expr_c, map(x, extract_vars, side)) - } else if (is_expression(x)) { + } else if (is_expression(x) & !is_formula(x)) { syms(all.vars(x)) } else if (is_formula(x)) { funs <- list("lhs" = f_lhs, "rhs" = f_rhs) From c6e3143835ea7052640cddcf0d1c95e520e9292d Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Tue, 18 Apr 2023 09:08:03 +0000 Subject: [PATCH 061/100] 241_allow_expressions: fix example for extract_vars() --- R/dev_utilities.R | 1 + man/extract_vars.Rd | 1 + 2 files changed, 2 insertions(+) diff --git a/R/dev_utilities.R b/R/dev_utilities.R index d21d07fb..45598e92 100644 --- a/R/dev_utilities.R +++ b/R/dev_utilities.R @@ -72,6 +72,7 @@ arg_name <- function(expr) { # nolint #' @export #' #' @examples +#' library(rlang) #' extract_vars(exprs(PARAMCD, (BASE - AVAL)/BASE + 100)) #' extract_vars(AVAL ~ ARMCD + AGEGR1) #' extract_vars(AVAL ~ ARMCD + AGEGR1, side = "rhs") diff --git a/man/extract_vars.Rd b/man/extract_vars.Rd index 81bbd009..94286672 100644 --- a/man/extract_vars.Rd +++ b/man/extract_vars.Rd @@ -18,6 +18,7 @@ A list of expressions Extract All Symbols from a List of Expressions } \examples{ +library(rlang) extract_vars(exprs(PARAMCD, (BASE - AVAL)/BASE + 100)) extract_vars(AVAL ~ ARMCD + AGEGR1) extract_vars(AVAL ~ ARMCD + AGEGR1, side = "rhs") From 8d995521125c400b59ed3d2494960b6379851844 Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Tue, 18 Apr 2023 09:15:26 +0000 Subject: [PATCH 062/100] 241_allow_expressions: style_files --- R/dev_utilities.R | 2 +- tests/testthat/test-dev_utilities.R | 11 +++++++---- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/R/dev_utilities.R b/R/dev_utilities.R index d2732c8d..02a6e3c4 100644 --- a/R/dev_utilities.R +++ b/R/dev_utilities.R @@ -73,7 +73,7 @@ arg_name <- function(expr) { # nolint #' #' @examples #' library(rlang) -#' extract_vars(exprs(PARAMCD, (BASE - AVAL)/BASE + 100)) +#' extract_vars(exprs(PARAMCD, (BASE - AVAL) / BASE + 100)) #' extract_vars(AVAL ~ ARMCD + AGEGR1) #' extract_vars(AVAL ~ ARMCD + AGEGR1, side = "rhs") extract_vars <- function(x, side = "lhs") { diff --git a/tests/testthat/test-dev_utilities.R b/tests/testthat/test-dev_utilities.R index 9677a1fd..0c83d82f 100644 --- a/tests/testthat/test-dev_utilities.R +++ b/tests/testthat/test-dev_utilities.R @@ -90,20 +90,23 @@ test_that("vars2chr Test 9: warning if quosures argument is used", { test_that("extract_vars Test 10: works with formulas (lhs)", { expect_equal( object = extract_vars(AVAL ~ ARMCD + AGEGR1), - expected = unname(exprs(AVAL))) + expected = unname(exprs(AVAL)) + ) }) ## Test 11: works with formulas (rhs) ---- test_that("extract_vars Test 11: works with formulas (rhs)", { expect_equal( object = extract_vars(AVAL ~ ARMCD + AGEGR1, side = "rhs"), - expected = unname(exprs(ARMCD, AGEGR1))) + expected = unname(exprs(ARMCD, AGEGR1)) + ) }) ## Test 12: works with calls ---- test_that("extract_vars Test 12: works with calls", { fun <- mean expect_equal( - object = extract_vars(expr({{fun}}((BASE - AVAL)/BASE * 100 , LLQ/2))), - expected = unname(exprs(BASE, AVAL, LLQ))) + object = extract_vars(expr({{ fun }}((BASE - AVAL) / BASE * 100, LLQ / 2))), + expected = unname(exprs(BASE, AVAL, LLQ)) + ) }) From b13883ed037df0af9a40dcb2c2ec95540f13def5 Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Tue, 18 Apr 2023 09:18:58 +0000 Subject: [PATCH 063/100] 241_allow_expressions: fix lintr check --- R/dev_utilities.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/dev_utilities.R b/R/dev_utilities.R index 02a6e3c4..4d37a178 100644 --- a/R/dev_utilities.R +++ b/R/dev_utilities.R @@ -81,7 +81,7 @@ extract_vars <- function(x, side = "lhs") { NULL } else if (is.list(x)) { do.call(expr_c, map(x, extract_vars, side)) - } else if (is_expression(x) & !is_formula(x)) { + } else if (is_expression(x) && !is_formula(x)) { syms(all.vars(x)) } else if (is_formula(x)) { funs <- list("lhs" = f_lhs, "rhs" = f_rhs) From 4aeeb690f2bdbba4fe43c0d7b4a3d454dc7230fa Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Tue, 18 Apr 2023 09:25:45 +0000 Subject: [PATCH 064/100] 241_allow_expressions: update man --- man/extract_vars.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/extract_vars.Rd b/man/extract_vars.Rd index 94286672..198ed3eb 100644 --- a/man/extract_vars.Rd +++ b/man/extract_vars.Rd @@ -19,7 +19,7 @@ Extract All Symbols from a List of Expressions } \examples{ library(rlang) -extract_vars(exprs(PARAMCD, (BASE - AVAL)/BASE + 100)) +extract_vars(exprs(PARAMCD, (BASE - AVAL) / BASE + 100)) extract_vars(AVAL ~ ARMCD + AGEGR1) extract_vars(AVAL ~ ARMCD + AGEGR1, side = "rhs") } From f6224195ef4e0e7a675119460b22afb6a055d29b Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 18 Apr 2023 11:02:25 +0000 Subject: [PATCH 065/100] renv update from pharmaverse/admiralci --- renv/profiles/4.0/renv/settings.dcf | 2 +- renv/profiles/4.0_legacy/renv/settings.dcf | 2 +- renv/profiles/4.1/renv/settings.dcf | 2 +- renv/profiles/4.2/renv/settings.dcf | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/renv/profiles/4.0/renv/settings.dcf b/renv/profiles/4.0/renv/settings.dcf index c4ab61bd..fd205f80 100644 --- a/renv/profiles/4.0/renv/settings.dcf +++ b/renv/profiles/4.0/renv/settings.dcf @@ -3,7 +3,7 @@ external.libraries: ignored.packages: admiral, admiraldev, admiral.test, admiralci package.dependency.fields: Imports, Depends, LinkingTo r.version: -snapshot.type: custom +snapshot.type: implicit use.cache: TRUE vcs.ignore.cellar: TRUE vcs.ignore.library: TRUE diff --git a/renv/profiles/4.0_legacy/renv/settings.dcf b/renv/profiles/4.0_legacy/renv/settings.dcf index c4ab61bd..fd205f80 100644 --- a/renv/profiles/4.0_legacy/renv/settings.dcf +++ b/renv/profiles/4.0_legacy/renv/settings.dcf @@ -3,7 +3,7 @@ external.libraries: ignored.packages: admiral, admiraldev, admiral.test, admiralci package.dependency.fields: Imports, Depends, LinkingTo r.version: -snapshot.type: custom +snapshot.type: implicit use.cache: TRUE vcs.ignore.cellar: TRUE vcs.ignore.library: TRUE diff --git a/renv/profiles/4.1/renv/settings.dcf b/renv/profiles/4.1/renv/settings.dcf index c4ab61bd..fd205f80 100644 --- a/renv/profiles/4.1/renv/settings.dcf +++ b/renv/profiles/4.1/renv/settings.dcf @@ -3,7 +3,7 @@ external.libraries: ignored.packages: admiral, admiraldev, admiral.test, admiralci package.dependency.fields: Imports, Depends, LinkingTo r.version: -snapshot.type: custom +snapshot.type: implicit use.cache: TRUE vcs.ignore.cellar: TRUE vcs.ignore.library: TRUE diff --git a/renv/profiles/4.2/renv/settings.dcf b/renv/profiles/4.2/renv/settings.dcf index c4ab61bd..fd205f80 100644 --- a/renv/profiles/4.2/renv/settings.dcf +++ b/renv/profiles/4.2/renv/settings.dcf @@ -3,7 +3,7 @@ external.libraries: ignored.packages: admiral, admiraldev, admiral.test, admiralci package.dependency.fields: Imports, Depends, LinkingTo r.version: -snapshot.type: custom +snapshot.type: implicit use.cache: TRUE vcs.ignore.cellar: TRUE vcs.ignore.library: TRUE From be0fe52b6142be464959c8441923b6ad49f6e8cd Mon Sep 17 00:00:00 2001 From: galachad Date: Mon, 24 Apr 2023 14:05:07 +0000 Subject: [PATCH 066/100] renv update from pharmaverse/admiralci --- renv.lock | 10 ---------- renv/profiles/4.0/renv.lock | 10 ---------- renv/profiles/4.1/renv.lock | 10 ---------- renv/profiles/4.2/renv.lock | 10 ---------- 4 files changed, 40 deletions(-) diff --git a/renv.lock b/renv.lock index a99fa094..932de771 100644 --- a/renv.lock +++ b/renv.lock @@ -120,16 +120,6 @@ ], "Hash": "e8a22846fff485f0be3770c2da758713" }, - "assertthat": { - "Package": "assertthat", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "tools" - ], - "Hash": "50c838a310445e954bc13f26f26a6ecf" - }, "backports": { "Package": "backports", "Version": "1.2.1", diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index a99fa094..932de771 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -120,16 +120,6 @@ ], "Hash": "e8a22846fff485f0be3770c2da758713" }, - "assertthat": { - "Package": "assertthat", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "tools" - ], - "Hash": "50c838a310445e954bc13f26f26a6ecf" - }, "backports": { "Package": "backports", "Version": "1.2.1", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index c1c5e689..94499def 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -114,16 +114,6 @@ ], "Hash": "e8a22846fff485f0be3770c2da758713" }, - "assertthat": { - "Package": "assertthat", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "tools" - ], - "Hash": "50c838a310445e954bc13f26f26a6ecf" - }, "backports": { "Package": "backports", "Version": "1.4.1", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 38a0bfc5..7a05bbc5 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -114,16 +114,6 @@ ], "Hash": "e8a22846fff485f0be3770c2da758713" }, - "assertthat": { - "Package": "assertthat", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "tools" - ], - "Hash": "50c838a310445e954bc13f26f26a6ecf" - }, "backports": { "Package": "backports", "Version": "1.4.1", From 0ffe5e84516c40e9b5d358827554ffa4ac152c27 Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Thu, 27 Apr 2023 15:16:09 +0000 Subject: [PATCH 067/100] 265_fix_suppress_warning: use any() --- R/warnings.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/warnings.R b/R/warnings.R index 13a905e5..8f6f3799 100644 --- a/R/warnings.R +++ b/R/warnings.R @@ -201,7 +201,7 @@ suppress_warning <- function(expr, regexpr) { withCallingHandlers( expr, warning = function(w) { - if (grepl(regexpr, w$message)) { + if (any(grepl(regexpr, w$message))) { invokeRestart("muffleWarning") } } From 0618d6fe94ab29d3b40a1963f56e3f1299bd63f0 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Wed, 3 May 2023 15:36:12 +0000 Subject: [PATCH 068/100] fix: #26 update badges (no favicon for dev) --- README.Rmd | 4 ++++ README.md | 7 +++++++ 2 files changed, 11 insertions(+) diff --git a/README.Rmd b/README.Rmd index eb397bdb..632fd2a8 100644 --- a/README.Rmd +++ b/README.Rmd @@ -36,6 +36,10 @@ Utility Functions and Development Tools for the Admiral Package Family +[](https://pharmaverse.org) +[![CRAN status](https://www.r-pkg.org/badges/version/admiraldev)](https://CRAN.R-project.org/package=admiraldev) +[![Test Coverage](https://raw.githubusercontent.com/pharmaverse/admiraldev/badges/main/test-coverage.svg)](https://github.com/pharmaverse/admiraldev/actions/workflows/common.yml) + diff --git a/README.md b/README.md index 75d7bc07..2a7340d0 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,13 @@ Utility Functions and Development Tools for the Admiral Package Family + +[](https://pharmaverse.org) +[![CRAN +status](https://www.r-pkg.org/badges/version/admiraldev)](https://CRAN.R-project.org/package=admiraldev) +[![Test +Coverage](https://raw.githubusercontent.com/pharmaverse/admiraldev/badges/main/test-coverage.svg)](https://github.com/pharmaverse/admiraldev/actions/workflows/common.yml) + ## Purpose From 252ee7860e3a9c3148af413b9fe4c6f18a0fd9af Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Wed, 3 May 2023 15:54:08 +0000 Subject: [PATCH 069/100] test: #104 add coverage for datasets.R --- tests/testthat/test-datasets.R | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 tests/testthat/test-datasets.R diff --git a/tests/testthat/test-datasets.R b/tests/testthat/test-datasets.R new file mode 100644 index 00000000..71d0fb57 --- /dev/null +++ b/tests/testthat/test-datasets.R @@ -0,0 +1,13 @@ +# get_dataset ---- +## Test 1: get_dataset works ---- +test_that("get_dataset Test 1: get_dataset works", { + expect_equal(NULL, get_dataset("one_to_many")) +}) + +## Test 2: get_dataset gives error works ---- +test_that("get_dataset Test 2: get_dataset works", { + expect_error( + get_dataset("test"), + "`name` must be one of 'one_to_many' or 'many_to_one' but is 'test'" + ) +}) From f8bb57cbb03e71a00462d153bd467fc68e27a19e Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Wed, 3 May 2023 15:55:30 +0000 Subject: [PATCH 070/100] fix: #246 update dplyr to 1.0.5 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d82db66d..d79eaa8d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -31,7 +31,7 @@ Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.1 Depends: R (>= 3.5) Imports: - dplyr (>= 0.8.4), + dplyr (>= 1.0.5), hms (>= 0.5.3), lifecycle (>= 0.1.0), lubridate (>= 1.7.4), From 516f8e7c1e9e0cb6496c739d80ca1af51c57a694 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 4 May 2023 18:21:17 +0000 Subject: [PATCH 071/100] chore: #26 no favicon for admiraldev --- README.Rmd | 1 - README.md | 1 - 2 files changed, 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index 632fd2a8..0a3dc4c0 100644 --- a/README.Rmd +++ b/README.Rmd @@ -36,7 +36,6 @@ Utility Functions and Development Tools for the Admiral Package Family -[](https://pharmaverse.org) [![CRAN status](https://www.r-pkg.org/badges/version/admiraldev)](https://CRAN.R-project.org/package=admiraldev) [![Test Coverage](https://raw.githubusercontent.com/pharmaverse/admiraldev/badges/main/test-coverage.svg)](https://github.com/pharmaverse/admiraldev/actions/workflows/common.yml) diff --git a/README.md b/README.md index 2a7340d0..cc8daf96 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,6 @@ Utility Functions and Development Tools for the Admiral Package Family -[](https://pharmaverse.org) [![CRAN status](https://www.r-pkg.org/badges/version/admiraldev)](https://CRAN.R-project.org/package=admiraldev) [![Test From 927c31e2c344288e5897e9a669ee6fbbdb0aacc0 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 4 May 2023 18:25:55 +0000 Subject: [PATCH 072/100] chore: #104 styler fix --- tests/testthat/test-datasets.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-datasets.R b/tests/testthat/test-datasets.R index 71d0fb57..563a1b4f 100644 --- a/tests/testthat/test-datasets.R +++ b/tests/testthat/test-datasets.R @@ -8,6 +8,6 @@ test_that("get_dataset Test 1: get_dataset works", { test_that("get_dataset Test 2: get_dataset works", { expect_error( get_dataset("test"), - "`name` must be one of 'one_to_many' or 'many_to_one' but is 'test'" + "`name` must be one of 'one_to_many' or 'many_to_one' but is 'test'" ) }) From faf119441577024b6f7fd8f8ce4c2f3ab277ee16 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 4 May 2023 19:01:08 +0000 Subject: [PATCH 073/100] test: #104 unassign one admiraldev_environment objects --- tests/testthat/test-assertions.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index 740ecd0b..837e50e8 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -1034,6 +1034,7 @@ test_that("assert_one_to_one Test 74: error if there is a one to many mapping", expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(DOMAIN), exprs(USUBJID)) ) + admiraldev_environment$one_to_many <- NULL }) ## Test 75: error if there is a many to one mapping ---- @@ -1041,6 +1042,7 @@ test_that("assert_one_to_one Test 75: error if there is a many to one mapping", expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(USUBJID), exprs(DOMAIN)) ) + admiraldev_environment$one_to_many <- NULL }) # assert_date_var ---- From 582a9545eb57bf36b3f848e2e92567bbe5c5890a Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 4 May 2023 19:04:51 +0000 Subject: [PATCH 074/100] chore: #104 typo in previous commit --- tests/testthat/test-assertions.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R index 837e50e8..00fe4626 100644 --- a/tests/testthat/test-assertions.R +++ b/tests/testthat/test-assertions.R @@ -1042,7 +1042,7 @@ test_that("assert_one_to_one Test 75: error if there is a many to one mapping", expect_error( assert_one_to_one(admiral.test::admiral_dm, exprs(USUBJID), exprs(DOMAIN)) ) - admiraldev_environment$one_to_many <- NULL + admiraldev_environment$many_to_one <- NULL }) # assert_date_var ---- From 1b0c5e9275d2a14fa5af713996b7e0a82e13ecf0 Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 16 May 2023 14:51:19 +0000 Subject: [PATCH 075/100] renv update from pharmaverse/admiralci --- .github/workflows/common.yml | 16 +- renv.lock | 311 ++--- renv/profiles/4.1/renv.lock | 7 +- renv/profiles/4.2/renv.lock | 258 ++-- renv/profiles/4.3/renv.lock | 1707 +++++++++++++++++++++++++++ renv/profiles/4.3/renv/.gitignore | 7 + renv/profiles/4.3/renv/settings.dcf | 10 + 7 files changed, 2044 insertions(+), 272 deletions(-) create mode 100644 renv/profiles/4.3/renv.lock create mode 100644 renv/profiles/4.3/renv/.gitignore create mode 100644 renv/profiles/4.3/renv/settings.dcf diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index 518c64af..59e069bd 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -45,25 +45,25 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/style.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" spellcheck: name: Spelling uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" readme: name: Render README uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main if: github.event_name == 'push' with: - r-version: "4.0" + r-version: "4.1" validation: name: Validation uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main if: github.event_name == 'release' with: - r-version: "4.0" + r-version: "4.1" check: name: Check uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main @@ -73,7 +73,7 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main if: github.event_name == 'push' with: - r-version: "4.0" + r-version: "4.1" # Whether to skip multiversion docs # Note that if you have multiple versions of docs, # your URL links are likely to break due to path changes @@ -85,7 +85,7 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" links: name: Links uses: pharmaverse/admiralci/.github/workflows/links.yml@main @@ -97,7 +97,7 @@ jobs: if: > github.event_name == 'push' || github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" # Whether to skip code coverage badge creation # Setting to 'false' will require you to create # an orphan branch called 'badges' in your repository @@ -107,4 +107,4 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" diff --git a/renv.lock b/renv.lock index 932de771..03dbcf3c 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.0.5", + "Version": "4.1.3", "Repositories": [ { "Name": "CRAN", @@ -8,38 +8,32 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2021-03-31" + "URL": "https://packagemanager.rstudio.com/cran/2022-03-10" } ] }, "Packages": { - "BH": { - "Package": "BH", - "Version": "1.75.0-0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "e4c04affc2cac20c8fec18385cd14691" - }, "DT": { "Package": "DT", - "Version": "0.17", + "Version": "0.21", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "crosstalk", "htmltools", "htmlwidgets", + "jquerylib", "jsonlite", "magrittr", "promises" ], - "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0" + "Hash": "45fa28dbf288cd606e13ca35d3d72437" }, "R.cache": { "Package": "R.cache", "Version": "0.15.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R.methodsS3", @@ -76,7 +70,7 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.10.1", + "Version": "2.11.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -87,28 +81,28 @@ "tools", "utils" ], - "Hash": "a9e316277ff12a43997266f2f6567780" + "Hash": "a7ecb8e60815c7a18648e84cd121b23a" }, "R6": { "Package": "R6", - "Version": "2.5.0", + "Version": "2.5.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "b203113193e70978a696b2809525649d" + "Hash": "470851b6d5d0ac559e9d01bb352b4021" }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.6", + "Version": "1.0.8", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods", "utils" ], - "Hash": "dbb5e436998a7eba5a9d682060533338" + "Hash": "22b546dd7e337f6c0c58a39983a496bc" }, "askpass": { "Package": "askpass", @@ -122,13 +116,13 @@ }, "backports": { "Package": "backports", - "Version": "1.2.1", + "Version": "1.4.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "644043219fc24e190c2f620c1a380a69" + "Hash": "c39fbec8a30d23e721980b8afb31984c" }, "base64enc": { "Package": "base64enc", @@ -142,23 +136,23 @@ }, "brew": { "Package": "brew", - "Version": "1.0-6", + "Version": "1.0-7", "Source": "Repository", "Repository": "RSPM", - "Hash": "92a5f887f9ae3035ac7afde22ba73ee9" + "Hash": "38875ea52350ff4b4c03849fc69736c8" }, "brio": { "Package": "brio", - "Version": "1.1.1", + "Version": "1.1.3", "Source": "Repository", "Repository": "RSPM", - "Hash": "36758510e65a457efeefa50e1e7f0576" + "Hash": "976cf154dfb043c012d87cddd8bca363" }, "bslib": { "Package": "bslib", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "grDevices", @@ -172,14 +166,14 @@ }, "cachem": { "Package": "cachem", - "Version": "1.0.4", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "fastmap", "rlang" ], - "Hash": "2703a46dcabfb902f10060b2bca9f708" + "Hash": "648c5b3d71e6a37e3043617489a0a0e9" }, "callr": { "Package": "callr", @@ -207,13 +201,13 @@ }, "clipr": { "Package": "clipr", - "Version": "0.7.1", + "Version": "0.8.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "utils" ], - "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7" + "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" }, "codetools": { "Package": "codetools", @@ -227,10 +221,10 @@ }, "commonmark": { "Package": "commonmark", - "Version": "1.7", + "Version": "1.8.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "0f22be39ec1d141fd03683c06f3a6e67" + "Hash": "2ba81b120c1655ab696c935ef33ea716" }, "covr": { "Package": "covr", @@ -261,7 +255,7 @@ }, "crayon": { "Package": "crayon", - "Version": "1.4.1", + "Version": "1.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -269,11 +263,11 @@ "methods", "utils" ], - "Hash": "e75525c55c70e5f4f78c9960a4b402e9" + "Hash": "741c2e098e98afe3dc26a7b0e5489f4e" }, "credentials": { "Package": "credentials", - "Version": "1.3.0", + "Version": "1.3.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -283,11 +277,11 @@ "openssl", "sys" ], - "Hash": "a96728288c75a814c900af9da84387be" + "Hash": "93762d0a34d78e6a025efdbfb5c6bb41" }, "crosstalk": { "Package": "crosstalk", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -296,17 +290,17 @@ "jsonlite", "lazyeval" ], - "Hash": "2b06f9e415a62b6762e4b8098d2aecbc" + "Hash": "6aa54f69598c32177e920eb3402e8293" }, "curl": { "Package": "curl", - "Version": "4.3", + "Version": "4.3.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "2b7d10581cc730804e9ed178c8374bd6" + "Hash": "022c42d49c28e95d69ca60446dbabf88" }, "cyclocomp": { "Package": "cyclocomp", @@ -338,19 +332,18 @@ }, "devtools": { "Package": "devtools", - "Version": "2.3.2", + "Version": "2.4.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "DT", "R", "callr", "cli", - "covr", "desc", "ellipsis", + "fs", "httr", - "jsonlite", + "lifecycle", "memoise", "pkgbuild", "pkgload", @@ -368,7 +361,7 @@ "utils", "withr" ], - "Hash": "415656f50722f5b6e6bcf80855ce11b9" + "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5" }, "diffdf": { "Package": "diffdf", @@ -383,7 +376,7 @@ }, "diffobj": { "Package": "diffobj", - "Version": "0.3.4", + "Version": "0.3.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -394,24 +387,24 @@ "tools", "utils" ], - "Hash": "feb5b7455eba422a2c110bb89852e6a3" + "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8" }, "digest": { "Package": "digest", - "Version": "0.6.27", + "Version": "0.6.29", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "a0cbe758a531d054b537d16dff4d58a1" + "Hash": "cf6b206a045a684728c3267ef7596190" }, "downlit": { "Package": "downlit", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "brio", @@ -428,31 +421,31 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.5", + "Version": "1.0.8", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "R6", - "ellipsis", "generics", "glue", "lifecycle", "magrittr", "methods", + "pillar", "rlang", "tibble", "tidyselect", "utils", "vctrs" ], - "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68" + "Hash": "ef47665e64228a17609d6df877bf86f2" }, "ellipsis": { "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "rlang" @@ -463,7 +456,7 @@ "Package": "evaluate", "Version": "0.15", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "methods" @@ -472,13 +465,15 @@ }, "fansi": { "Package": "fansi", - "Version": "0.4.2", + "Version": "1.0.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "R" + "R", + "grDevices", + "utils" ], - "Hash": "fea074fb67fe4c25d47ad09087da847d" + "Hash": "f28149c2d7a1342a834b314e95e67260" }, "fastmap": { "Package": "fastmap", @@ -487,31 +482,43 @@ "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "htmltools", + "rlang" + ], + "Hash": "55624ed409e46c5f358b2c060be87f67" + }, "fs": { "Package": "fs", - "Version": "1.5.0", + "Version": "1.5.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "44594a07a42e5f91fac9f93fda6d0109" + "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" }, "generics": { "Package": "generics", - "Version": "0.1.0", + "Version": "0.1.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "4d243a9c10b00589889fe32314ffd902" + "Hash": "177475892cf4a55865868527654a7741" }, "gert": { "Package": "gert", - "Version": "1.3.0", + "Version": "1.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -522,11 +529,11 @@ "sys", "zip" ], - "Hash": "56f398846cd40937be6b435a66bd3f37" + "Hash": "8fddce7cbd59467106266a6e93e253b4" }, "gh": { "Package": "gh", - "Version": "1.2.0", + "Version": "1.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -536,11 +543,11 @@ "ini", "jsonlite" ], - "Hash": "05129b4387282404780d2f8593636388" + "Hash": "38c2580abbda249bd6afeec00d14f531" }, "git2r": { "Package": "git2r", - "Version": "0.28.0", + "Version": "0.29.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -548,7 +555,7 @@ "graphics", "utils" ], - "Hash": "f64fd34026f6025de71a4354800e6d79" + "Hash": "b114135c4749076bd5ef74a5827b6f62" }, "gitcreds": { "Package": "gitcreds", @@ -559,28 +566,29 @@ }, "glue": { "Package": "glue", - "Version": "1.4.2", + "Version": "1.6.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "6efd734b14c6471cfe443345f3e35e29" + "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e" }, "highr": { "Package": "highr", - "Version": "0.8", + "Version": "0.9", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "R" + "R", + "xfun" ], - "Hash": "4dc5bb88961e347a0f4d8aad597cbfac" + "Hash": "8eb36c8125038e648e5d111c0d7b2ed4" }, "hms": { "Package": "hms", - "Version": "1.0.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -591,13 +599,13 @@ "rlang", "vctrs" ], - "Hash": "bf552cdd96f5969873afdac7311c7d0d" + "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca" }, "htmltools": { "Package": "htmltools", "Version": "0.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "base64enc", @@ -611,7 +619,7 @@ }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.5.3", + "Version": "1.5.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -620,15 +628,14 @@ "jsonlite", "yaml" ], - "Hash": "6fdaa86d0700f8b3e92ee3c445a5a10d" + "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb" }, "httpuv": { "Package": "httpuv", - "Version": "1.5.5", + "Version": "1.6.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "BH", "R", "R6", "Rcpp", @@ -636,7 +643,7 @@ "promises", "utils" ], - "Hash": "b9d5d39be2150cf86538b8488334b8f8" + "Hash": "97fe71f0a4a1c9890e6c2128afa04bc0" }, "httr": { "Package": "httr", @@ -674,23 +681,23 @@ }, "jquerylib": { "Package": "jquerylib", - "Version": "0.1.3", + "Version": "0.1.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "htmltools" ], - "Hash": "5ff50b36f7f0832f8421745af333e73c" + "Hash": "5aab57a3bd297eee1c1d862735972182" }, "jsonlite": { "Package": "jsonlite", - "Version": "1.7.2", + "Version": "1.8.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods" ], - "Hash": "98138e0994d41508c7a6b84a0600cfcb" + "Hash": "d07e729b27b372429d42d24d503613a0" }, "knitr": { "Package": "knitr", @@ -711,15 +718,14 @@ }, "later": { "Package": "later", - "Version": "1.1.0.1", + "Version": "1.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "BH", "Rcpp", "rlang" ], - "Hash": "d0a62b247165aabf397fded504660d8a" + "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e" }, "lazyeval": { "Package": "lazyeval", @@ -735,7 +741,7 @@ "Package": "lifecycle", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "glue", @@ -768,44 +774,44 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.7.10", + "Version": "1.8.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "Rcpp", + "cpp11", "generics", "methods" ], - "Hash": "1ebfdc8a3cfe8fe19184f5481972b092" + "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a" }, "magrittr": { "Package": "magrittr", - "Version": "2.0.1", + "Version": "2.0.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "41287f1ac7d28a92f0a286ed507928d3" + "Hash": "cdc87ecd81934679d1557633d8e1fe51" }, "memoise": { "Package": "memoise", - "Version": "2.0.0", + "Version": "2.0.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "cachem", "rlang" ], - "Hash": "a0bc51650201a56d00a4798523cc91b3" + "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" }, "mime": { "Package": "mime", - "Version": "0.10", + "Version": "0.12", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "tools" ], - "Hash": "26fa77e707223e1ce042b2b5d09993dc" + "Hash": "18e9c28c1d3ca1560ce30658b22ce104" }, "miniUI": { "Package": "miniUI", @@ -821,17 +827,17 @@ }, "openssl": { "Package": "openssl", - "Version": "1.4.3", + "Version": "2.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "askpass" ], - "Hash": "a399e4773075fc2375b71f45fca186c4" + "Hash": "cf4329aac12c2c44089974559c18e446" }, "pillar": { "Package": "pillar", - "Version": "1.5.1", + "Version": "1.7.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -839,17 +845,18 @@ "crayon", "ellipsis", "fansi", + "glue", "lifecycle", "rlang", "utf8", "utils", "vctrs" ], - "Hash": "24622aa4a0d3de3463c34513edca99b2" + "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e" }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.2.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -863,7 +870,7 @@ "rprojroot", "withr" ], - "Hash": "725fcc30222d4d11ec68efb8ff11a9af" + "Hash": "66d2adfed274daf81ccfe77d974c3b9b" }, "pkgconfig": { "Package": "pkgconfig", @@ -907,7 +914,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.2.0", + "Version": "1.2.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -915,14 +922,13 @@ "crayon", "desc", "methods", - "pkgbuild", "rlang", "rprojroot", "rstudioapi", "utils", "withr" ], - "Hash": "cb57de933545960a86f03513e4bd2911" + "Hash": "7533cd805940821bf23eaf3c8d4c1735" }, "praise": { "Package": "praise", @@ -991,14 +997,14 @@ }, "ragg": { "Package": "ragg", - "Version": "1.1.2", + "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "3f0ac98597bebdc31b747def3eb9b6ca" + "Hash": "14932bb6f2739c771ca4ceaba6b4248e" }, "rappdirs": { "Package": "rappdirs", @@ -1012,14 +1018,14 @@ }, "rcmdcheck": { "Package": "rcmdcheck", - "Version": "1.3.3", + "Version": "1.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R6", "callr", "cli", - "crayon", + "curl", "desc", "digest", "pkgbuild", @@ -1030,7 +1036,7 @@ "withr", "xopen" ], - "Hash": "ed95895886dab6d2a584da45503555da" + "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, "rematch2": { "Package": "rematch2", @@ -1046,7 +1052,7 @@ "Package": "remotes", "Version": "2.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "methods", @@ -1068,13 +1074,13 @@ }, "rex": { "Package": "rex", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "lazyeval" ], - "Hash": "093584b944440c5cd07a696b3c8e0e4c" + "Hash": "ae34cd56890607370665bee5bd17812f" }, "rlang": { "Package": "rlang", @@ -1112,7 +1118,7 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1123,7 +1129,6 @@ "commonmark", "cpp11", "desc", - "digest", "knitr", "methods", "pkgload", @@ -1135,7 +1140,7 @@ "withr", "xml2" ], - "Hash": "da1f278262e563c835345872f2fef537" + "Hash": "7b153c746193b143c14baa072bae4e27" }, "rprojroot": { "Package": "rprojroot", @@ -1156,7 +1161,7 @@ }, "rversions": { "Package": "rversions", - "Version": "2.0.2", + "Version": "2.1.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1164,13 +1169,13 @@ "utils", "xml2" ], - "Hash": "0ec41191f744d0f5afad8c6f35cc36e4" + "Hash": "f88fab00907b312f8b23ec13e2d437cb" }, "sass": { "Package": "sass", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R6", "fs", @@ -1182,20 +1187,20 @@ }, "sessioninfo": { "Package": "sessioninfo", - "Version": "1.1.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ + "R", "cli", "tools", - "utils", - "withr" + "utils" ], - "Hash": "308013098befe37484df72c39cf90d6e" + "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f" }, "shiny": { "Package": "shiny", - "Version": "1.6.0", + "Version": "1.7.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1205,9 +1210,9 @@ "cachem", "commonmark", "crayon", - "digest", "ellipsis", "fastmap", + "fontawesome", "glue", "grDevices", "htmltools", @@ -1225,7 +1230,7 @@ "withr", "xtable" ], - "Hash": "6e3b6ae7fe02b5859e4bb277f218b8ae" + "Hash": "00344c227c7bd0ab5d78052c5d736c44" }, "sourcetools": { "Package": "sourcetools", @@ -1284,7 +1289,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.5.3", + "Version": "1.7.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1293,7 +1298,7 @@ "tools", "utils" ], - "Hash": "a063ebea753c92910a4cca7b18bc1f05" + "Hash": "bba431031d30789535745a9627ac9271" }, "stringr": { "Package": "stringr", @@ -1336,14 +1341,14 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.1", + "Version": "1.0.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "cpp11" ], - "Hash": "6e899d7c097698d50ec87b1d8e65f246" + "Hash": "90b28393209827327de889f49935140a" }, "testthat": { "Package": "testthat", @@ -1377,7 +1382,7 @@ }, "textshaping": { "Package": "textshaping", - "Version": "0.3.3", + "Version": "0.3.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1385,11 +1390,11 @@ "cpp11", "systemfonts" ], - "Hash": "fff317575e7191e2d077292309bed575" + "Hash": "1ab6223d3670fac7143202cb6a2d43d5" }, "tibble": { "Package": "tibble", - "Version": "3.1.0", + "Version": "3.1.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1405,11 +1410,11 @@ "utils", "vctrs" ], - "Hash": "4d894a114dbd4ecafeda5074e7c538e6" + "Hash": "8a8f02d1934dfd6431c671361510dd0b" }, "tidyr": { "Package": "tidyr", - "Version": "1.1.3", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1427,11 +1432,11 @@ "utils", "vctrs" ], - "Hash": "450d7dfaedde58e28586b854eeece4fa" + "Hash": "d8b95b7fee945d7da6888cf7eb71a49c" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.0", + "Version": "1.1.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1442,21 +1447,21 @@ "rlang", "vctrs" ], - "Hash": "6ea435c354e8448819627cf686f66e0a" + "Hash": "17f6da8cfd7002760a859915ce7eef8f" }, "tinytex": { "Package": "tinytex", - "Version": "0.31", + "Version": "0.37", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - "Hash": "25b572f764f3c19fef9aac33b5724f3d" + "Hash": "a80abeb527a977e4bef21873d29222dd" }, "usethis": { "Package": "usethis", - "Version": "2.0.1", + "Version": "2.1.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1483,17 +1488,17 @@ "withr", "yaml" ], - "Hash": "360e904f9e623286e1a0c6ca0a98c5f6" + "Hash": "c499f488e6dd7718accffaee5bc5a79b" }, "utf8": { "Package": "utf8", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7" + "Hash": "c9c462b759a5cc844ae25b5942654d13" }, "vctrs": { "Package": "vctrs", @@ -1534,16 +1539,16 @@ }, "withr": { "Package": "withr", - "Version": "2.4.3", + "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "grDevices", "graphics", "stats" ], - "Hash": "a376b424c4817cda4920bbbeb3364e85" + "Hash": "c0e49a9760983e81e55cdd9be92e7182" }, "xfun": { "Package": "xfun", @@ -1560,7 +1565,7 @@ "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "methods" @@ -1602,17 +1607,17 @@ }, "yaml": { "Package": "yaml", - "Version": "2.2.1", + "Version": "2.3.5", "Source": "Repository", "Repository": "RSPM", - "Hash": "2826c5d9efb0a88f657c7a679c7106db" + "Hash": "458bb38374d73bf83b1bb85e353da200" }, "zip": { "Package": "zip", - "Version": "2.1.1", + "Version": "2.2.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "3bc8405c637d988801ec5ea88372d0c2" + "Hash": "c7eef2996ac270a18c2715c997a727c5" } } } diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 94499def..03dbcf3c 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -8,7 +8,7 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2022-03-10" + "URL": "https://packagemanager.rstudio.com/cran/2022-03-10" } ] }, @@ -1118,7 +1118,7 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1129,7 +1129,6 @@ "commonmark", "cpp11", "desc", - "digest", "knitr", "methods", "pkgload", @@ -1141,7 +1140,7 @@ "withr", "xml2" ], - "Hash": "da1f278262e563c835345872f2fef537" + "Hash": "7b153c746193b143c14baa072bae4e27" }, "rprojroot": { "Package": "rprojroot", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 7a05bbc5..dada8221 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -8,14 +8,14 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2022-10-31" + "URL": "https://packagemanager.rstudio.com/cran/2023-03-15" } ] }, "Packages": { "DT": { "Package": "DT", - "Version": "0.26", + "Version": "0.27", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -27,7 +27,7 @@ "magrittr", "promises" ], - "Hash": "c66a72c4d3499e14ae179ccb742e740a" + "Hash": "3444e6ed78763f9f13aaa39f2481eb34" }, "R.cache": { "Package": "R.cache", @@ -70,7 +70,7 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.12.1", + "Version": "2.12.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -81,7 +81,7 @@ "tools", "utils" ], - "Hash": "1ed133420fcd2b93cf55a383b38fe27c" + "Hash": "325f01db13da12c04d8f6e7be36ff514" }, "R6": { "Package": "R6", @@ -95,14 +95,14 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.9", + "Version": "1.0.10", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods", "utils" ], - "Hash": "e9c08b94391e9f3f97355841229124f2" + "Hash": "e749cae40fa9ef469b6050959517453c" }, "askpass": { "Package": "askpass", @@ -150,38 +150,40 @@ }, "bslib": { "Package": "bslib", - "Version": "0.4.0", + "Version": "0.4.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", + "base64enc", "cachem", "grDevices", "htmltools", "jquerylib", "jsonlite", "memoise", + "mime", "rlang", "sass" ], - "Hash": "be5ee090716ce1671be6cd5d7c34d091" + "Hash": "a7fbf03946ad741129dc81098722fca1" }, "cachem": { "Package": "cachem", - "Version": "1.0.6", + "Version": "1.0.7", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "fastmap", "rlang" ], - "Hash": "648c5b3d71e6a37e3043617489a0a0e9" + "Hash": "cda74447c42f529de601fe4d4050daef" }, "callr": { "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -192,14 +194,14 @@ }, "cli": { "Package": "cli", - "Version": "3.4.1", + "Version": "3.6.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "0d297d01734d2bcea40197bd4971a764" + "Hash": "3177a5a16c243adc199ba33117bd9657" }, "clipr": { "Package": "clipr", @@ -296,13 +298,13 @@ }, "curl": { "Package": "curl", - "Version": "4.3.3", + "Version": "5.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "0eb86baa62f06e8855258fa5a8048667" + "Hash": "e4f97056611e8e6b8b852d13b7400cf1" }, "cyclocomp": { "Package": "cyclocomp", @@ -394,14 +396,14 @@ }, "digest": { "Package": "digest", - "Version": "0.6.30", + "Version": "0.6.31", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "bf1cd206a5d170d132ef75c7537b9bdb" + "Hash": "8b708f296afd9ae69f450f9640be8990" }, "downlit": { "Package": "downlit", @@ -425,12 +427,13 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.10", + "Version": "1.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "R6", + "cli", "generics", "glue", "lifecycle", @@ -443,7 +446,7 @@ "utils", "vctrs" ], - "Hash": "539412282059f7f0c07295723d23f987" + "Hash": "d3c34618017e7ae252d46d79a1b9ec32" }, "ellipsis": { "Package": "ellipsis", @@ -458,18 +461,18 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.17", + "Version": "0.20", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "9171b012a55a1ef53f1442b1d798a3b4" + "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c" }, "fansi": { "Package": "fansi", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -477,18 +480,18 @@ "grDevices", "utils" ], - "Hash": "83a8afdbe71839506baa9f90eebad7ec" + "Hash": "1d9e7ad3c8312a192dea7d3db0274fde" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" + "Hash": "f7736a18de97dea803bde0a2daaafb27" }, "fontawesome": { "Package": "fontawesome", - "Version": "0.4.0", + "Version": "0.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -496,18 +499,18 @@ "htmltools", "rlang" ], - "Hash": "c5a628c2570aa86a96cc6ef739d8bfda" + "Hash": "e80750aec5717dedc019ad7ee40e4a7c" }, "fs": { "Package": "fs", - "Version": "1.5.2", + "Version": "1.6.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" + "Hash": "f4dcd23b67e33d851d2079f703e8b985" }, "generics": { "Package": "generics", @@ -522,7 +525,7 @@ }, "gert": { "Package": "gert", - "Version": "1.9.1", + "Version": "1.9.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -533,26 +536,27 @@ "sys", "zip" ], - "Hash": "9a091a6d2fb91e43afd4337e2dcef2e7" + "Hash": "9122b3958e749badb5c939f498038b57" }, "gh": { "Package": "gh", - "Version": "1.3.1", + "Version": "1.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "cli", "gitcreds", - "httr", + "httr2", "ini", - "jsonlite" + "jsonlite", + "rlang" ], - "Hash": "b6a12054ee13dce0f6696c019c10e539" + "Hash": "03533b1c875028233598f848fda44c4c" }, "git2r": { "Package": "git2r", - "Version": "0.30.1", + "Version": "0.31.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -560,7 +564,7 @@ "graphics", "utils" ], - "Hash": "e0c6a04a3e7b90e64213d09128f74f1b" + "Hash": "acb972e0be37f83b9c762d962d75a188" }, "gitcreds": { "Package": "gitcreds", @@ -585,14 +589,14 @@ }, "highr": { "Package": "highr", - "Version": "0.9", + "Version": "0.10", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "xfun" ], - "Hash": "8eb36c8125038e648e5d111c0d7b2ed4" + "Hash": "06230136b2d2b9ba5805e1963fa6e890" }, "hms": { "Package": "hms", @@ -611,36 +615,39 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.3", + "Version": "0.5.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "base64enc", "digest", + "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "6496090a9e00f8354b811d1a2d47b566" + "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7" }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.5.4", + "Version": "1.6.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "grDevices", "htmltools", "jsonlite", + "knitr", + "rmarkdown", "yaml" ], - "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb" + "Hash": "b677ee5954471eaa974c0d099a343a1a" }, "httpuv": { "Package": "httpuv", - "Version": "1.6.6", + "Version": "1.6.9", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -651,11 +658,11 @@ "promises", "utils" ], - "Hash": "fd090e236ae2dc0f0cdf33a9ec83afb6" + "Hash": "1046aa31a57eae8b357267a56a0b6d8b" }, "httr": { "Package": "httr", - "Version": "1.4.4", + "Version": "1.4.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -666,7 +673,26 @@ "mime", "openssl" ], - "Hash": "57557fac46471f0dbbf44705cc6a5c8c" + "Hash": "f6844033201269bec3ca0097bc6c97b3" + }, + "httr2": { + "Package": "httr2", + "Version": "0.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "cli", + "curl", + "glue", + "magrittr", + "openssl", + "rappdirs", + "rlang", + "withr" + ], + "Hash": "5c09fe33064978ede54de42309c8b532" }, "hunspell": { "Package": "hunspell", @@ -699,17 +725,17 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods" ], - "Hash": "8b1bd0be62956f2a6b91ce84fac79a45" + "Hash": "a4269a09a9b865579b2635c77e572374" }, "knitr": { "Package": "knitr", - "Version": "1.40", + "Version": "1.42", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -717,12 +743,11 @@ "evaluate", "highr", "methods", - "stringr", "tools", "xfun", "yaml" ], - "Hash": "caea8b0f899a0b1738444b9bc47067e7" + "Hash": "8329a9bcc82943c8069104d4be3ee22d" }, "later": { "Package": "later", @@ -783,16 +808,16 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.8.0", + "Version": "1.9.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "cpp11", "generics", - "methods" + "methods", + "timechange" ], - "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a" + "Hash": "e25f18436e3efd42c7c590a1c4c15390" }, "magrittr": { "Package": "magrittr", @@ -839,13 +864,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.4", + "Version": "2.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "askpass" ], - "Hash": "e86c5ffeb8474a9e03d75f5d2919683e" + "Hash": "0f7cd2962e3044bb940cca4f4b5cecbe" }, "pillar": { "Package": "pillar", @@ -866,7 +891,7 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.3.1", + "Version": "1.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -877,10 +902,11 @@ "crayon", "desc", "prettyunits", + "processx", "rprojroot", "withr" ], - "Hash": "66d2adfed274daf81ccfe77d974c3b9b" + "Hash": "d6c3008d79653a0f267703288230105e" }, "pkgconfig": { "Package": "pkgconfig", @@ -896,7 +922,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "bslib", @@ -924,7 +950,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.1", + "Version": "1.3.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -940,7 +966,7 @@ "utils", "withr" ], - "Hash": "3c0918b1792c75de2e640d1d8d12dead" + "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2" }, "praise": { "Package": "praise", @@ -1009,26 +1035,29 @@ }, "purrr": { "Package": "purrr", - "Version": 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"Version": "2.3.7", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "0d0056cc5383fbc240ccd0cb584bf436" + }, + "zip": { + "Package": "zip", + "Version": "2.3.0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "d98c94dacb7e0efcf83b0a133a705504" + } + } +} diff --git a/renv/profiles/4.3/renv/.gitignore b/renv/profiles/4.3/renv/.gitignore new file mode 100644 index 00000000..0ec0cbba --- /dev/null +++ b/renv/profiles/4.3/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/profiles/4.3/renv/settings.dcf b/renv/profiles/4.3/renv/settings.dcf new file mode 100644 index 00000000..fd205f80 --- /dev/null +++ b/renv/profiles/4.3/renv/settings.dcf @@ -0,0 +1,10 @@ +bioconductor.version: +external.libraries: +ignored.packages: admiral, admiraldev, admiral.test, admiralci +package.dependency.fields: Imports, Depends, LinkingTo +r.version: +snapshot.type: implicit +use.cache: TRUE +vcs.ignore.cellar: TRUE +vcs.ignore.library: TRUE +vcs.ignore.local: TRUE From 5238d352bd695ad99c3d98a657913d62f08d8cda Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Wed, 17 May 2023 07:56:47 +0000 Subject: [PATCH 076/100] renv update from pharmaverse/admiralci --- .github/workflows/common.yml | 16 +- renv.lock | 311 +++-- renv/profiles/4.0/renv.lock | 2 +- renv/profiles/4.1/renv.lock | 9 +- renv/profiles/4.2/renv.lock | 258 ++-- renv/profiles/4.3/renv.lock | 1707 --------------------------- renv/profiles/4.3/renv/.gitignore | 7 - renv/profiles/4.3/renv/settings.dcf | 10 - 8 files changed, 274 insertions(+), 2046 deletions(-) delete mode 100644 renv/profiles/4.3/renv.lock delete mode 100644 renv/profiles/4.3/renv/.gitignore delete mode 100644 renv/profiles/4.3/renv/settings.dcf diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index 59e069bd..518c64af 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -45,25 +45,25 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/style.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.1" + r-version: "4.0" spellcheck: name: Spelling uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.1" + r-version: "4.0" readme: name: Render README uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main if: github.event_name == 'push' with: - r-version: "4.1" + r-version: "4.0" validation: name: Validation uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main if: github.event_name == 'release' with: - r-version: "4.1" + r-version: "4.0" check: name: Check uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main @@ -73,7 +73,7 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main if: github.event_name == 'push' with: - r-version: "4.1" + r-version: "4.0" # Whether to skip multiversion docs # Note that if you have multiple versions of docs, # your URL links are likely to break due to path changes @@ -85,7 +85,7 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.1" + r-version: "4.0" links: name: Links uses: pharmaverse/admiralci/.github/workflows/links.yml@main @@ -97,7 +97,7 @@ jobs: if: > github.event_name == 'push' || github.event_name == 'pull_request' with: - r-version: "4.1" + r-version: "4.0" # Whether to skip code coverage badge creation # Setting to 'false' will require you to create # an orphan branch called 'badges' in your repository @@ -107,4 +107,4 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.1" + r-version: "4.0" diff --git a/renv.lock b/renv.lock index 03dbcf3c..932de771 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.1.3", + "Version": "4.0.5", "Repositories": [ { "Name": "CRAN", @@ -8,32 +8,38 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.rstudio.com/cran/2022-03-10" + "URL": "https://packagemanager.posit.co/cran/2021-03-31" } ] }, "Packages": { + "BH": { + "Package": "BH", + "Version": "1.75.0-0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "e4c04affc2cac20c8fec18385cd14691" + }, "DT": { "Package": "DT", - "Version": "0.21", + "Version": "0.17", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "crosstalk", "htmltools", "htmlwidgets", - "jquerylib", "jsonlite", "magrittr", "promises" ], - "Hash": "45fa28dbf288cd606e13ca35d3d72437" + "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0" }, "R.cache": { "Package": "R.cache", "Version": "0.15.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R.methodsS3", @@ -70,7 +76,7 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.11.0", + "Version": "2.10.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -81,28 +87,28 @@ "tools", "utils" ], - "Hash": "a7ecb8e60815c7a18648e84cd121b23a" + "Hash": "a9e316277ff12a43997266f2f6567780" }, "R6": { "Package": "R6", - "Version": "2.5.1", + "Version": "2.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "470851b6d5d0ac559e9d01bb352b4021" + "Hash": "b203113193e70978a696b2809525649d" }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.8", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods", "utils" ], - "Hash": "22b546dd7e337f6c0c58a39983a496bc" + "Hash": "dbb5e436998a7eba5a9d682060533338" }, "askpass": { "Package": "askpass", @@ -116,13 +122,13 @@ }, "backports": { "Package": "backports", - "Version": "1.4.1", + "Version": "1.2.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "c39fbec8a30d23e721980b8afb31984c" + "Hash": "644043219fc24e190c2f620c1a380a69" }, "base64enc": { "Package": "base64enc", @@ -136,23 +142,23 @@ }, "brew": { "Package": "brew", - "Version": "1.0-7", + "Version": "1.0-6", "Source": "Repository", "Repository": "RSPM", - "Hash": "38875ea52350ff4b4c03849fc69736c8" + "Hash": "92a5f887f9ae3035ac7afde22ba73ee9" }, "brio": { "Package": "brio", - "Version": "1.1.3", + "Version": "1.1.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "976cf154dfb043c012d87cddd8bca363" + "Hash": "36758510e65a457efeefa50e1e7f0576" }, "bslib": { "Package": "bslib", "Version": "0.3.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", @@ -166,14 +172,14 @@ }, "cachem": { "Package": "cachem", - "Version": "1.0.6", + "Version": "1.0.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "fastmap", "rlang" ], - "Hash": "648c5b3d71e6a37e3043617489a0a0e9" + "Hash": "2703a46dcabfb902f10060b2bca9f708" }, "callr": { "Package": "callr", @@ -201,13 +207,13 @@ }, "clipr": { "Package": "clipr", - "Version": "0.8.0", + "Version": "0.7.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "utils" ], - "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" + "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7" }, "codetools": { "Package": "codetools", @@ -221,10 +227,10 @@ }, "commonmark": { "Package": "commonmark", - "Version": "1.8.0", + "Version": "1.7", "Source": "Repository", "Repository": "RSPM", - "Hash": "2ba81b120c1655ab696c935ef33ea716" + "Hash": "0f22be39ec1d141fd03683c06f3a6e67" }, "covr": { "Package": "covr", @@ -255,7 +261,7 @@ }, "crayon": { "Package": "crayon", - "Version": "1.5.0", + "Version": "1.4.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -263,11 +269,11 @@ "methods", "utils" ], - "Hash": "741c2e098e98afe3dc26a7b0e5489f4e" + "Hash": "e75525c55c70e5f4f78c9960a4b402e9" }, "credentials": { "Package": "credentials", - "Version": "1.3.2", + "Version": "1.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -277,11 +283,11 @@ "openssl", "sys" ], - "Hash": "93762d0a34d78e6a025efdbfb5c6bb41" + "Hash": "a96728288c75a814c900af9da84387be" }, "crosstalk": { "Package": "crosstalk", - "Version": "1.2.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -290,17 +296,17 @@ "jsonlite", "lazyeval" ], - "Hash": "6aa54f69598c32177e920eb3402e8293" + "Hash": "2b06f9e415a62b6762e4b8098d2aecbc" }, "curl": { "Package": "curl", - "Version": "4.3.2", + "Version": "4.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "022c42d49c28e95d69ca60446dbabf88" + "Hash": "2b7d10581cc730804e9ed178c8374bd6" }, "cyclocomp": { "Package": "cyclocomp", @@ -332,18 +338,19 @@ }, "devtools": { "Package": "devtools", - "Version": "2.4.3", + "Version": "2.3.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ + "DT", "R", "callr", "cli", + "covr", "desc", "ellipsis", - "fs", "httr", - "lifecycle", + "jsonlite", "memoise", "pkgbuild", "pkgload", @@ -361,7 +368,7 @@ "utils", "withr" ], - "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5" + "Hash": "415656f50722f5b6e6bcf80855ce11b9" }, "diffdf": { "Package": "diffdf", @@ -376,7 +383,7 @@ }, "diffobj": { "Package": "diffobj", - "Version": "0.3.5", + "Version": "0.3.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -387,24 +394,24 @@ "tools", "utils" ], - "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8" + "Hash": "feb5b7455eba422a2c110bb89852e6a3" }, "digest": { "Package": "digest", - "Version": "0.6.29", + "Version": "0.6.27", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "cf6b206a045a684728c3267ef7596190" + "Hash": "a0cbe758a531d054b537d16dff4d58a1" }, "downlit": { "Package": "downlit", "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "brio", @@ -421,31 +428,31 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.8", + "Version": "1.0.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "R6", + "ellipsis", "generics", "glue", "lifecycle", "magrittr", "methods", - "pillar", "rlang", "tibble", "tidyselect", "utils", "vctrs" ], - "Hash": "ef47665e64228a17609d6df877bf86f2" + "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68" }, "ellipsis": { "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "rlang" @@ -456,7 +463,7 @@ "Package": "evaluate", "Version": "0.15", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods" @@ -465,15 +472,13 @@ }, "fansi": { "Package": "fansi", - "Version": "1.0.2", + "Version": "0.4.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "R", - "grDevices", - "utils" + "R" ], - "Hash": "f28149c2d7a1342a834b314e95e67260" + "Hash": "fea074fb67fe4c25d47ad09087da847d" }, "fastmap": { "Package": "fastmap", @@ -482,43 +487,31 @@ "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" }, - "fontawesome": { - "Package": "fontawesome", - "Version": "0.2.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "htmltools", - "rlang" - ], - "Hash": "55624ed409e46c5f358b2c060be87f67" - }, "fs": { "Package": "fs", - "Version": "1.5.2", + "Version": "1.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" + "Hash": "44594a07a42e5f91fac9f93fda6d0109" }, "generics": { "Package": "generics", - "Version": "0.1.2", + "Version": "0.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "177475892cf4a55865868527654a7741" + "Hash": "4d243a9c10b00589889fe32314ffd902" }, "gert": { "Package": "gert", - "Version": "1.5.0", + "Version": "1.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -529,11 +522,11 @@ "sys", "zip" ], - "Hash": "8fddce7cbd59467106266a6e93e253b4" + "Hash": "56f398846cd40937be6b435a66bd3f37" }, "gh": { "Package": "gh", - "Version": "1.3.0", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -543,11 +536,11 @@ "ini", "jsonlite" ], - "Hash": "38c2580abbda249bd6afeec00d14f531" + "Hash": "05129b4387282404780d2f8593636388" }, "git2r": { "Package": "git2r", - "Version": "0.29.0", + "Version": "0.28.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -555,7 +548,7 @@ "graphics", "utils" ], - "Hash": "b114135c4749076bd5ef74a5827b6f62" + "Hash": "f64fd34026f6025de71a4354800e6d79" }, "gitcreds": { "Package": "gitcreds", @@ -566,29 +559,28 @@ }, "glue": { "Package": "glue", - "Version": "1.6.2", + "Version": "1.4.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e" + "Hash": "6efd734b14c6471cfe443345f3e35e29" }, "highr": { "Package": "highr", - "Version": "0.9", + "Version": "0.8", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "R", - "xfun" + "R" ], - "Hash": "8eb36c8125038e648e5d111c0d7b2ed4" + "Hash": "4dc5bb88961e347a0f4d8aad597cbfac" }, "hms": { "Package": "hms", - "Version": "1.1.1", + "Version": "1.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -599,13 +591,13 @@ "rlang", "vctrs" ], - "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca" + "Hash": "bf552cdd96f5969873afdac7311c7d0d" }, "htmltools": { "Package": "htmltools", "Version": "0.5.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "base64enc", @@ -619,7 +611,7 @@ }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.5.4", + "Version": "1.5.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -628,14 +620,15 @@ "jsonlite", "yaml" ], - "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb" + "Hash": "6fdaa86d0700f8b3e92ee3c445a5a10d" }, "httpuv": { "Package": "httpuv", - "Version": "1.6.5", + "Version": "1.5.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ + "BH", "R", "R6", "Rcpp", @@ -643,7 +636,7 @@ "promises", "utils" ], - "Hash": "97fe71f0a4a1c9890e6c2128afa04bc0" + "Hash": "b9d5d39be2150cf86538b8488334b8f8" }, "httr": { "Package": "httr", @@ -681,23 +674,23 @@ }, "jquerylib": { "Package": "jquerylib", - "Version": "0.1.4", + "Version": "0.1.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "htmltools" ], - "Hash": "5aab57a3bd297eee1c1d862735972182" + "Hash": "5ff50b36f7f0832f8421745af333e73c" }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.0", + "Version": "1.7.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods" ], - "Hash": "d07e729b27b372429d42d24d503613a0" + "Hash": "98138e0994d41508c7a6b84a0600cfcb" }, "knitr": { "Package": "knitr", @@ -718,14 +711,15 @@ }, "later": { "Package": "later", - "Version": "1.3.0", + "Version": "1.1.0.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ + "BH", "Rcpp", "rlang" ], - "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e" + "Hash": "d0a62b247165aabf397fded504660d8a" }, "lazyeval": { "Package": "lazyeval", @@ -741,7 +735,7 @@ "Package": "lifecycle", "Version": "1.0.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "glue", @@ -774,44 +768,44 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.8.0", + "Version": "1.7.10", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "cpp11", + "Rcpp", "generics", "methods" ], - "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a" + "Hash": "1ebfdc8a3cfe8fe19184f5481972b092" }, "magrittr": { "Package": "magrittr", - "Version": "2.0.2", + "Version": "2.0.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "cdc87ecd81934679d1557633d8e1fe51" + "Hash": "41287f1ac7d28a92f0a286ed507928d3" }, "memoise": { "Package": "memoise", - "Version": "2.0.1", + "Version": "2.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "cachem", "rlang" ], - "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" + "Hash": "a0bc51650201a56d00a4798523cc91b3" }, "mime": { "Package": "mime", - "Version": "0.12", + "Version": "0.10", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "tools" ], - "Hash": "18e9c28c1d3ca1560ce30658b22ce104" + "Hash": "26fa77e707223e1ce042b2b5d09993dc" }, "miniUI": { "Package": "miniUI", @@ -827,17 +821,17 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.0", + "Version": "1.4.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "askpass" ], - "Hash": "cf4329aac12c2c44089974559c18e446" + "Hash": "a399e4773075fc2375b71f45fca186c4" }, "pillar": { "Package": "pillar", - "Version": "1.7.0", + "Version": "1.5.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -845,18 +839,17 @@ "crayon", "ellipsis", "fansi", - "glue", "lifecycle", "rlang", "utf8", "utils", "vctrs" ], - "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e" + "Hash": "24622aa4a0d3de3463c34513edca99b2" }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.3.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -870,7 +863,7 @@ "rprojroot", "withr" ], - "Hash": "66d2adfed274daf81ccfe77d974c3b9b" + "Hash": "725fcc30222d4d11ec68efb8ff11a9af" }, "pkgconfig": { "Package": "pkgconfig", @@ -914,7 +907,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.2.4", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -922,13 +915,14 @@ "crayon", "desc", "methods", + "pkgbuild", "rlang", "rprojroot", "rstudioapi", "utils", "withr" ], - "Hash": "7533cd805940821bf23eaf3c8d4c1735" + "Hash": "cb57de933545960a86f03513e4bd2911" }, "praise": { "Package": "praise", @@ -997,14 +991,14 @@ }, "ragg": { "Package": "ragg", - "Version": "1.2.2", + "Version": "1.1.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "14932bb6f2739c771ca4ceaba6b4248e" + "Hash": "3f0ac98597bebdc31b747def3eb9b6ca" }, "rappdirs": { "Package": "rappdirs", @@ -1018,14 +1012,14 @@ }, "rcmdcheck": { "Package": "rcmdcheck", - "Version": "1.4.0", + "Version": "1.3.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R6", "callr", "cli", - "curl", + "crayon", "desc", "digest", "pkgbuild", @@ -1036,7 +1030,7 @@ "withr", "xopen" ], - "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" + "Hash": "ed95895886dab6d2a584da45503555da" }, "rematch2": { "Package": "rematch2", @@ -1052,7 +1046,7 @@ "Package": "remotes", "Version": "2.4.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods", @@ -1074,13 +1068,13 @@ }, "rex": { "Package": "rex", - "Version": "1.2.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "lazyeval" ], - "Hash": "ae34cd56890607370665bee5bd17812f" + "Hash": "093584b944440c5cd07a696b3c8e0e4c" }, "rlang": { "Package": "rlang", @@ -1118,7 +1112,7 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.3", + "Version": "7.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1129,6 +1123,7 @@ "commonmark", "cpp11", "desc", + "digest", "knitr", "methods", "pkgload", @@ -1140,7 +1135,7 @@ "withr", "xml2" ], - "Hash": "7b153c746193b143c14baa072bae4e27" + "Hash": "da1f278262e563c835345872f2fef537" }, "rprojroot": { "Package": "rprojroot", @@ -1161,7 +1156,7 @@ }, "rversions": { "Package": "rversions", - "Version": "2.1.1", + "Version": "2.0.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1169,13 +1164,13 @@ "utils", "xml2" ], - "Hash": "f88fab00907b312f8b23ec13e2d437cb" + "Hash": "0ec41191f744d0f5afad8c6f35cc36e4" }, "sass": { "Package": "sass", "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R6", "fs", @@ -1187,20 +1182,20 @@ }, "sessioninfo": { "Package": "sessioninfo", - "Version": "1.2.2", + "Version": "1.1.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "R", "cli", "tools", - "utils" + "utils", + "withr" ], - "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f" + "Hash": "308013098befe37484df72c39cf90d6e" }, "shiny": { "Package": "shiny", - "Version": "1.7.1", + "Version": "1.6.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1210,9 +1205,9 @@ "cachem", "commonmark", "crayon", + "digest", "ellipsis", "fastmap", - "fontawesome", "glue", "grDevices", "htmltools", @@ -1230,7 +1225,7 @@ "withr", "xtable" ], - "Hash": "00344c227c7bd0ab5d78052c5d736c44" + "Hash": "6e3b6ae7fe02b5859e4bb277f218b8ae" }, "sourcetools": { "Package": "sourcetools", @@ -1289,7 +1284,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.6", + "Version": "1.5.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1298,7 +1293,7 @@ "tools", "utils" ], - "Hash": "bba431031d30789535745a9627ac9271" + "Hash": "a063ebea753c92910a4cca7b18bc1f05" }, "stringr": { "Package": "stringr", @@ -1341,14 +1336,14 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.4", + "Version": "1.0.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "cpp11" ], - "Hash": "90b28393209827327de889f49935140a" + "Hash": "6e899d7c097698d50ec87b1d8e65f246" }, "testthat": { "Package": "testthat", @@ -1382,7 +1377,7 @@ }, "textshaping": { "Package": "textshaping", - "Version": "0.3.6", + "Version": "0.3.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1390,11 +1385,11 @@ "cpp11", "systemfonts" ], - "Hash": "1ab6223d3670fac7143202cb6a2d43d5" + "Hash": "fff317575e7191e2d077292309bed575" }, "tibble": { "Package": "tibble", - "Version": "3.1.6", + "Version": "3.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1410,11 +1405,11 @@ "utils", "vctrs" ], - "Hash": "8a8f02d1934dfd6431c671361510dd0b" + "Hash": "4d894a114dbd4ecafeda5074e7c538e6" }, "tidyr": { "Package": "tidyr", - "Version": "1.2.0", + "Version": "1.1.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1432,11 +1427,11 @@ "utils", "vctrs" ], - "Hash": "d8b95b7fee945d7da6888cf7eb71a49c" + "Hash": "450d7dfaedde58e28586b854eeece4fa" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.2", + "Version": "1.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1447,21 +1442,21 @@ "rlang", "vctrs" ], - "Hash": "17f6da8cfd7002760a859915ce7eef8f" + "Hash": "6ea435c354e8448819627cf686f66e0a" }, "tinytex": { "Package": "tinytex", - "Version": "0.37", + "Version": "0.31", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - "Hash": "a80abeb527a977e4bef21873d29222dd" + "Hash": "25b572f764f3c19fef9aac33b5724f3d" }, "usethis": { "Package": "usethis", - "Version": "2.1.5", + "Version": "2.0.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1488,17 +1483,17 @@ "withr", "yaml" ], - "Hash": "c499f488e6dd7718accffaee5bc5a79b" + "Hash": "360e904f9e623286e1a0c6ca0a98c5f6" }, "utf8": { "Package": "utf8", - "Version": "1.2.2", + "Version": "1.2.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "c9c462b759a5cc844ae25b5942654d13" + "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7" }, "vctrs": { "Package": "vctrs", @@ -1539,16 +1534,16 @@ }, "withr": { "Package": "withr", - "Version": "2.5.0", + "Version": "2.4.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", "graphics", "stats" ], - "Hash": "c0e49a9760983e81e55cdd9be92e7182" + "Hash": "a376b424c4817cda4920bbbeb3364e85" }, "xfun": { "Package": "xfun", @@ -1565,7 +1560,7 @@ "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods" @@ -1607,17 +1602,17 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.5", + "Version": "2.2.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "458bb38374d73bf83b1bb85e353da200" + "Hash": "2826c5d9efb0a88f657c7a679c7106db" }, "zip": { "Package": "zip", - "Version": "2.2.0", + "Version": "2.1.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "c7eef2996ac270a18c2715c997a727c5" + "Hash": "3bc8405c637d988801ec5ea88372d0c2" } } } diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index 932de771..3414f902 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -13,7 +13,7 @@ ] }, "Packages": { - "BH": { + "BH": { "Package": "BH", "Version": "1.75.0-0", "Source": "Repository", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 03dbcf3c..a1b20e23 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -8,7 +8,7 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.rstudio.com/cran/2022-03-10" + "URL": "https://packagemanager.posit.co/cran/2022-03-10" } ] }, @@ -16,7 +16,7 @@ "DT": { "Package": "DT", "Version": "0.21", - "Source": "Repository", + "Source": "Repository", "Repository": "RSPM", "Requirements": [ "crosstalk", @@ -1118,7 +1118,7 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.3", + "Version": "7.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1129,6 +1129,7 @@ "commonmark", "cpp11", "desc", + "digest", "knitr", "methods", "pkgload", @@ -1140,7 +1141,7 @@ "withr", "xml2" ], - "Hash": "7b153c746193b143c14baa072bae4e27" + "Hash": "da1f278262e563c835345872f2fef537" }, "rprojroot": { "Package": "rprojroot", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index dada8221..7a05bbc5 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -8,14 +8,14 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.rstudio.com/cran/2023-03-15" + "URL": "https://packagemanager.posit.co/cran/2022-10-31" } ] }, "Packages": { "DT": { "Package": "DT", - "Version": "0.27", + "Version": "0.26", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -27,7 +27,7 @@ "magrittr", "promises" ], - "Hash": "3444e6ed78763f9f13aaa39f2481eb34" + "Hash": "c66a72c4d3499e14ae179ccb742e740a" }, "R.cache": { "Package": "R.cache", @@ -70,7 +70,7 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.12.2", + "Version": "2.12.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -81,7 +81,7 @@ "tools", "utils" ], - "Hash": "325f01db13da12c04d8f6e7be36ff514" + "Hash": "1ed133420fcd2b93cf55a383b38fe27c" }, "R6": { "Package": "R6", @@ -95,14 +95,14 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.10", + "Version": "1.0.9", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods", "utils" ], - "Hash": "e749cae40fa9ef469b6050959517453c" + "Hash": "e9c08b94391e9f3f97355841229124f2" }, "askpass": { "Package": "askpass", @@ -150,40 +150,38 @@ }, "bslib": { "Package": "bslib", - "Version": "0.4.2", + "Version": "0.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "base64enc", "cachem", "grDevices", "htmltools", "jquerylib", "jsonlite", "memoise", - "mime", "rlang", "sass" ], - "Hash": "a7fbf03946ad741129dc81098722fca1" + "Hash": "be5ee090716ce1671be6cd5d7c34d091" }, "cachem": { "Package": "cachem", - "Version": "1.0.7", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "fastmap", "rlang" ], - "Hash": "cda74447c42f529de601fe4d4050daef" + "Hash": "648c5b3d71e6a37e3043617489a0a0e9" }, "callr": { "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -194,14 +192,14 @@ }, "cli": { "Package": "cli", - "Version": "3.6.0", + "Version": "3.4.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "3177a5a16c243adc199ba33117bd9657" + "Hash": "0d297d01734d2bcea40197bd4971a764" }, "clipr": { "Package": "clipr", @@ -298,13 +296,13 @@ }, "curl": { "Package": "curl", - "Version": "5.0.0", + "Version": "4.3.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "e4f97056611e8e6b8b852d13b7400cf1" + "Hash": "0eb86baa62f06e8855258fa5a8048667" }, "cyclocomp": { "Package": "cyclocomp", @@ -396,14 +394,14 @@ }, "digest": { "Package": "digest", - "Version": "0.6.31", + "Version": "0.6.30", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "8b708f296afd9ae69f450f9640be8990" + "Hash": "bf1cd206a5d170d132ef75c7537b9bdb" }, "downlit": { "Package": "downlit", @@ -427,13 +425,12 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.1.0", + "Version": "1.0.10", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "R6", - "cli", "generics", "glue", "lifecycle", @@ -446,7 +443,7 @@ "utils", "vctrs" ], - "Hash": "d3c34618017e7ae252d46d79a1b9ec32" + "Hash": "539412282059f7f0c07295723d23f987" }, "ellipsis": { "Package": "ellipsis", @@ -461,18 +458,18 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.20", + "Version": "0.17", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c" + "Hash": "9171b012a55a1ef53f1442b1d798a3b4" }, "fansi": { "Package": "fansi", - "Version": "1.0.4", + "Version": "1.0.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -480,18 +477,18 @@ "grDevices", "utils" ], - "Hash": "1d9e7ad3c8312a192dea7d3db0274fde" + "Hash": "83a8afdbe71839506baa9f90eebad7ec" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.1.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" }, "fontawesome": { "Package": "fontawesome", - "Version": "0.5.0", + "Version": "0.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -499,18 +496,18 @@ "htmltools", "rlang" ], - "Hash": "e80750aec5717dedc019ad7ee40e4a7c" + "Hash": "c5a628c2570aa86a96cc6ef739d8bfda" }, "fs": { "Package": "fs", - "Version": "1.6.1", + "Version": "1.5.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "f4dcd23b67e33d851d2079f703e8b985" + "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" }, "generics": { "Package": "generics", @@ -525,7 +522,7 @@ }, "gert": { "Package": "gert", - "Version": "1.9.2", + "Version": "1.9.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -536,27 +533,26 @@ "sys", "zip" ], - "Hash": "9122b3958e749badb5c939f498038b57" + "Hash": "9a091a6d2fb91e43afd4337e2dcef2e7" }, "gh": { "Package": "gh", - "Version": "1.4.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "cli", "gitcreds", - "httr2", + "httr", "ini", - "jsonlite", - "rlang" + "jsonlite" ], - "Hash": "03533b1c875028233598f848fda44c4c" + "Hash": "b6a12054ee13dce0f6696c019c10e539" }, "git2r": { "Package": "git2r", - "Version": "0.31.0", + "Version": "0.30.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -564,7 +560,7 @@ "graphics", "utils" ], - "Hash": "acb972e0be37f83b9c762d962d75a188" + "Hash": "e0c6a04a3e7b90e64213d09128f74f1b" }, "gitcreds": { "Package": "gitcreds", @@ -589,14 +585,14 @@ }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.9", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "xfun" ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" + "Hash": "8eb36c8125038e648e5d111c0d7b2ed4" }, "hms": { "Package": "hms", @@ -615,39 +611,36 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.4", + "Version": "0.5.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "base64enc", "digest", - "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7" + "Hash": "6496090a9e00f8354b811d1a2d47b566" }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.6.1", + "Version": "1.5.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "grDevices", "htmltools", "jsonlite", - "knitr", - "rmarkdown", "yaml" ], - "Hash": "b677ee5954471eaa974c0d099a343a1a" + "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb" }, "httpuv": { "Package": "httpuv", - "Version": "1.6.9", + "Version": "1.6.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -658,11 +651,11 @@ "promises", "utils" ], - "Hash": "1046aa31a57eae8b357267a56a0b6d8b" + "Hash": "fd090e236ae2dc0f0cdf33a9ec83afb6" }, "httr": { "Package": "httr", - "Version": "1.4.5", + "Version": "1.4.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -673,26 +666,7 @@ "mime", "openssl" ], - "Hash": "f6844033201269bec3ca0097bc6c97b3" - }, - "httr2": { - "Package": "httr2", - "Version": "0.2.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", - "cli", - "curl", - "glue", - "magrittr", - "openssl", - "rappdirs", - "rlang", - "withr" - ], - "Hash": "5c09fe33064978ede54de42309c8b532" + "Hash": "57557fac46471f0dbbf44705cc6a5c8c" }, "hunspell": { "Package": "hunspell", @@ -725,17 +699,17 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.4", + "Version": "1.8.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods" ], - "Hash": "a4269a09a9b865579b2635c77e572374" + "Hash": "8b1bd0be62956f2a6b91ce84fac79a45" }, "knitr": { "Package": "knitr", - "Version": "1.42", + "Version": "1.40", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -743,11 +717,12 @@ "evaluate", "highr", "methods", + "stringr", "tools", "xfun", "yaml" ], - "Hash": "8329a9bcc82943c8069104d4be3ee22d" + "Hash": "caea8b0f899a0b1738444b9bc47067e7" }, "later": { "Package": "later", @@ -808,16 +783,16 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.9.2", + "Version": "1.8.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", + "cpp11", "generics", - "methods", - "timechange" + "methods" ], - "Hash": "e25f18436e3efd42c7c590a1c4c15390" + "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a" }, "magrittr": { "Package": "magrittr", @@ -864,13 +839,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.6", + "Version": "2.0.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "askpass" ], - "Hash": "0f7cd2962e3044bb940cca4f4b5cecbe" + "Hash": "e86c5ffeb8474a9e03d75f5d2919683e" }, "pillar": { "Package": "pillar", @@ -891,7 +866,7 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.4.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -902,11 +877,10 @@ "crayon", "desc", "prettyunits", - "processx", "rprojroot", "withr" ], - "Hash": "d6c3008d79653a0f267703288230105e" + "Hash": "66d2adfed274daf81ccfe77d974c3b9b" }, "pkgconfig": { "Package": "pkgconfig", @@ -922,7 +896,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "bslib", @@ -950,7 +924,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.2", + "Version": "1.3.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -966,7 +940,7 @@ "utils", "withr" ], - "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2" + "Hash": "3c0918b1792c75de2e640d1d8d12dead" }, "praise": { "Package": "praise", @@ -1035,29 +1009,26 @@ }, "purrr": { "Package": "purrr", - "Version": "1.0.1", + "Version": "0.3.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "cli", - "lifecycle", "magrittr", - "rlang", - "vctrs" + "rlang" ], - "Hash": "d71c815267c640f17ddbf7f16144b4bb" + "Hash": "54842a2443c76267152eface28d9e90a" }, "ragg": { "Package": "ragg", - "Version": "1.2.5", + "Version": "1.2.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9" + "Hash": "0db17bd5a1d4abfec76487b6f5dd957b" }, "rappdirs": { "Package": "rappdirs", @@ -1137,18 +1108,18 @@ }, "rlang": { "Package": "rlang", - "Version": "1.1.0", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "dc079ccd156cde8647360f473c1fa718" + "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.20", + "Version": "2.17", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1167,13 +1138,13 @@ "xfun", "yaml" ], - "Hash": "716fde5382293cc94a71f68c85b78d19" + "Hash": "e97c8be593e010f93520e8215c0f9189" }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.3", + "Version": "7.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -1182,6 +1153,7 @@ "commonmark", "cpp11", "desc", + "digest", "knitr", "methods", "pkgload", @@ -1193,7 +1165,7 @@ "withr", "xml2" ], - "Hash": "7b153c746193b143c14baa072bae4e27" + "Hash": "da1f278262e563c835345872f2fef537" }, "rprojroot": { "Package": "rprojroot", @@ -1226,7 +1198,7 @@ }, "sass": { "Package": "sass", - "Version": "0.4.5", + "Version": "0.4.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1236,7 +1208,7 @@ "rappdirs", "rlang" ], - "Hash": "2bb4371a4c80115518261866eab6ab11" + "Hash": "1b191143d7d3444d504277843f3a95fe" }, "sessioninfo": { "Package": "sessioninfo", @@ -1253,7 +1225,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.4", + "Version": "1.7.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1283,17 +1255,17 @@ "withr", "xtable" ], - "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5" + "Hash": "fe12df67fdb3b1142325cc54f100cc06" }, "sourcetools": { "Package": "sourcetools", - "Version": "0.1.7-1", + "Version": "0.1.7", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "5f5a7629f956619d519205ec475fe647" + "Hash": "947e4e02a79effa5d512473e10f41797" }, "spelling": { "Package": "spelling", @@ -1342,7 +1314,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.12", + "Version": "1.7.8", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1351,30 +1323,26 @@ "tools", "utils" ], - "Hash": "ca8bd84263c77310739d2cf64d84d7c9" + "Hash": "a68b980681bcbc84c7a67003fa796bfb" }, "stringr": { "Package": "stringr", - "Version": "1.5.0", + "Version": "1.4.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "cli", "glue", - "lifecycle", "magrittr", - "rlang", - "stringi", - "vctrs" + "stringi" ], - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8" + "Hash": "a66ad12140cd34d4f9dfcc19e84fc2a5" }, "styler": { "Package": "styler", "Version": "1.9.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R.cache", @@ -1411,7 +1379,7 @@ "Package": "testthat", "Version": "3.1.7", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -1451,7 +1419,7 @@ }, "tibble": { "Package": "tibble", - "Version": "3.2.0", + "Version": "3.1.8", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1466,30 +1434,29 @@ "utils", "vctrs" ], - "Hash": "37695ff125982007d42a59ad10982ff2" + "Hash": "56b6934ef0f8c68225949a8672fe1a8f" }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "cli", "cpp11", "dplyr", + "ellipsis", "glue", "lifecycle", "magrittr", "purrr", "rlang", - "stringr", "tibble", "tidyselect", "utils", "vctrs" ], - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" + "Hash": "cdb403db0de33ccd1b6f53b83736efa8" }, "tidyselect": { "Package": "tidyselect", @@ -1507,26 +1474,15 @@ ], "Hash": "79540e5fcd9e0435af547d885f184fd5" }, - "timechange": { - "Package": "timechange", - "Version": "0.2.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "cpp11" - ], - "Hash": "8548b44f79a35ba1791308b61e6012d7" - }, "tinytex": { "Package": "tinytex", - "Version": "0.44", + "Version": "0.42", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - "Hash": "c0f007e2eeed7722ce13d42b84a22e07" + "Hash": "7629c6c1540835d5248e6e7df265fa74" }, "urlchecker": { "Package": "urlchecker", @@ -1575,17 +1531,17 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "1fe17157424bb09c48a8b3b550c753bc" + "Hash": "c9c462b759a5cc844ae25b5942654d13" }, "vctrs": { "Package": "vctrs", - "Version": "0.5.2", + "Version": "0.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1595,7 +1551,7 @@ "lifecycle", "rlang" ], - "Hash": "e4ffa94ceed5f124d429a5a5f0f5b378" + "Hash": "001fd6a5ebfff8316baf9fb2b5516dc9" }, "waldo": { "Package": "waldo", @@ -1616,10 +1572,10 @@ }, "whisker": { "Package": "whisker", - "Version": "0.4.1", + "Version": "0.4", "Source": "Repository", "Repository": "RSPM", - "Hash": "c6abfa47a46d281a7d5159d0a8891e88" + "Hash": "ca970b96d894e90397ed20637a0c1bbe" }, "withr": { "Package": "withr", @@ -1636,14 +1592,14 @@ }, "xfun": { "Package": "xfun", - "Version": "0.37", + "Version": "0.34", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "stats", "tools" ], - "Hash": "a6860e1400a8fd1ddb6d9b4230cc34ab" + "Hash": "9eba2411b0b1f879797141bd24df7407" }, "xml2": { "Package": "xml2", @@ -1691,10 +1647,10 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.7", + "Version": "2.3.6", "Source": "Repository", "Repository": "RSPM", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436" + "Hash": "9b570515751dcbae610f29885e025b41" }, "zip": { "Package": "zip", diff --git a/renv/profiles/4.3/renv.lock b/renv/profiles/4.3/renv.lock deleted file mode 100644 index 5192711f..00000000 --- a/renv/profiles/4.3/renv.lock +++ /dev/null @@ -1,1707 +0,0 @@ -{ - "R": { - "Version": "4.3.0", - "Repositories": [ - { - "Name": "CRAN", - "URL": "https://cloud.r-project.org" - }, - { - "Name": "RSPM", - "URL": "https://packagemanager.rstudio.com/cran/2023-04-20" - } - ] - }, - "Packages": { - "DT": { - "Package": "DT", - "Version": "0.27", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": 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"6c85f015dee9cc7710ddd20f86881f58" - }, - "xtable": { - "Package": "xtable", - "Version": "1.8-4", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "stats", - "utils" - ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" - }, - "yaml": { - "Package": "yaml", - "Version": "2.3.7", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436" - }, - "zip": { - "Package": "zip", - "Version": "2.3.0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "d98c94dacb7e0efcf83b0a133a705504" - } - } -} diff --git a/renv/profiles/4.3/renv/.gitignore b/renv/profiles/4.3/renv/.gitignore deleted file mode 100644 index 0ec0cbba..00000000 --- a/renv/profiles/4.3/renv/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -library/ -local/ -cellar/ -lock/ -python/ -sandbox/ -staging/ diff --git a/renv/profiles/4.3/renv/settings.dcf b/renv/profiles/4.3/renv/settings.dcf deleted file mode 100644 index fd205f80..00000000 --- a/renv/profiles/4.3/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: admiral, admiraldev, admiral.test, admiralci -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE From e7a82234e2e30ceabc63fc1e0c08ee087c105319 Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Wed, 17 May 2023 08:26:56 +0000 Subject: [PATCH 077/100] renv update from pharmaverse/admiralci --- renv/profiles/4.0/renv.lock | 2 +- renv/profiles/4.1/renv.lock | 2 +- renv/profiles/4.2/renv.lock | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock index 3414f902..932de771 100644 --- a/renv/profiles/4.0/renv.lock +++ b/renv/profiles/4.0/renv.lock @@ -13,7 +13,7 @@ ] }, "Packages": { - "BH": { + "BH": { "Package": "BH", "Version": "1.75.0-0", "Source": "Repository", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index a1b20e23..94499def 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -16,7 +16,7 @@ "DT": { "Package": "DT", "Version": "0.21", - "Source": "Repository", + "Source": "Repository", "Repository": "RSPM", "Requirements": [ "crosstalk", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 7a05bbc5..88e86259 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -12,7 +12,7 @@ } ] }, - "Packages": { + "Packages": { "DT": { "Package": "DT", "Version": "0.26", From 609298f37c5bbb302ebdc3bb5f8fb8aa3b908ce1 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 17 May 2023 09:59:16 +0000 Subject: [PATCH 078/100] renv update from pharmaverse/admiralci --- .github/workflows/common.yml | 16 +- renv.lock | 311 ++--- renv/profiles/4.1/renv.lock | 7 +- renv/profiles/4.2/renv.lock | 260 ++-- renv/profiles/4.3/renv.lock | 1707 +++++++++++++++++++++++++++ renv/profiles/4.3/renv/.gitignore | 7 + renv/profiles/4.3/renv/settings.dcf | 10 + 7 files changed, 2045 insertions(+), 273 deletions(-) create mode 100644 renv/profiles/4.3/renv.lock create mode 100644 renv/profiles/4.3/renv/.gitignore create mode 100644 renv/profiles/4.3/renv/settings.dcf diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml index 518c64af..59e069bd 100644 --- a/.github/workflows/common.yml +++ b/.github/workflows/common.yml @@ -45,25 +45,25 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/style.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" spellcheck: name: Spelling uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" readme: name: Render README uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main if: github.event_name == 'push' with: - r-version: "4.0" + r-version: "4.1" validation: name: Validation uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main if: github.event_name == 'release' with: - r-version: "4.0" + r-version: "4.1" check: name: Check uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main @@ -73,7 +73,7 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main if: github.event_name == 'push' with: - r-version: "4.0" + r-version: "4.1" # Whether to skip multiversion docs # Note that if you have multiple versions of docs, # your URL links are likely to break due to path changes @@ -85,7 +85,7 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" links: name: Links uses: pharmaverse/admiralci/.github/workflows/links.yml@main @@ -97,7 +97,7 @@ jobs: if: > github.event_name == 'push' || github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" # Whether to skip code coverage badge creation # Setting to 'false' will require you to create # an orphan branch called 'badges' in your repository @@ -107,4 +107,4 @@ jobs: uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main if: github.event_name == 'pull_request' with: - r-version: "4.0" + r-version: "4.1" diff --git a/renv.lock b/renv.lock index 932de771..03dbcf3c 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.0.5", + "Version": "4.1.3", "Repositories": [ { "Name": "CRAN", @@ -8,38 +8,32 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2021-03-31" + "URL": "https://packagemanager.rstudio.com/cran/2022-03-10" } ] }, "Packages": { - "BH": { - "Package": "BH", - "Version": "1.75.0-0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "e4c04affc2cac20c8fec18385cd14691" - }, "DT": { "Package": "DT", - "Version": "0.17", + "Version": "0.21", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "crosstalk", "htmltools", "htmlwidgets", + "jquerylib", "jsonlite", "magrittr", "promises" ], - "Hash": "56b33b77f4cffd78ff96b8e5a69eabb0" + "Hash": "45fa28dbf288cd606e13ca35d3d72437" }, "R.cache": { "Package": "R.cache", "Version": "0.15.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R.methodsS3", @@ -76,7 +70,7 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.10.1", + "Version": "2.11.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -87,28 +81,28 @@ "tools", "utils" ], - "Hash": "a9e316277ff12a43997266f2f6567780" + "Hash": "a7ecb8e60815c7a18648e84cd121b23a" }, "R6": { "Package": "R6", - "Version": "2.5.0", + "Version": "2.5.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "b203113193e70978a696b2809525649d" + "Hash": "470851b6d5d0ac559e9d01bb352b4021" }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.6", + "Version": "1.0.8", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods", "utils" ], - "Hash": "dbb5e436998a7eba5a9d682060533338" + "Hash": "22b546dd7e337f6c0c58a39983a496bc" }, "askpass": { "Package": "askpass", @@ -122,13 +116,13 @@ }, "backports": { "Package": "backports", - "Version": "1.2.1", + "Version": "1.4.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "644043219fc24e190c2f620c1a380a69" + "Hash": "c39fbec8a30d23e721980b8afb31984c" }, "base64enc": { "Package": "base64enc", @@ -142,23 +136,23 @@ }, "brew": { "Package": "brew", - "Version": "1.0-6", + "Version": "1.0-7", "Source": "Repository", "Repository": "RSPM", - "Hash": "92a5f887f9ae3035ac7afde22ba73ee9" + "Hash": "38875ea52350ff4b4c03849fc69736c8" }, "brio": { "Package": "brio", - "Version": "1.1.1", + "Version": "1.1.3", "Source": "Repository", "Repository": "RSPM", - "Hash": "36758510e65a457efeefa50e1e7f0576" + "Hash": "976cf154dfb043c012d87cddd8bca363" }, "bslib": { "Package": "bslib", "Version": "0.3.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "grDevices", @@ -172,14 +166,14 @@ }, "cachem": { "Package": "cachem", - "Version": "1.0.4", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "fastmap", "rlang" ], - "Hash": "2703a46dcabfb902f10060b2bca9f708" + "Hash": "648c5b3d71e6a37e3043617489a0a0e9" }, "callr": { "Package": "callr", @@ -207,13 +201,13 @@ }, "clipr": { "Package": "clipr", - "Version": "0.7.1", + "Version": "0.8.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "utils" ], - "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7" + "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" }, "codetools": { "Package": "codetools", @@ -227,10 +221,10 @@ }, "commonmark": { "Package": "commonmark", - "Version": "1.7", + "Version": "1.8.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "0f22be39ec1d141fd03683c06f3a6e67" + "Hash": "2ba81b120c1655ab696c935ef33ea716" }, "covr": { "Package": "covr", @@ -261,7 +255,7 @@ }, "crayon": { "Package": "crayon", - "Version": "1.4.1", + "Version": "1.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -269,11 +263,11 @@ "methods", "utils" ], - "Hash": "e75525c55c70e5f4f78c9960a4b402e9" + "Hash": "741c2e098e98afe3dc26a7b0e5489f4e" }, "credentials": { "Package": "credentials", - "Version": "1.3.0", + "Version": "1.3.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -283,11 +277,11 @@ "openssl", "sys" ], - "Hash": "a96728288c75a814c900af9da84387be" + "Hash": "93762d0a34d78e6a025efdbfb5c6bb41" }, "crosstalk": { "Package": "crosstalk", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -296,17 +290,17 @@ "jsonlite", "lazyeval" ], - "Hash": "2b06f9e415a62b6762e4b8098d2aecbc" + "Hash": "6aa54f69598c32177e920eb3402e8293" }, "curl": { "Package": "curl", - "Version": "4.3", + "Version": "4.3.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "2b7d10581cc730804e9ed178c8374bd6" + "Hash": "022c42d49c28e95d69ca60446dbabf88" }, "cyclocomp": { "Package": "cyclocomp", @@ -338,19 +332,18 @@ }, "devtools": { "Package": "devtools", - "Version": "2.3.2", + "Version": "2.4.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "DT", "R", "callr", "cli", - "covr", "desc", "ellipsis", + "fs", "httr", - "jsonlite", + "lifecycle", "memoise", "pkgbuild", "pkgload", @@ -368,7 +361,7 @@ "utils", "withr" ], - "Hash": "415656f50722f5b6e6bcf80855ce11b9" + "Hash": "fc35e13bb582e5fe6f63f3d647a4cbe5" }, "diffdf": { "Package": "diffdf", @@ -383,7 +376,7 @@ }, "diffobj": { "Package": "diffobj", - "Version": "0.3.4", + "Version": "0.3.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -394,24 +387,24 @@ "tools", "utils" ], - "Hash": "feb5b7455eba422a2c110bb89852e6a3" + "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8" }, "digest": { "Package": "digest", - "Version": "0.6.27", + "Version": "0.6.29", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "a0cbe758a531d054b537d16dff4d58a1" + "Hash": "cf6b206a045a684728c3267ef7596190" }, "downlit": { "Package": "downlit", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "brio", @@ -428,31 +421,31 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.5", + "Version": "1.0.8", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "R6", - "ellipsis", "generics", "glue", "lifecycle", "magrittr", "methods", + "pillar", "rlang", "tibble", "tidyselect", "utils", "vctrs" ], - "Hash": "d0d76c11ec807eb3f000eba4e3eb0f68" + "Hash": "ef47665e64228a17609d6df877bf86f2" }, "ellipsis": { "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "rlang" @@ -463,7 +456,7 @@ "Package": "evaluate", "Version": "0.15", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "methods" @@ -472,13 +465,15 @@ }, "fansi": { "Package": "fansi", - "Version": "0.4.2", + "Version": "1.0.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "R" + "R", + "grDevices", + "utils" ], - "Hash": "fea074fb67fe4c25d47ad09087da847d" + "Hash": "f28149c2d7a1342a834b314e95e67260" }, "fastmap": { "Package": "fastmap", @@ -487,31 +482,43 @@ "Repository": "RSPM", "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "htmltools", + "rlang" + ], + "Hash": "55624ed409e46c5f358b2c060be87f67" + }, "fs": { "Package": "fs", - "Version": "1.5.0", + "Version": "1.5.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "44594a07a42e5f91fac9f93fda6d0109" + "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" }, "generics": { "Package": "generics", - "Version": "0.1.0", + "Version": "0.1.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "4d243a9c10b00589889fe32314ffd902" + "Hash": "177475892cf4a55865868527654a7741" }, "gert": { "Package": "gert", - "Version": "1.3.0", + "Version": "1.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -522,11 +529,11 @@ "sys", "zip" ], - "Hash": "56f398846cd40937be6b435a66bd3f37" + "Hash": "8fddce7cbd59467106266a6e93e253b4" }, "gh": { "Package": "gh", - "Version": "1.2.0", + "Version": "1.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -536,11 +543,11 @@ "ini", "jsonlite" ], - "Hash": "05129b4387282404780d2f8593636388" + "Hash": "38c2580abbda249bd6afeec00d14f531" }, "git2r": { "Package": "git2r", - "Version": "0.28.0", + "Version": "0.29.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -548,7 +555,7 @@ "graphics", "utils" ], - "Hash": "f64fd34026f6025de71a4354800e6d79" + "Hash": "b114135c4749076bd5ef74a5827b6f62" }, "gitcreds": { "Package": "gitcreds", @@ -559,28 +566,29 @@ }, "glue": { "Package": "glue", - "Version": "1.4.2", + "Version": "1.6.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "6efd734b14c6471cfe443345f3e35e29" + "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e" }, "highr": { "Package": "highr", - "Version": "0.8", + "Version": "0.9", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "R" + "R", + "xfun" ], - "Hash": "4dc5bb88961e347a0f4d8aad597cbfac" + "Hash": "8eb36c8125038e648e5d111c0d7b2ed4" }, "hms": { "Package": "hms", - "Version": "1.0.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -591,13 +599,13 @@ "rlang", "vctrs" ], - "Hash": "bf552cdd96f5969873afdac7311c7d0d" + "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca" }, "htmltools": { "Package": "htmltools", "Version": "0.5.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "base64enc", @@ -611,7 +619,7 @@ }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.5.3", + "Version": "1.5.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -620,15 +628,14 @@ "jsonlite", "yaml" ], - "Hash": "6fdaa86d0700f8b3e92ee3c445a5a10d" + "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb" }, "httpuv": { "Package": "httpuv", - "Version": "1.5.5", + "Version": "1.6.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "BH", "R", "R6", "Rcpp", @@ -636,7 +643,7 @@ "promises", "utils" ], - "Hash": "b9d5d39be2150cf86538b8488334b8f8" + "Hash": "97fe71f0a4a1c9890e6c2128afa04bc0" }, "httr": { "Package": "httr", @@ -674,23 +681,23 @@ }, "jquerylib": { "Package": "jquerylib", - "Version": "0.1.3", + "Version": "0.1.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "htmltools" ], - "Hash": "5ff50b36f7f0832f8421745af333e73c" + "Hash": "5aab57a3bd297eee1c1d862735972182" }, "jsonlite": { "Package": "jsonlite", - "Version": "1.7.2", + "Version": "1.8.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods" ], - "Hash": "98138e0994d41508c7a6b84a0600cfcb" + "Hash": "d07e729b27b372429d42d24d503613a0" }, "knitr": { "Package": "knitr", @@ -711,15 +718,14 @@ }, "later": { "Package": "later", - "Version": "1.1.0.1", + "Version": "1.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ - "BH", "Rcpp", "rlang" ], - "Hash": "d0a62b247165aabf397fded504660d8a" + "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e" }, "lazyeval": { "Package": "lazyeval", @@ -735,7 +741,7 @@ "Package": "lifecycle", "Version": "1.0.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "glue", @@ -768,44 +774,44 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.7.10", + "Version": "1.8.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "Rcpp", + "cpp11", "generics", "methods" ], - "Hash": "1ebfdc8a3cfe8fe19184f5481972b092" + "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a" }, "magrittr": { "Package": "magrittr", - "Version": "2.0.1", + "Version": "2.0.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "41287f1ac7d28a92f0a286ed507928d3" + "Hash": "cdc87ecd81934679d1557633d8e1fe51" }, "memoise": { "Package": "memoise", - "Version": "2.0.0", + "Version": "2.0.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "cachem", "rlang" ], - "Hash": "a0bc51650201a56d00a4798523cc91b3" + "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" }, "mime": { "Package": "mime", - "Version": "0.10", + "Version": "0.12", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "tools" ], - "Hash": "26fa77e707223e1ce042b2b5d09993dc" + "Hash": "18e9c28c1d3ca1560ce30658b22ce104" }, "miniUI": { "Package": "miniUI", @@ -821,17 +827,17 @@ }, "openssl": { "Package": "openssl", - "Version": "1.4.3", + "Version": "2.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "askpass" ], - "Hash": "a399e4773075fc2375b71f45fca186c4" + "Hash": "cf4329aac12c2c44089974559c18e446" }, "pillar": { "Package": "pillar", - "Version": "1.5.1", + "Version": "1.7.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -839,17 +845,18 @@ "crayon", "ellipsis", "fansi", + "glue", "lifecycle", "rlang", "utf8", "utils", "vctrs" ], - "Hash": "24622aa4a0d3de3463c34513edca99b2" + "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e" }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.2.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -863,7 +870,7 @@ "rprojroot", "withr" ], - "Hash": "725fcc30222d4d11ec68efb8ff11a9af" + "Hash": "66d2adfed274daf81ccfe77d974c3b9b" }, "pkgconfig": { "Package": "pkgconfig", @@ -907,7 +914,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.2.0", + "Version": "1.2.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -915,14 +922,13 @@ "crayon", "desc", "methods", - "pkgbuild", "rlang", "rprojroot", "rstudioapi", "utils", "withr" ], - "Hash": "cb57de933545960a86f03513e4bd2911" + "Hash": "7533cd805940821bf23eaf3c8d4c1735" }, "praise": { "Package": "praise", @@ -991,14 +997,14 @@ }, "ragg": { "Package": "ragg", - "Version": "1.1.2", + "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "3f0ac98597bebdc31b747def3eb9b6ca" + "Hash": "14932bb6f2739c771ca4ceaba6b4248e" }, "rappdirs": { "Package": "rappdirs", @@ -1012,14 +1018,14 @@ }, "rcmdcheck": { "Package": "rcmdcheck", - "Version": "1.3.3", + "Version": "1.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R6", "callr", "cli", - "crayon", + "curl", "desc", "digest", "pkgbuild", @@ -1030,7 +1036,7 @@ "withr", "xopen" ], - "Hash": "ed95895886dab6d2a584da45503555da" + "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" }, "rematch2": { "Package": "rematch2", @@ -1046,7 +1052,7 @@ "Package": "remotes", "Version": "2.4.2", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "methods", @@ -1068,13 +1074,13 @@ }, "rex": { "Package": "rex", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "lazyeval" ], - "Hash": "093584b944440c5cd07a696b3c8e0e4c" + "Hash": "ae34cd56890607370665bee5bd17812f" }, "rlang": { "Package": "rlang", @@ -1112,7 +1118,7 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1123,7 +1129,6 @@ "commonmark", "cpp11", "desc", - "digest", "knitr", "methods", "pkgload", @@ -1135,7 +1140,7 @@ "withr", "xml2" ], - "Hash": "da1f278262e563c835345872f2fef537" + "Hash": "7b153c746193b143c14baa072bae4e27" }, "rprojroot": { "Package": "rprojroot", @@ -1156,7 +1161,7 @@ }, "rversions": { "Package": "rversions", - "Version": "2.0.2", + "Version": "2.1.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1164,13 +1169,13 @@ "utils", "xml2" ], - "Hash": "0ec41191f744d0f5afad8c6f35cc36e4" + "Hash": "f88fab00907b312f8b23ec13e2d437cb" }, "sass": { "Package": "sass", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R6", "fs", @@ -1182,20 +1187,20 @@ }, "sessioninfo": { "Package": "sessioninfo", - "Version": "1.1.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ + "R", "cli", "tools", - "utils", - "withr" + "utils" ], - "Hash": "308013098befe37484df72c39cf90d6e" + "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f" }, "shiny": { "Package": "shiny", - "Version": "1.6.0", + "Version": "1.7.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1205,9 +1210,9 @@ "cachem", "commonmark", "crayon", - "digest", "ellipsis", "fastmap", + "fontawesome", "glue", "grDevices", "htmltools", @@ -1225,7 +1230,7 @@ "withr", "xtable" ], - "Hash": "6e3b6ae7fe02b5859e4bb277f218b8ae" + "Hash": "00344c227c7bd0ab5d78052c5d736c44" }, "sourcetools": { "Package": "sourcetools", @@ -1284,7 +1289,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.5.3", + "Version": "1.7.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1293,7 +1298,7 @@ "tools", "utils" ], - "Hash": "a063ebea753c92910a4cca7b18bc1f05" + "Hash": "bba431031d30789535745a9627ac9271" }, "stringr": { "Package": "stringr", @@ -1336,14 +1341,14 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.1", + "Version": "1.0.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "cpp11" ], - "Hash": "6e899d7c097698d50ec87b1d8e65f246" + "Hash": "90b28393209827327de889f49935140a" }, "testthat": { "Package": "testthat", @@ -1377,7 +1382,7 @@ }, "textshaping": { "Package": "textshaping", - "Version": "0.3.3", + "Version": "0.3.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1385,11 +1390,11 @@ "cpp11", "systemfonts" ], - "Hash": "fff317575e7191e2d077292309bed575" + "Hash": "1ab6223d3670fac7143202cb6a2d43d5" }, "tibble": { "Package": "tibble", - "Version": "3.1.0", + "Version": "3.1.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1405,11 +1410,11 @@ "utils", "vctrs" ], - "Hash": "4d894a114dbd4ecafeda5074e7c538e6" + "Hash": "8a8f02d1934dfd6431c671361510dd0b" }, "tidyr": { "Package": "tidyr", - "Version": "1.1.3", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1427,11 +1432,11 @@ "utils", "vctrs" ], - "Hash": "450d7dfaedde58e28586b854eeece4fa" + "Hash": "d8b95b7fee945d7da6888cf7eb71a49c" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.0", + "Version": "1.1.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1442,21 +1447,21 @@ "rlang", "vctrs" ], - "Hash": "6ea435c354e8448819627cf686f66e0a" + "Hash": "17f6da8cfd7002760a859915ce7eef8f" }, "tinytex": { "Package": "tinytex", - "Version": "0.31", + "Version": "0.37", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - "Hash": "25b572f764f3c19fef9aac33b5724f3d" + "Hash": "a80abeb527a977e4bef21873d29222dd" }, "usethis": { "Package": "usethis", - "Version": "2.0.1", + "Version": "2.1.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1483,17 +1488,17 @@ "withr", "yaml" ], - "Hash": "360e904f9e623286e1a0c6ca0a98c5f6" + "Hash": "c499f488e6dd7718accffaee5bc5a79b" }, "utf8": { "Package": "utf8", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7" + "Hash": "c9c462b759a5cc844ae25b5942654d13" }, "vctrs": { "Package": "vctrs", @@ -1534,16 +1539,16 @@ }, "withr": { "Package": "withr", - "Version": "2.4.3", + "Version": "2.5.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "grDevices", "graphics", "stats" ], - "Hash": "a376b424c4817cda4920bbbeb3364e85" + "Hash": "c0e49a9760983e81e55cdd9be92e7182" }, "xfun": { "Package": "xfun", @@ -1560,7 +1565,7 @@ "Package": "xml2", "Version": "1.3.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "methods" @@ -1602,17 +1607,17 @@ }, "yaml": { "Package": "yaml", - "Version": "2.2.1", + "Version": "2.3.5", "Source": "Repository", "Repository": "RSPM", - "Hash": "2826c5d9efb0a88f657c7a679c7106db" + "Hash": "458bb38374d73bf83b1bb85e353da200" }, "zip": { "Package": "zip", - "Version": "2.1.1", + "Version": "2.2.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "3bc8405c637d988801ec5ea88372d0c2" + "Hash": "c7eef2996ac270a18c2715c997a727c5" } } } diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 94499def..03dbcf3c 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -8,7 +8,7 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2022-03-10" + "URL": "https://packagemanager.rstudio.com/cran/2022-03-10" } ] }, @@ -1118,7 +1118,7 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1129,7 +1129,6 @@ "commonmark", "cpp11", "desc", - "digest", "knitr", "methods", "pkgload", @@ -1141,7 +1140,7 @@ "withr", "xml2" ], - "Hash": "da1f278262e563c835345872f2fef537" + "Hash": "7b153c746193b143c14baa072bae4e27" }, "rprojroot": { "Package": "rprojroot", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 88e86259..dada8221 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -8,14 +8,14 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2022-10-31" + "URL": "https://packagemanager.rstudio.com/cran/2023-03-15" } ] }, - "Packages": { + "Packages": { "DT": { "Package": "DT", - "Version": "0.26", + "Version": "0.27", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -27,7 +27,7 @@ "magrittr", "promises" ], - "Hash": "c66a72c4d3499e14ae179ccb742e740a" + "Hash": "3444e6ed78763f9f13aaa39f2481eb34" }, "R.cache": { "Package": "R.cache", @@ -70,7 +70,7 @@ }, "R.utils": { "Package": "R.utils", - "Version": "2.12.1", + "Version": "2.12.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -81,7 +81,7 @@ "tools", "utils" ], - "Hash": "1ed133420fcd2b93cf55a383b38fe27c" + "Hash": "325f01db13da12c04d8f6e7be36ff514" }, "R6": { "Package": "R6", @@ -95,14 +95,14 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.9", + "Version": "1.0.10", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods", "utils" ], - "Hash": "e9c08b94391e9f3f97355841229124f2" + "Hash": "e749cae40fa9ef469b6050959517453c" }, "askpass": { "Package": "askpass", @@ -150,38 +150,40 @@ }, "bslib": { "Package": "bslib", - "Version": "0.4.0", + "Version": "0.4.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", + "base64enc", "cachem", "grDevices", "htmltools", "jquerylib", "jsonlite", "memoise", + "mime", "rlang", "sass" ], - "Hash": "be5ee090716ce1671be6cd5d7c34d091" + "Hash": "a7fbf03946ad741129dc81098722fca1" }, "cachem": { "Package": "cachem", - "Version": "1.0.6", + "Version": "1.0.7", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "fastmap", "rlang" ], - "Hash": "648c5b3d71e6a37e3043617489a0a0e9" + "Hash": "cda74447c42f529de601fe4d4050daef" }, "callr": { "Package": "callr", "Version": "3.7.3", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -192,14 +194,14 @@ }, "cli": { "Package": "cli", - "Version": "3.4.1", + "Version": "3.6.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "0d297d01734d2bcea40197bd4971a764" + "Hash": "3177a5a16c243adc199ba33117bd9657" }, "clipr": { "Package": "clipr", @@ -296,13 +298,13 @@ }, "curl": { "Package": "curl", - "Version": "4.3.3", + "Version": "5.0.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "0eb86baa62f06e8855258fa5a8048667" + "Hash": "e4f97056611e8e6b8b852d13b7400cf1" }, "cyclocomp": { "Package": "cyclocomp", @@ -394,14 +396,14 @@ }, "digest": { "Package": "digest", - "Version": "0.6.30", + "Version": "0.6.31", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "bf1cd206a5d170d132ef75c7537b9bdb" + "Hash": "8b708f296afd9ae69f450f9640be8990" }, "downlit": { "Package": "downlit", @@ -425,12 +427,13 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.10", + "Version": "1.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "R6", + "cli", "generics", "glue", "lifecycle", @@ -443,7 +446,7 @@ "utils", "vctrs" ], - "Hash": "539412282059f7f0c07295723d23f987" + "Hash": "d3c34618017e7ae252d46d79a1b9ec32" }, "ellipsis": { "Package": "ellipsis", @@ -458,18 +461,18 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.17", + "Version": "0.20", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "9171b012a55a1ef53f1442b1d798a3b4" + "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c" }, "fansi": { "Package": "fansi", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -477,18 +480,18 @@ "grDevices", "utils" ], - "Hash": "83a8afdbe71839506baa9f90eebad7ec" + "Hash": "1d9e7ad3c8312a192dea7d3db0274fde" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "RSPM", - "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" + "Hash": "f7736a18de97dea803bde0a2daaafb27" }, "fontawesome": { "Package": "fontawesome", - "Version": "0.4.0", + "Version": "0.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -496,18 +499,18 @@ "htmltools", "rlang" ], - "Hash": "c5a628c2570aa86a96cc6ef739d8bfda" + "Hash": "e80750aec5717dedc019ad7ee40e4a7c" }, "fs": { "Package": "fs", - "Version": "1.5.2", + "Version": "1.6.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" + "Hash": "f4dcd23b67e33d851d2079f703e8b985" }, "generics": { "Package": "generics", @@ -522,7 +525,7 @@ }, "gert": { "Package": "gert", - "Version": "1.9.1", + "Version": "1.9.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -533,26 +536,27 @@ "sys", "zip" ], - "Hash": "9a091a6d2fb91e43afd4337e2dcef2e7" + "Hash": "9122b3958e749badb5c939f498038b57" }, "gh": { "Package": "gh", - "Version": "1.3.1", + "Version": "1.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "cli", "gitcreds", - "httr", + "httr2", "ini", - "jsonlite" + "jsonlite", + "rlang" ], - "Hash": "b6a12054ee13dce0f6696c019c10e539" + "Hash": "03533b1c875028233598f848fda44c4c" }, "git2r": { "Package": "git2r", - "Version": "0.30.1", + "Version": "0.31.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -560,7 +564,7 @@ "graphics", "utils" ], - "Hash": "e0c6a04a3e7b90e64213d09128f74f1b" + "Hash": "acb972e0be37f83b9c762d962d75a188" }, "gitcreds": { "Package": "gitcreds", @@ -585,14 +589,14 @@ }, "highr": { "Package": "highr", - "Version": "0.9", + "Version": "0.10", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "xfun" ], - "Hash": "8eb36c8125038e648e5d111c0d7b2ed4" + "Hash": "06230136b2d2b9ba5805e1963fa6e890" }, "hms": { "Package": "hms", @@ -611,36 +615,39 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.3", + "Version": "0.5.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "base64enc", "digest", + "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "6496090a9e00f8354b811d1a2d47b566" + "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7" }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.5.4", + "Version": "1.6.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "grDevices", "htmltools", "jsonlite", + "knitr", + "rmarkdown", "yaml" ], - "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb" + "Hash": "b677ee5954471eaa974c0d099a343a1a" }, "httpuv": { "Package": "httpuv", - "Version": "1.6.6", + "Version": "1.6.9", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -651,11 +658,11 @@ "promises", "utils" ], - "Hash": "fd090e236ae2dc0f0cdf33a9ec83afb6" + "Hash": "1046aa31a57eae8b357267a56a0b6d8b" }, "httr": { "Package": "httr", - "Version": "1.4.4", + "Version": "1.4.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -666,7 +673,26 @@ "mime", "openssl" ], - "Hash": "57557fac46471f0dbbf44705cc6a5c8c" + "Hash": "f6844033201269bec3ca0097bc6c97b3" + }, + "httr2": { + "Package": "httr2", + "Version": "0.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R6", + "cli", + "curl", + "glue", + "magrittr", + "openssl", + "rappdirs", + "rlang", + "withr" + ], + "Hash": "5c09fe33064978ede54de42309c8b532" }, "hunspell": { "Package": "hunspell", @@ -699,17 +725,17 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "methods" ], - "Hash": "8b1bd0be62956f2a6b91ce84fac79a45" + "Hash": "a4269a09a9b865579b2635c77e572374" }, "knitr": { "Package": "knitr", - "Version": "1.40", + "Version": "1.42", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -717,12 +743,11 @@ "evaluate", "highr", "methods", - "stringr", "tools", "xfun", "yaml" ], - "Hash": "caea8b0f899a0b1738444b9bc47067e7" + "Hash": "8329a9bcc82943c8069104d4be3ee22d" }, "later": { "Package": "later", @@ -783,16 +808,16 @@ }, "lubridate": { "Package": "lubridate", - "Version": "1.8.0", + "Version": "1.9.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "cpp11", "generics", - "methods" + "methods", + "timechange" ], - "Hash": "2ff5eedb6ee38fb1b81205c73be1be5a" + "Hash": "e25f18436e3efd42c7c590a1c4c15390" }, "magrittr": { "Package": "magrittr", @@ -839,13 +864,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.4", + "Version": "2.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "askpass" ], - "Hash": "e86c5ffeb8474a9e03d75f5d2919683e" + "Hash": "0f7cd2962e3044bb940cca4f4b5cecbe" }, "pillar": { "Package": "pillar", @@ -866,7 +891,7 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.3.1", + "Version": "1.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -877,10 +902,11 @@ "crayon", "desc", "prettyunits", + "processx", "rprojroot", "withr" ], - "Hash": "66d2adfed274daf81ccfe77d974c3b9b" + "Hash": "d6c3008d79653a0f267703288230105e" }, "pkgconfig": { "Package": "pkgconfig", @@ -896,7 +922,7 @@ "Package": "pkgdown", "Version": "2.0.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "bslib", @@ -924,7 +950,7 @@ }, "pkgload": { "Package": "pkgload", - "Version": "1.3.1", + "Version": "1.3.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -940,7 +966,7 @@ "utils", "withr" ], - "Hash": "3c0918b1792c75de2e640d1d8d12dead" + "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2" }, "praise": { "Package": "praise", @@ -1009,26 +1035,29 @@ }, "purrr": { "Package": "purrr", - "Version": "0.3.5", + "Version": "1.0.1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", + "cli", + "lifecycle", "magrittr", - "rlang" + "rlang", + "vctrs" ], - "Hash": "54842a2443c76267152eface28d9e90a" + "Hash": "d71c815267c640f17ddbf7f16144b4bb" }, "ragg": { "Package": "ragg", - "Version": "1.2.4", + "Version": "1.2.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "0db17bd5a1d4abfec76487b6f5dd957b" + "Hash": "690bc058ea2b1b8a407d3cfe3dce3ef9" }, "rappdirs": { "Package": "rappdirs", @@ -1108,18 +1137,18 @@ }, "rlang": { "Package": "rlang", - "Version": "1.0.6", + "Version": "1.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" + "Hash": "dc079ccd156cde8647360f473c1fa718" }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.17", + "Version": "2.20", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1138,13 +1167,13 @@ "xfun", "yaml" ], - "Hash": "e97c8be593e010f93520e8215c0f9189" + "Hash": "716fde5382293cc94a71f68c85b78d19" }, "roxygen2": { "Package": "roxygen2", - "Version": "7.2.1", + "Version": "7.2.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -1153,7 +1182,6 @@ "commonmark", "cpp11", "desc", - "digest", "knitr", "methods", "pkgload", @@ -1165,7 +1193,7 @@ "withr", "xml2" ], - "Hash": "da1f278262e563c835345872f2fef537" + "Hash": "7b153c746193b143c14baa072bae4e27" }, "rprojroot": { "Package": "rprojroot", @@ -1198,7 +1226,7 @@ }, "sass": { "Package": "sass", - "Version": "0.4.2", + "Version": "0.4.5", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1208,7 +1236,7 @@ "rappdirs", "rlang" ], - "Hash": "1b191143d7d3444d504277843f3a95fe" + "Hash": "2bb4371a4c80115518261866eab6ab11" }, "sessioninfo": { "Package": "sessioninfo", @@ -1225,7 +1253,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.7.3", + "Version": "1.7.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1255,17 +1283,17 @@ "withr", "xtable" ], - "Hash": "fe12df67fdb3b1142325cc54f100cc06" + "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5" }, "sourcetools": { "Package": "sourcetools", - "Version": "0.1.7", + "Version": "0.1.7-1", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R" ], - "Hash": "947e4e02a79effa5d512473e10f41797" + "Hash": "5f5a7629f956619d519205ec475fe647" }, "spelling": { "Package": "spelling", @@ -1314,7 +1342,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.7.8", + "Version": "1.7.12", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1323,26 +1351,30 @@ "tools", "utils" ], - "Hash": "a68b980681bcbc84c7a67003fa796bfb" + "Hash": "ca8bd84263c77310739d2cf64d84d7c9" }, "stringr": { "Package": "stringr", - "Version": "1.4.1", + "Version": "1.5.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", + "cli", "glue", + "lifecycle", "magrittr", - "stringi" + "rlang", + "stringi", + "vctrs" ], - "Hash": "a66ad12140cd34d4f9dfcc19e84fc2a5" + "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8" }, "styler": { "Package": "styler", "Version": "1.9.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R.cache", @@ -1379,7 +1411,7 @@ "Package": "testthat", "Version": "3.1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "R6", @@ -1419,7 +1451,7 @@ }, "tibble": { "Package": "tibble", - "Version": "3.1.8", + "Version": "3.2.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1434,29 +1466,30 @@ "utils", "vctrs" ], - "Hash": "56b6934ef0f8c68225949a8672fe1a8f" + "Hash": "37695ff125982007d42a59ad10982ff2" }, "tidyr": { "Package": "tidyr", - "Version": "1.2.1", + "Version": "1.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", + "cli", "cpp11", "dplyr", - "ellipsis", "glue", "lifecycle", "magrittr", "purrr", "rlang", + "stringr", "tibble", "tidyselect", "utils", "vctrs" ], - "Hash": "cdb403db0de33ccd1b6f53b83736efa8" + "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" }, "tidyselect": { "Package": "tidyselect", @@ -1474,15 +1507,26 @@ ], "Hash": "79540e5fcd9e0435af547d885f184fd5" }, + "timechange": { + "Package": "timechange", + "Version": "0.2.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "cpp11" + ], + "Hash": "8548b44f79a35ba1791308b61e6012d7" + }, "tinytex": { "Package": "tinytex", - "Version": "0.42", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - 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b/renv/profiles/4.3/renv/settings.dcf new file mode 100644 index 00000000..fd205f80 --- /dev/null +++ b/renv/profiles/4.3/renv/settings.dcf @@ -0,0 +1,10 @@ +bioconductor.version: +external.libraries: +ignored.packages: admiral, admiraldev, admiral.test, admiralci +package.dependency.fields: Imports, Depends, LinkingTo +r.version: +snapshot.type: implicit +use.cache: TRUE +vcs.ignore.cellar: TRUE +vcs.ignore.library: TRUE +vcs.ignore.local: TRUE From a1ecb0bb5a8fae8e1c7907e4877afc20861dee23 Mon Sep 17 00:00:00 2001 From: galachad Date: Wed, 17 May 2023 11:11:58 +0000 Subject: [PATCH 079/100] renv update from pharmaverse/admiralci --- renv/profiles/4.0/renv.lock | 1618 ------------------- renv/profiles/4.0/renv/.gitignore | 7 - renv/profiles/4.0/renv/settings.dcf | 10 - renv/profiles/4.0_legacy/renv.lock | 1640 -------------------- renv/profiles/4.0_legacy/renv/.gitignore | 7 - renv/profiles/4.0_legacy/renv/settings.dcf | 10 - 6 files changed, 3292 deletions(-) delete mode 100644 renv/profiles/4.0/renv.lock delete mode 100644 renv/profiles/4.0/renv/.gitignore delete mode 100644 renv/profiles/4.0/renv/settings.dcf delete mode 100644 renv/profiles/4.0_legacy/renv.lock delete mode 100644 renv/profiles/4.0_legacy/renv/.gitignore delete mode 100644 renv/profiles/4.0_legacy/renv/settings.dcf diff --git a/renv/profiles/4.0/renv.lock b/renv/profiles/4.0/renv.lock deleted file mode 100644 index 932de771..00000000 --- a/renv/profiles/4.0/renv.lock +++ /dev/null @@ -1,1618 +0,0 @@ -{ - "R": { - "Version": "4.0.5", - "Repositories": [ - { - "Name": "CRAN", - "URL": "https://cloud.r-project.org" - }, - { - "Name": "RSPM", - "URL": "https://packagemanager.posit.co/cran/2021-03-31" - } - ] - }, - "Packages": { - "BH": { - "Package": "BH", - "Version": "1.75.0-0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "e4c04affc2cac20c8fec18385cd14691" - }, - "DT": { - "Package": "DT", - "Version": "0.17", - "Source": "Repository", - "Repository": "RSPM", - 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"Repository": "RSPM", - "Requirements": [ - "xfun" - ], - "Hash": "25b572f764f3c19fef9aac33b5724f3d" - }, - "usethis": { - "Package": "usethis", - "Version": "2.0.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "cli", - "clipr", - "crayon", - "curl", - "desc", - "fs", - "gert", - "gh", - "glue", - "jsonlite", - "lifecycle", - "purrr", - "rappdirs", - "rlang", - "rprojroot", - "rstudioapi", - "stats", - "utils", - "whisker", - "withr", - "yaml" - ], - "Hash": "360e904f9e623286e1a0c6ca0a98c5f6" - }, - "utf8": { - "Package": "utf8", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "c3ad47dc6da0751f18ed53c4613e3ac7" - }, - "vctrs": { - "Package": "vctrs", - "Version": "0.3.7", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "ellipsis", - "glue", - "rlang" - ], - "Hash": "5540dc30a203a43a1ce5dc6a89532b3b" - }, - "waldo": { - "Package": "waldo", - "Version": 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"d4d71a75dd3ea9eb5fa28cc21f9585e2" - }, - "xmlparsedata": { - "Package": "xmlparsedata", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R" - ], - "Hash": "45e4bf3c46476896e821fc0a408fb4fc" - }, - "xopen": { - "Package": "xopen", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "processx" - ], - "Hash": "6c85f015dee9cc7710ddd20f86881f58" - }, - "xtable": { - "Package": "xtable", - "Version": "1.8-4", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "stats", - "utils" - ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" - }, - "yaml": { - "Package": "yaml", - "Version": "2.2.1", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "2826c5d9efb0a88f657c7a679c7106db" - }, - "zip": { - "Package": "zip", - "Version": "2.1.1", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "3bc8405c637d988801ec5ea88372d0c2" - } - } -} diff --git a/renv/profiles/4.0_legacy/renv/.gitignore b/renv/profiles/4.0_legacy/renv/.gitignore deleted file mode 100644 index 0ec0cbba..00000000 --- a/renv/profiles/4.0_legacy/renv/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -library/ -local/ -cellar/ -lock/ -python/ -sandbox/ -staging/ diff --git a/renv/profiles/4.0_legacy/renv/settings.dcf b/renv/profiles/4.0_legacy/renv/settings.dcf deleted file mode 100644 index fd205f80..00000000 --- a/renv/profiles/4.0_legacy/renv/settings.dcf +++ /dev/null @@ -1,10 +0,0 @@ -bioconductor.version: -external.libraries: -ignored.packages: admiral, admiraldev, admiral.test, admiralci -package.dependency.fields: Imports, Depends, LinkingTo -r.version: -snapshot.type: implicit -use.cache: TRUE -vcs.ignore.cellar: TRUE -vcs.ignore.library: TRUE -vcs.ignore.local: TRUE From 0be3ab11b1fe8633dd3a2b51535c0a5a4dda1bb7 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 18 May 2023 18:05:14 +0000 Subject: [PATCH 080/100] feat: #272 follow deprecation strategy --- R/quo.R | 35 +++++++++++----------------------- man/add_suffix_to_vars.Rd | 6 +----- man/assert_order_vars.Rd | 7 +++++++ man/expr_c.Rd | 6 +----- man/quo_c.Rd | 10 ++++------ man/quo_not_missing.Rd | 10 ++++------ man/replace_symbol_in_expr.Rd | 6 +----- man/replace_symbol_in_quo.Rd | 10 ++++------ man/replace_values_by_names.Rd | 10 ++++------ tests/testthat/test-quo.R | 27 +++++++++++++------------- 10 files changed, 51 insertions(+), 76 deletions(-) diff --git a/R/quo.R b/R/quo.R index a0d7f938..50134c9e 100644 --- a/R/quo.R +++ b/R/quo.R @@ -9,12 +9,12 @@ #' @return An object of class `quosures` #' #' -#' @keywords quo -#' @family quo +#' @keywords deprecated +#' @family deprecated #' #' @export quo_c <- function(...) { - deprecate_warn( + deprecate_stop( "0.10.0", "quo_c()", "expr_c()", @@ -23,10 +23,6 @@ quo_c <- function(...) { "instead of quosures created by `vars()`." ) ) - inputs <- unlist(list(...), recursive = TRUE) - stopifnot(all(map_lgl(inputs, is_quosure))) - is_null <- map_lgl(inputs, quo_is_null) - rlang::as_quosures(inputs[!is_null]) } #' Concatenate One or More Expressions @@ -64,12 +60,12 @@ expr_c <- function(...) { #' @return TRUE or error. #' #' -#' @keywords quo -#' @family quo +#' @keywords deprecated +#' @family deprecated #' #' @export quo_not_missing <- function(x) { - deprecate_warn( + deprecate_stop( "0.3.0", "quo_not_missing()", details = paste( @@ -78,15 +74,6 @@ quo_not_missing <- function(x) { sep = "\n" ) ) - !rlang::quo_is_missing(x) - - if (is.null(missing(x)) || quo_is_missing(x)) { - stop(paste0( - "Argument `", - deparse(substitute(x)), - "` is missing, with no default" - )) - } } @@ -97,8 +84,8 @@ quo_not_missing <- function(x) { #' @param quosures *Deprecated*, please use `expressions` instead. #' #' -#' @keywords quo -#' @family quo +#' @keywords deprecated +#' @family deprecated #' #' #' @return A list of expressions @@ -109,7 +96,7 @@ quo_not_missing <- function(x) { #' replace_values_by_names(exprs(AVAL, ADT = convert_dtc_to_dt(EXSTDTC))) replace_values_by_names <- function(expressions, quosures) { if (!missing(quosures)) { - deprecate_warn( + deprecate_stop( "0.10.0", "replace_values_by_names(quosures = )", "replace_values_by_names(expressions = )" @@ -143,8 +130,8 @@ replace_values_by_names <- function(expressions, quosures) { #' @return The quosure where every occurrence of the symbol `target` is replaced #' by `replace` #' -#' @keywords quo -#' @family quo +#' @keywords deprecated +#' @family deprecated #' #' @export replace_symbol_in_quo <- function(quosure, diff --git a/man/add_suffix_to_vars.Rd b/man/add_suffix_to_vars.Rd index 8d561d7a..d3d069ce 100644 --- a/man/add_suffix_to_vars.Rd +++ b/man/add_suffix_to_vars.Rd @@ -36,11 +36,7 @@ add_suffix_to_vars(exprs(ADT, desc(AVAL), AVALC), vars = exprs(AVAL), suffix = " \seealso{ Helpers for working with Quosures: \code{\link{expr_c}()}, -\code{\link{quo_c}()}, -\code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_expr}()}, -\code{\link{replace_symbol_in_quo}()}, -\code{\link{replace_values_by_names}()} +\code{\link{replace_symbol_in_expr}()} } \concept{quo} \keyword{quo} diff --git a/man/assert_order_vars.Rd b/man/assert_order_vars.Rd index 9e662627..7b9221e5 100644 --- a/man/assert_order_vars.Rd +++ b/man/assert_order_vars.Rd @@ -25,5 +25,12 @@ This function is \emph{deprecated}, please use \code{assert_expr_list()} instead Checks if an argument is a valid list of order variables/expressions created using \code{exprs()} } +\seealso{ +Other deprecated: +\code{\link{quo_c}()}, +\code{\link{quo_not_missing}()}, +\code{\link{replace_symbol_in_quo}()}, +\code{\link{replace_values_by_names}()} +} \concept{deprecated} \keyword{deprecated} diff --git a/man/expr_c.Rd b/man/expr_c.Rd index 8dc253ad..c946e74c 100644 --- a/man/expr_c.Rd +++ b/man/expr_c.Rd @@ -18,11 +18,7 @@ Concatenate One or More Expressions \seealso{ Helpers for working with Quosures: \code{\link{add_suffix_to_vars}()}, -\code{\link{quo_c}()}, -\code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_expr}()}, -\code{\link{replace_symbol_in_quo}()}, -\code{\link{replace_values_by_names}()} +\code{\link{replace_symbol_in_expr}()} } \concept{quo} \keyword{quo} diff --git a/man/quo_c.Rd b/man/quo_c.Rd index dad6a5ab..08403d92 100644 --- a/man/quo_c.Rd +++ b/man/quo_c.Rd @@ -19,13 +19,11 @@ An object of class \code{quosures} This function is \emph{deprecated}, please use \code{expr_c()} instead. } \seealso{ -Helpers for working with Quosures: -\code{\link{add_suffix_to_vars}()}, -\code{\link{expr_c}()}, +Other deprecated: +\code{\link{assert_order_vars}()}, \code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_expr}()}, \code{\link{replace_symbol_in_quo}()}, \code{\link{replace_values_by_names}()} } -\concept{quo} -\keyword{quo} +\concept{deprecated} +\keyword{deprecated} diff --git a/man/quo_not_missing.Rd b/man/quo_not_missing.Rd index d1161bc0..bc279ad5 100644 --- a/man/quo_not_missing.Rd +++ b/man/quo_not_missing.Rd @@ -16,13 +16,11 @@ TRUE or error. Check Whether an Argument Is Not a Quosure of a Missing Argument } \seealso{ -Helpers for working with Quosures: -\code{\link{add_suffix_to_vars}()}, -\code{\link{expr_c}()}, +Other deprecated: +\code{\link{assert_order_vars}()}, \code{\link{quo_c}()}, -\code{\link{replace_symbol_in_expr}()}, \code{\link{replace_symbol_in_quo}()}, \code{\link{replace_values_by_names}()} } -\concept{quo} -\keyword{quo} +\concept{deprecated} +\keyword{deprecated} diff --git a/man/replace_symbol_in_expr.Rd b/man/replace_symbol_in_expr.Rd index 248eb19a..9c74d915 100644 --- a/man/replace_symbol_in_expr.Rd +++ b/man/replace_symbol_in_expr.Rd @@ -31,11 +31,7 @@ replace_symbol_in_expr(expr(desc(AVAL)), target = AVAL, replace = AVAL.join) \seealso{ Helpers for working with Quosures: \code{\link{add_suffix_to_vars}()}, -\code{\link{expr_c}()}, -\code{\link{quo_c}()}, -\code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_quo}()}, -\code{\link{replace_values_by_names}()} +\code{\link{expr_c}()} } \author{ Stefan Bundfuss diff --git a/man/replace_symbol_in_quo.Rd b/man/replace_symbol_in_quo.Rd index 57b3752a..c8d1d21d 100644 --- a/man/replace_symbol_in_quo.Rd +++ b/man/replace_symbol_in_quo.Rd @@ -24,13 +24,11 @@ by \code{replace} This function is \emph{deprecated}, please use \code{replace_symbol_in_expr()} instead. } \seealso{ -Helpers for working with Quosures: -\code{\link{add_suffix_to_vars}()}, -\code{\link{expr_c}()}, +Other deprecated: +\code{\link{assert_order_vars}()}, \code{\link{quo_c}()}, \code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_expr}()}, \code{\link{replace_values_by_names}()} } -\concept{quo} -\keyword{quo} +\concept{deprecated} +\keyword{deprecated} diff --git a/man/replace_values_by_names.Rd b/man/replace_values_by_names.Rd index b407b5c9..e913e146 100644 --- a/man/replace_values_by_names.Rd +++ b/man/replace_values_by_names.Rd @@ -22,13 +22,11 @@ library(rlang) replace_values_by_names(exprs(AVAL, ADT = convert_dtc_to_dt(EXSTDTC))) } \seealso{ -Helpers for working with Quosures: -\code{\link{add_suffix_to_vars}()}, -\code{\link{expr_c}()}, +Other deprecated: +\code{\link{assert_order_vars}()}, \code{\link{quo_c}()}, \code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_expr}()}, \code{\link{replace_symbol_in_quo}()} } -\concept{quo} -\keyword{quo} +\concept{deprecated} +\keyword{deprecated} diff --git a/tests/testthat/test-quo.R b/tests/testthat/test-quo.R index e0644054..579cd728 100644 --- a/tests/testthat/test-quo.R +++ b/tests/testthat/test-quo.R @@ -1,9 +1,9 @@ # quo_c ---- ## Test 1: issues deprecation warning ---- test_that("quo_c Test 1: issues deprecation warning", { - expect_warning( + expect_error( quo_c(quo(USUBJID), quo(STUDYID)), - class = "lifecycle_warning_deprecated" + class = "lifecycle_error_deprecated" ) }) @@ -12,13 +12,13 @@ test_that("quo_c Test 2: `quo_c` works in concatenating and indexing quosures", x <- quo(USUBJID) y <- quo(STUDYID) - expect_equal( - expected = quo(USUBJID), - object = quo_c(x, NULL, y)[[1]] + expect_error( + quo_c(x, NULL, y)[[1]], + class = "lifecycle_error_deprecated" ) - expect_equal( - expected = quo(STUDYID), - object = quo_c(x, NULL, y)[[2]] + expect_error( + object = quo_c(x, NULL, y)[[2]], + class = "lifecycle_error_deprecated" ) }) @@ -27,7 +27,8 @@ test_that("quo_c Test 3: `quo_c` returns error if non-quosures are input", { USUBJID <- "01-701-1015" # nolint expect_error( - object = quo_c(quo(USUBJID), USUBJID) + object = quo_c(quo(USUBJID), USUBJID), + class = "lifecycle_error_deprecated" ) }) @@ -77,9 +78,9 @@ test_that("quo_not_missing Test 8: issues deprecation warning", { x <- enquo(x) !isTRUE(quo_not_missing(x)) } - expect_warning( + expect_error( test_fun(my_variable), - class = "lifecycle_warning_deprecated" + class = "lifecycle_error_deprecated" ) }) @@ -134,9 +135,9 @@ test_that("replace_values_by_names Test 11: names of argument is NULL", { ## Test 12: warning if quosures argument is used ---- test_that("replace_values_by_names Test 12: warning if quosures argument is used", { - expect_warning( + expect_error( replace_values_by_names(quosures = rlang::quos(STUDYID, USUBJID)), - class = "lifecycle_warning_deprecated" + class = "lifecycle_error_deprecated" ) }) From aa34609703961465d675377965c7badcc395681c Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 18 May 2023 19:05:11 +0000 Subject: [PATCH 081/100] docs: #253 add snippet about importFrom --- vignettes/programming_strategy.Rmd | 1 + 1 file changed, 1 insertion(+) diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index 0212a3d3..ef21e2d4 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -524,6 +524,7 @@ If a package is used only in examples and/or unit tests then it should be listed Functions from other packages have to be explicitly imported by using the `@importFrom` tag in the `R/admiral-package.R` file. To import the `if_else()` and `mutate()` function from `dplyr` the following line would have to be included in that file: `#' @importFrom dplyr if_else mutate`. +By using the `@importFrom` tag, it is easier to track all of our dependencies in one place and improves code readability. Some of these functions become critically important while using admiral and should be included as an export. This applies to functions which are frequently From 03fdb9d059229d2d95f17fb5b2b23fb460cec6a9 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 18 May 2023 19:28:28 +0000 Subject: [PATCH 082/100] docs: #72 add guidance on default/permitted --- vignettes/programming_strategy.Rmd | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index ef21e2d4..83704cbf 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -389,8 +389,12 @@ An example is given below: The following fields are mandatory: * `@param`: One entry per function argument. -The following attributes should be described: expected data type (e.g. `data.frame`, `logical`, `numeric` etc.), default value (if any), permitted values (if applicable), optionality (i.e. is this a required argument). -If the expected input is a dataset then the required variables should be clearly stated. +The following attributes should be described: expected data type (e.g. `data.frame`, `logical`, `numeric` etc.), permitted values (if applicable), optionality (i.e. is this a required argument). If the expected input is a dataset then the required variables should be clearly stated. Describing the default value becomes difficult to maintain and subject to manual error when it is already declared in the function arguments. The description for permitted values should be written as a separate line italicizing the phrase "Permitted Values", example below: + +``` +#' *Permitted Values*: example description of permitted values here +``` + * `@details`: A natural-language description of the derivation used inside the function. * `@keyword`: One applicable tag to the function - identical to family. * `@family`: One applicable tag to the function - identical to keyword. From abfab73dd0344b11ca35be3ef8a53e3dbe31794b Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 18 May 2023 19:28:28 +0000 Subject: [PATCH 083/100] docs: #72 add guidance on default/permitted --- NEWS.md | 2 +- vignettes/programming_strategy.Rmd | 8 ++++++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index b5c4380a..5e08ae9d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -18,7 +18,7 @@ expressions (#241) ## Documentation - The deprecation strategy was updated regarding unit tests for deprecated -functions/arguments in phase 1. (#247) +functions/arguments in phase 1 and 2. (#247, #272) # admiraldev 0.3.0 diff --git a/vignettes/programming_strategy.Rmd b/vignettes/programming_strategy.Rmd index ef21e2d4..83704cbf 100644 --- a/vignettes/programming_strategy.Rmd +++ b/vignettes/programming_strategy.Rmd @@ -389,8 +389,12 @@ An example is given below: The following fields are mandatory: * `@param`: One entry per function argument. -The following attributes should be described: expected data type (e.g. `data.frame`, `logical`, `numeric` etc.), default value (if any), permitted values (if applicable), optionality (i.e. is this a required argument). -If the expected input is a dataset then the required variables should be clearly stated. +The following attributes should be described: expected data type (e.g. `data.frame`, `logical`, `numeric` etc.), permitted values (if applicable), optionality (i.e. is this a required argument). If the expected input is a dataset then the required variables should be clearly stated. Describing the default value becomes difficult to maintain and subject to manual error when it is already declared in the function arguments. The description for permitted values should be written as a separate line italicizing the phrase "Permitted Values", example below: + +``` +#' *Permitted Values*: example description of permitted values here +``` + * `@details`: A natural-language description of the derivation used inside the function. * `@keyword`: One applicable tag to the function - identical to family. * `@family`: One applicable tag to the function - identical to keyword. From 883331f31db042d5ebf331c00ca96c0b0f93b854 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Fri, 19 May 2023 16:51:39 +0000 Subject: [PATCH 084/100] docs: #272 #253 #72 properly update news --- NEWS.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 5e08ae9d..38d11f5f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -14,11 +14,20 @@ expressions (#241) ## Breaking Changes - `assert_order_vars()` was deprecated in favor of `assert_expr_list()`. (#241) +- The following functions have been deprecated from previous admiral versions using the next phase of the deprecation process: (#272) + + - `quo_c()` + - `quo_not_missing()` + - `replace_values_by_names()` + - `replace_symbol_in_quo()` + ## Documentation - The deprecation strategy was updated regarding unit tests for deprecated -functions/arguments in phase 1 and 2. (#247, #272) +functions/arguments in phase 1. (#247) + +- The programming strategy was updated regarding permitted values and calling functions from package dependencies (#72, #253) # admiraldev 0.3.0 From 7f9369ae7f84daa3b421728d66032fc02a1dfd2d Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Fri, 19 May 2023 19:17:02 +0000 Subject: [PATCH 085/100] fix: #272 fix deprecation warnings to correct ver --- R/quo.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/quo.R b/R/quo.R index 50134c9e..623041b7 100644 --- a/R/quo.R +++ b/R/quo.R @@ -15,7 +15,7 @@ #' @export quo_c <- function(...) { deprecate_stop( - "0.10.0", + "0.3.0", "quo_c()", "expr_c()", details = paste( @@ -97,7 +97,7 @@ quo_not_missing <- function(x) { replace_values_by_names <- function(expressions, quosures) { if (!missing(quosures)) { deprecate_stop( - "0.10.0", + "0.3.0", "replace_values_by_names(quosures = )", "replace_values_by_names(expressions = )" ) @@ -138,7 +138,7 @@ replace_symbol_in_quo <- function(quosure, target, replace) { deprecate_stop( - "0.10.0", + "0.3.0", "replace_symbol_in_quo()", "replace_symbol_in_expr()", details = paste( From 1e3422e852480391c08be775d443fdbc0c64a9f7 Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Mon, 22 May 2023 15:40:52 +0000 Subject: [PATCH 086/100] docs: #272 address feedback about deprecation --- NEWS.md | 3 +-- R/quo.R | 4 ++-- man/add_suffix_to_vars.Rd | 3 ++- man/assert_order_vars.Rd | 3 +-- man/expr_c.Rd | 3 ++- man/quo_c.Rd | 3 +-- man/quo_not_missing.Rd | 3 +-- man/replace_symbol_in_expr.Rd | 3 ++- man/replace_symbol_in_quo.Rd | 3 +-- man/replace_values_by_names.Rd | 13 ++++++------- 10 files changed, 19 insertions(+), 22 deletions(-) diff --git a/NEWS.md b/NEWS.md index 38d11f5f..b3ec78a8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -18,9 +18,8 @@ expressions (#241) - `quo_c()` - `quo_not_missing()` - - `replace_values_by_names()` - `replace_symbol_in_quo()` - +- The `quosures` argument was replaced by the `expressions` argument in `replace_values_by_names()`. ## Documentation diff --git a/R/quo.R b/R/quo.R index 623041b7..a5870a6f 100644 --- a/R/quo.R +++ b/R/quo.R @@ -84,8 +84,8 @@ quo_not_missing <- function(x) { #' @param quosures *Deprecated*, please use `expressions` instead. #' #' -#' @keywords deprecated -#' @family deprecated +#' @keywords quo +#' @family quo #' #' #' @return A list of expressions diff --git a/man/add_suffix_to_vars.Rd b/man/add_suffix_to_vars.Rd index d3d069ce..f0981e61 100644 --- a/man/add_suffix_to_vars.Rd +++ b/man/add_suffix_to_vars.Rd @@ -36,7 +36,8 @@ add_suffix_to_vars(exprs(ADT, desc(AVAL), AVALC), vars = exprs(AVAL), suffix = " \seealso{ Helpers for working with Quosures: \code{\link{expr_c}()}, -\code{\link{replace_symbol_in_expr}()} +\code{\link{replace_symbol_in_expr}()}, +\code{\link{replace_values_by_names}()} } \concept{quo} \keyword{quo} diff --git a/man/assert_order_vars.Rd b/man/assert_order_vars.Rd index 7b9221e5..b17ce75a 100644 --- a/man/assert_order_vars.Rd +++ b/man/assert_order_vars.Rd @@ -29,8 +29,7 @@ using \code{exprs()} Other deprecated: \code{\link{quo_c}()}, \code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_quo}()}, -\code{\link{replace_values_by_names}()} +\code{\link{replace_symbol_in_quo}()} } \concept{deprecated} \keyword{deprecated} diff --git a/man/expr_c.Rd b/man/expr_c.Rd index c946e74c..312f238e 100644 --- a/man/expr_c.Rd +++ b/man/expr_c.Rd @@ -18,7 +18,8 @@ Concatenate One or More Expressions \seealso{ Helpers for working with Quosures: \code{\link{add_suffix_to_vars}()}, -\code{\link{replace_symbol_in_expr}()} +\code{\link{replace_symbol_in_expr}()}, +\code{\link{replace_values_by_names}()} } \concept{quo} \keyword{quo} diff --git a/man/quo_c.Rd b/man/quo_c.Rd index 08403d92..672877ae 100644 --- a/man/quo_c.Rd +++ b/man/quo_c.Rd @@ -22,8 +22,7 @@ This function is \emph{deprecated}, please use \code{expr_c()} instead. Other deprecated: \code{\link{assert_order_vars}()}, \code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_quo}()}, -\code{\link{replace_values_by_names}()} +\code{\link{replace_symbol_in_quo}()} } \concept{deprecated} \keyword{deprecated} diff --git a/man/quo_not_missing.Rd b/man/quo_not_missing.Rd index bc279ad5..7e45b673 100644 --- a/man/quo_not_missing.Rd +++ b/man/quo_not_missing.Rd @@ -19,8 +19,7 @@ Check Whether an Argument Is Not a Quosure of a Missing Argument Other deprecated: \code{\link{assert_order_vars}()}, \code{\link{quo_c}()}, -\code{\link{replace_symbol_in_quo}()}, -\code{\link{replace_values_by_names}()} +\code{\link{replace_symbol_in_quo}()} } \concept{deprecated} \keyword{deprecated} diff --git a/man/replace_symbol_in_expr.Rd b/man/replace_symbol_in_expr.Rd index 9c74d915..61b95436 100644 --- a/man/replace_symbol_in_expr.Rd +++ b/man/replace_symbol_in_expr.Rd @@ -31,7 +31,8 @@ replace_symbol_in_expr(expr(desc(AVAL)), target = AVAL, replace = AVAL.join) \seealso{ Helpers for working with Quosures: \code{\link{add_suffix_to_vars}()}, -\code{\link{expr_c}()} +\code{\link{expr_c}()}, +\code{\link{replace_values_by_names}()} } \author{ Stefan Bundfuss diff --git a/man/replace_symbol_in_quo.Rd b/man/replace_symbol_in_quo.Rd index c8d1d21d..ccbb3200 100644 --- a/man/replace_symbol_in_quo.Rd +++ b/man/replace_symbol_in_quo.Rd @@ -27,8 +27,7 @@ This function is \emph{deprecated}, please use \code{replace_symbol_in_expr()} i Other deprecated: \code{\link{assert_order_vars}()}, \code{\link{quo_c}()}, -\code{\link{quo_not_missing}()}, -\code{\link{replace_values_by_names}()} +\code{\link{quo_not_missing}()} } \concept{deprecated} \keyword{deprecated} diff --git a/man/replace_values_by_names.Rd b/man/replace_values_by_names.Rd index e913e146..0ad71aa3 100644 --- a/man/replace_values_by_names.Rd +++ b/man/replace_values_by_names.Rd @@ -22,11 +22,10 @@ library(rlang) replace_values_by_names(exprs(AVAL, ADT = convert_dtc_to_dt(EXSTDTC))) } \seealso{ -Other deprecated: -\code{\link{assert_order_vars}()}, -\code{\link{quo_c}()}, -\code{\link{quo_not_missing}()}, -\code{\link{replace_symbol_in_quo}()} +Helpers for working with Quosures: +\code{\link{add_suffix_to_vars}()}, +\code{\link{expr_c}()}, +\code{\link{replace_symbol_in_expr}()} } -\concept{deprecated} -\keyword{deprecated} +\concept{quo} +\keyword{quo} From dc12c853a7afd507be93eddc86be6464e2b9af27 Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 30 May 2023 06:24:49 +0000 Subject: [PATCH 087/100] renv update from pharmaverse/admiralci --- .Rprofile | 13 +++++++++++++ renv.lock | 2 +- renv/profiles/4.1/renv.lock | 2 +- renv/profiles/4.2/renv.lock | 2 +- renv/profiles/4.3/renv.lock | 2 +- 5 files changed, 17 insertions(+), 4 deletions(-) diff --git a/.Rprofile b/.Rprofile index 3ac58f50..85d4f44f 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,5 +1,18 @@ +# Set renv profile base on R version. +renv_profile <- paste(R.version$major, substr(R.version$minor, 1,1), sep = ".") +if (file.exists("./renv/profile")){ + message("Using renv profile from `renv/profile` file.") +} else if (renv_profile %in% c("4.1", "4.2", "4.3")) { + message("Set renv profile to", renv_profile) + Sys.setenv("RENV_PROFILE" = renv_profile) +} else { + message("Using default renv profile") +} + if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) { source("renv/activate.R") } else { options(repos = c(CRAN = "https://cran.rstudio.com")) } + + diff --git a/renv.lock b/renv.lock index 03dbcf3c..7708d4e2 100644 --- a/renv.lock +++ b/renv.lock @@ -8,7 +8,7 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.rstudio.com/cran/2022-03-10" + "URL": "https://packagemanager.posit.co/cran/2022-03-10" } ] }, diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 03dbcf3c..7708d4e2 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -8,7 +8,7 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.rstudio.com/cran/2022-03-10" + "URL": "https://packagemanager.posit.co/cran/2022-03-10" } ] }, diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index dada8221..4a96e80f 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -8,7 +8,7 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.rstudio.com/cran/2023-03-15" + "URL": "https://packagemanager.posit.co/cran/2023-03-15" } ] }, diff --git a/renv/profiles/4.3/renv.lock b/renv/profiles/4.3/renv.lock index 5192711f..b875a5b8 100644 --- a/renv/profiles/4.3/renv.lock +++ b/renv/profiles/4.3/renv.lock @@ -8,7 +8,7 @@ }, { "Name": "RSPM", - "URL": "https://packagemanager.rstudio.com/cran/2023-04-20" + "URL": "https://packagemanager.posit.co/cran/2023-04-20" } ] }, From a0f14fe599681ffb9808ef0faf11fce82447499d Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 30 May 2023 06:54:21 +0000 Subject: [PATCH 088/100] renv update from pharmaverse/admiralci --- .Rprofile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.Rprofile b/.Rprofile index 85d4f44f..2a2e95ef 100644 --- a/.Rprofile +++ b/.Rprofile @@ -3,10 +3,10 @@ renv_profile <- paste(R.version$major, substr(R.version$minor, 1,1), sep = ".") if (file.exists("./renv/profile")){ message("Using renv profile from `renv/profile` file.") } else if (renv_profile %in% c("4.1", "4.2", "4.3")) { - message("Set renv profile to", renv_profile) + message("Set renv profile to `", renv_profile, "`") Sys.setenv("RENV_PROFILE" = renv_profile) } else { - message("Using default renv profile") + message("This repository do not contains the renv profile for your R version.") } if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) { From 43d06729c713b6fd938d2de41ce7f0743f204530 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adam=20Fory=C5=9B?= Date: Tue, 30 May 2023 09:39:41 +0200 Subject: [PATCH 089/100] Update DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 39064a9f..9a9ad929 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,7 +28,7 @@ Encoding: UTF-8 Language: en-US LazyData: false Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.1 +RoxygenNote: 7.2.3 Depends: R (>= 3.5) Imports: dplyr (>= 1.0.5), From 2ec93f67ac026aa5313271f642a331dcfec37240 Mon Sep 17 00:00:00 2001 From: Adam Forys Date: Tue, 30 May 2023 09:41:54 +0000 Subject: [PATCH 090/100] Update pr_review_guidance urls --- .lycheeignore | 3 +++ vignettes/pr_review_guidance.Rmd | 12 ++++++------ 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/.lycheeignore b/.lycheeignore index 99cd3aca..bbe5ed81 100644 --- a/.lycheeignore +++ b/.lycheeignore @@ -11,3 +11,6 @@ tj-actions/branch-names@v5.2 file:///home/runner/work/admiraldev/admiraldev/.github/workflows/pkgdown file:///home/runner/work/admiraldev/admiraldev/.github/workflows/style.yml%60 file:///home/runner/work/admiraldev/admiraldev/.github/workflows/sd-repo +https://packagemanager.posit.co/cran/2021-05-03/ +https://packagemanager.posit.co/cran/2022-01-03/ +https://packagemanager.posit.co/cran/2023-04-20/ diff --git a/vignettes/pr_review_guidance.Rmd b/vignettes/pr_review_guidance.Rmd index d8ca399c..da7c8390 100644 --- a/vignettes/pr_review_guidance.Rmd +++ b/vignettes/pr_review_guidance.Rmd @@ -177,12 +177,12 @@ for (pkg in base_recommended_pkgs) { assign(".lib.loc", ".library", envir = environment(.libPaths)) r_version <- getRversion() -if (grepl("^4.0", r_version)) { - options(repos = "https://cran.microsoft.com/snapshot/2021-03-31") -} else if (grepl("^4.1", r_version)) { - options(repos = "https://cran.microsoft.com/snapshot/2022-03-10") -} else if (grepl("release", r_version)) { - options(repos = "https://cran.microsoft.com/snapshot/2022-06-23") +if (grepl("^4.1", r_version)) { + options(repos = "https://packagemanager.posit.co/cran/2021-05-03/") +} else if (grepl("^4.2", r_version)) { + options(repos = "https://packagemanager.posit.co/cran/2022-01-03/") +} else if (grepl("^4.3", r_version)) { + options(repos = "https://packagemanager.posit.co/cran/2023-04-20/") } else { options(repos = "https://cran.rstudio.com") } From e9dffe9c47128489e6ab01ff4bd6bc693b2ed0a6 Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 30 May 2023 09:48:02 +0000 Subject: [PATCH 091/100] renv update from pharmaverse/admiralci --- .Rprofile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rprofile b/.Rprofile index 2a2e95ef..5b3aa735 100644 --- a/.Rprofile +++ b/.Rprofile @@ -9,7 +9,7 @@ if (file.exists("./renv/profile")){ message("This repository do not contains the renv profile for your R version.") } -if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) { +if (Sys.getenv("GITHUB_ACTIONS") == "") { source("renv/activate.R") } else { options(repos = c(CRAN = "https://cran.rstudio.com")) From fc1b46c0f0c7b13bc630327938fd9a2f7299f777 Mon Sep 17 00:00:00 2001 From: galachad Date: Tue, 30 May 2023 09:59:16 +0000 Subject: [PATCH 092/100] renv update from pharmaverse/admiralci --- renv/settings.dcf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/renv/settings.dcf b/renv/settings.dcf index c4ab61bd..fd205f80 100644 --- a/renv/settings.dcf +++ b/renv/settings.dcf @@ -3,7 +3,7 @@ external.libraries: ignored.packages: admiral, admiraldev, admiral.test, admiralci package.dependency.fields: Imports, Depends, LinkingTo r.version: -snapshot.type: custom +snapshot.type: implicit use.cache: TRUE vcs.ignore.cellar: TRUE vcs.ignore.library: TRUE From 11b079fa8740950e2de373635eb8b618f18a965d Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Thu, 1 Jun 2023 19:48:09 +0000 Subject: [PATCH 093/100] fix merge conflict --- README.md | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index cc8daf96..d4566c2a 100644 --- a/README.md +++ b/README.md @@ -6,11 +6,6 @@ Utility Functions and Development Tools for the Admiral Package Family -[![CRAN -status](https://www.r-pkg.org/badges/version/admiraldev)](https://CRAN.R-project.org/package=admiraldev) -[![Test -Coverage](https://raw.githubusercontent.com/pharmaverse/admiraldev/badges/main/test-coverage.svg)](https://github.com/pharmaverse/admiraldev/actions/workflows/common.yml) - ## Purpose @@ -22,7 +17,7 @@ functions/Addins to assist developers of `{admiral}` or `{admiral}` extension packages as well as functions to help with rendering documentation. -**NOTE:** This package is not intended for standalone use but rather as +__NOTE:__ This package is not intended for standalone use but rather as a central dependency for `{admiral}` and its extension packages ## Installation @@ -33,11 +28,13 @@ The package is available from CRAN and can be installed by running To install the latest development version of the package directly from GitHub use the following code: - if (!requireNamespace("remotes", quietly = TRUE)) { - install.packages("remotes") - } +``` +if (!requireNamespace("remotes", quietly = TRUE)) { + install.packages("remotes") +} - remotes::install_github("pharmaverse/admiraldev", ref = "devel") +remotes::install_github("pharmaverse/admiraldev", ref = "devel") +``` ## Release Schedule From 294d32716d150bc576a6eb2b7c9dcd5d257ba02c Mon Sep 17 00:00:00 2001 From: Zelos Zhu Date: Mon, 5 Jun 2023 14:55:10 +0000 Subject: [PATCH 094/100] turn CRAN dates on --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index e9425344..22293eab 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -11,7 +11,7 @@ repo: issue: https://github.com/pharmaverse/admiraldev/issues/ user: https://github.com/ news: - cran_dates: false + cran_dates: true reference: - title: Assertion Functions From 647b6c73d7096e514873c3ef4530299aa66a0d3b Mon Sep 17 00:00:00 2001 From: dgrassellyb Date: Tue, 6 Jun 2023 08:51:11 +0000 Subject: [PATCH 095/100] renv update from pharmaverse/admiralci --- renv.lock | 49 +++++++++++++++++----------------- renv/profiles/4.1/renv.lock | 53 +++++++++++++++++++------------------ renv/profiles/4.2/renv.lock | 20 +++++++------- renv/profiles/4.3/renv.lock | 2 +- 4 files changed, 63 insertions(+), 61 deletions(-) diff --git a/renv.lock b/renv.lock index 7708d4e2..66174483 100644 --- a/renv.lock +++ b/renv.lock @@ -421,12 +421,13 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.8", + "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", + "cli", "generics", "glue", "lifecycle", @@ -439,7 +440,7 @@ "utils", "vctrs" ], - "Hash": "ef47665e64228a17609d6df877bf86f2" + "Hash": "eb5742d256a0d9306d85ea68756d8187" }, "ellipsis": { "Package": "ellipsis", @@ -739,15 +740,16 @@ }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.1", + "Version": "1.0.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", + "cli", "glue", "rlang" ], - "Hash": "a6b6d352e3ed897373ab19d8395c98d0" + "Hash": "001cecbeac1cff9301bdc3775ee46a86" }, "lintr": { "Package": "lintr", @@ -837,13 +839,11 @@ }, "pillar": { "Package": "pillar", - "Version": "1.7.0", + "Version": "1.9.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "cli", - "crayon", - "ellipsis", "fansi", "glue", "lifecycle", @@ -852,7 +852,7 @@ "utils", "vctrs" ], - "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e" + "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, "pkgbuild": { "Package": "pkgbuild", @@ -1084,14 +1084,14 @@ }, "rlang": { "Package": "rlang", - "Version": "1.0.6", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" + "Hash": "dc079ccd156cde8647360f473c1fa718" }, "rmarkdown": { "Package": "rmarkdown", @@ -1394,12 +1394,11 @@ }, "tibble": { "Package": "tibble", - "Version": "3.1.6", + "Version": "3.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", - "ellipsis", "fansi", "lifecycle", "magrittr", @@ -1410,7 +1409,7 @@ "utils", "vctrs" ], - "Hash": "8a8f02d1934dfd6431c671361510dd0b" + "Hash": "37695ff125982007d42a59ad10982ff2" }, "tidyr": { "Package": "tidyr", @@ -1436,18 +1435,19 @@ }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.2", + "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", - "ellipsis", + "cli", "glue", - "purrr", + "lifecycle", "rlang", - "vctrs" + "vctrs", + "withr" ], - "Hash": "17f6da8cfd7002760a859915ce7eef8f" + "Hash": "79540e5fcd9e0435af547d885f184fd5" }, "tinytex": { "Package": "tinytex", @@ -1502,16 +1502,17 @@ }, "vctrs": { "Package": "vctrs", - "Version": "0.4.1", + "Version": "0.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", "glue", + "lifecycle", "rlang" ], - "Hash": "8b54f22e2a58c4f275479c92ce041a57" + "Hash": "7e877404388794361277be95d8445de8" }, "waldo": { "Package": "waldo", diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 7708d4e2..2bfb572c 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -12,7 +12,7 @@ } ] }, - "Packages": { + "Packages": { "DT": { "Package": "DT", "Version": "0.21", @@ -421,12 +421,13 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.8", + "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", + "cli", "generics", "glue", "lifecycle", @@ -439,7 +440,7 @@ "utils", "vctrs" ], - "Hash": "ef47665e64228a17609d6df877bf86f2" + "Hash": "eb5742d256a0d9306d85ea68756d8187" }, "ellipsis": { "Package": "ellipsis", @@ -739,15 +740,16 @@ }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.1", + "Version": "1.0.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", + "cli", "glue", "rlang" ], - "Hash": "a6b6d352e3ed897373ab19d8395c98d0" + "Hash": "001cecbeac1cff9301bdc3775ee46a86" }, "lintr": { "Package": "lintr", @@ -837,13 +839,11 @@ }, "pillar": { "Package": "pillar", - "Version": "1.7.0", + "Version": "1.9.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "cli", - "crayon", - "ellipsis", "fansi", "glue", "lifecycle", @@ -852,7 +852,7 @@ "utils", "vctrs" ], - "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e" + "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, "pkgbuild": { "Package": "pkgbuild", @@ -1084,14 +1084,14 @@ }, "rlang": { "Package": "rlang", - "Version": "1.0.6", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "4ed1f8336c8d52c3e750adcdc57228a7" + "Hash": "dc079ccd156cde8647360f473c1fa718" }, "rmarkdown": { "Package": "rmarkdown", @@ -1394,12 +1394,11 @@ }, "tibble": { "Package": "tibble", - "Version": "3.1.6", + "Version": "3.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", - "ellipsis", "fansi", "lifecycle", "magrittr", @@ -1410,7 +1409,7 @@ "utils", "vctrs" ], - "Hash": "8a8f02d1934dfd6431c671361510dd0b" + "Hash": "37695ff125982007d42a59ad10982ff2" }, "tidyr": { "Package": "tidyr", @@ -1436,18 +1435,19 @@ }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.2", + "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", - "ellipsis", + "cli", "glue", - "purrr", + "lifecycle", "rlang", - "vctrs" + "vctrs", + "withr" ], - "Hash": "17f6da8cfd7002760a859915ce7eef8f" + "Hash": "79540e5fcd9e0435af547d885f184fd5" }, "tinytex": { "Package": "tinytex", @@ -1502,16 +1502,17 @@ }, "vctrs": { "Package": "vctrs", - "Version": "0.4.1", + "Version": "0.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", "glue", + "lifecycle", "rlang" ], - "Hash": "8b54f22e2a58c4f275479c92ce041a57" + "Hash": "7e877404388794361277be95d8445de8" }, "waldo": { "Package": "waldo", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index 4a96e80f..a3dec833 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -12,7 +12,7 @@ } ] }, - "Packages": { + "Packages": { "DT": { "Package": "DT", "Version": "0.27", @@ -427,9 +427,9 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.1.0", + "Version": "1.1.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -446,7 +446,7 @@ "utils", "vctrs" ], - "Hash": "d3c34618017e7ae252d46d79a1b9ec32" + "Hash": "eb5742d256a0d9306d85ea68756d8187" }, "ellipsis": { "Package": "ellipsis", @@ -874,9 +874,9 @@ }, "pillar": { "Package": "pillar", - "Version": "1.8.1", + "Version": "1.9.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "cli", "fansi", @@ -887,7 +887,7 @@ "utils", "vctrs" ], - "Hash": "f2316df30902c81729ae9de95ad5a608" + "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, "pkgbuild": { "Package": "pkgbuild", @@ -1585,9 +1585,9 @@ }, "vctrs": { "Package": "vctrs", - "Version": "0.5.2", + "Version": "0.6.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "cli", @@ -1595,7 +1595,7 @@ "lifecycle", "rlang" ], - "Hash": "e4ffa94ceed5f124d429a5a5f0f5b378" + "Hash": "7e877404388794361277be95d8445de8" }, "waldo": { "Package": "waldo", diff --git a/renv/profiles/4.3/renv.lock b/renv/profiles/4.3/renv.lock index b875a5b8..691871a8 100644 --- a/renv/profiles/4.3/renv.lock +++ b/renv/profiles/4.3/renv.lock @@ -12,7 +12,7 @@ } ] }, - "Packages": { + "Packages": { "DT": { "Package": "DT", "Version": "0.27", From 328d19b2c206ed9ab9713e734634396c2d9796b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?= <56442075+dgrassellyb@users.noreply.github.com> Date: Tue, 6 Jun 2023 13:26:54 +0200 Subject: [PATCH 096/100] Update .Rprofile --- .Rprofile | 23 ++++++++++------------- 1 file changed, 10 insertions(+), 13 deletions(-) diff --git a/.Rprofile b/.Rprofile index 5b3aa735..673ea47a 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,18 +1,15 @@ # Set renv profile base on R version. -renv_profile <- paste(R.version$major, substr(R.version$minor, 1,1), sep = ".") -if (file.exists("./renv/profile")){ - message("Using renv profile from `renv/profile` file.") -} else if (renv_profile %in% c("4.1", "4.2", "4.3")) { - message("Set renv profile to `", renv_profile, "`") - Sys.setenv("RENV_PROFILE" = renv_profile) -} else { - message("This repository do not contains the renv profile for your R version.") -} - -if (Sys.getenv("GITHUB_ACTIONS") == "") { +if ((Sys.getenv("GITHUB_ACTIONS") == "") & (Sys.getenv("CODESPACE_NAME") == "")) { + renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") + if (file.exists("./renv/profile")) { + message("Using renv profile from `renv/profile` file.") + } else if (renv_profile %in% c("4.1", "4.2", "4.3")) { + message("Set renv profile to `", renv_profile, "`") + Sys.setenv("RENV_PROFILE" = renv_profile) + } else { + message("This repository do not contains the renv profile for your R version.") + } source("renv/activate.R") } else { options(repos = c(CRAN = "https://cran.rstudio.com")) } - - From 861aa36a946e8909cb210a5387af2cf48d6ba16d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?= <56442075+dgrassellyb@users.noreply.github.com> Date: Tue, 6 Jun 2023 13:31:26 +0200 Subject: [PATCH 097/100] Update .Rprofile --- .Rprofile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rprofile b/.Rprofile index 673ea47a..1c4c4d97 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,5 +1,5 @@ # Set renv profile base on R version. -if ((Sys.getenv("GITHUB_ACTIONS") == "") & (Sys.getenv("CODESPACE_NAME") == "")) { +if ((Sys.getenv("GITHUB_ACTIONS") == "") & (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) { renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") if (file.exists("./renv/profile")) { message("Using renv profile from `renv/profile` file.") From c35b76df41ad4927b9bff3b004228ab42f06bc0a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?= <56442075+dgrassellyb@users.noreply.github.com> Date: Tue, 6 Jun 2023 13:33:21 +0200 Subject: [PATCH 098/100] Update .Rprofile --- .Rprofile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rprofile b/.Rprofile index 1c4c4d97..77ae067e 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,5 +1,5 @@ # Set renv profile base on R version. -if ((Sys.getenv("GITHUB_ACTIONS") == "") & (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) { +if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) { renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".") if (file.exists("./renv/profile")) { message("Using renv profile from `renv/profile` file.") From 370c26758a60d58c325b92c91a70ac1dec72af64 Mon Sep 17 00:00:00 2001 From: cicdguy Date: Tue, 6 Jun 2023 13:50:02 +0000 Subject: [PATCH 099/100] renv update from pharmaverse/admiralci --- renv/profiles/4.1/renv.lock | 2 +- renv/profiles/4.2/renv.lock | 2 +- renv/profiles/4.3/renv.lock | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/renv/profiles/4.1/renv.lock b/renv/profiles/4.1/renv.lock index 2bfb572c..0f3ac2c8 100644 --- a/renv/profiles/4.1/renv.lock +++ b/renv/profiles/4.1/renv.lock @@ -12,7 +12,7 @@ } ] }, - "Packages": { + "Packages": { "DT": { "Package": "DT", "Version": "0.21", diff --git a/renv/profiles/4.2/renv.lock b/renv/profiles/4.2/renv.lock index a3dec833..0bb8fc56 100644 --- a/renv/profiles/4.2/renv.lock +++ b/renv/profiles/4.2/renv.lock @@ -12,7 +12,7 @@ } ] }, - "Packages": { + "Packages": { "DT": { "Package": "DT", "Version": "0.27", diff --git a/renv/profiles/4.3/renv.lock b/renv/profiles/4.3/renv.lock index 691871a8..b875a5b8 100644 --- a/renv/profiles/4.3/renv.lock +++ b/renv/profiles/4.3/renv.lock @@ -12,7 +12,7 @@ } ] }, - "Packages": { + "Packages": { "DT": { "Package": "DT", "Version": "0.27", From 1347b682505b46910518ffbcea36f995878ff183 Mon Sep 17 00:00:00 2001 From: bms63 Date: Tue, 6 Jun 2023 15:29:06 +0000 Subject: [PATCH 100/100] trigger wfs