From d93acd0a55f8629370092ec9e40a20df5c7c127f Mon Sep 17 00:00:00 2001 From: "The Carpentries Apprentice (beta)" <64428345+carpentries-bot@users.noreply.github.com> Date: Tue, 1 Oct 2024 09:23:36 +0100 Subject: [PATCH] [actions] update 13 packages (#99) Co-authored-by: zkamvar --- renv/activate.R | 105 ++++++++++++++++++-- renv/profiles/lesson-requirements/renv.lock | 59 ++++++----- 2 files changed, 125 insertions(+), 39 deletions(-) diff --git a/renv/activate.R b/renv/activate.R index d13f9932..c360bf29 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.7" + version <- "1.0.9" attr(version, "sha") <- NULL # the project directory @@ -98,6 +98,66 @@ local({ unloadNamespace("renv") # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + `%||%` <- function(x, y) { if (is.null(x)) y else x } @@ -142,7 +202,10 @@ local({ # compute common indent indent <- regexpr("[^[:space:]]", lines) common <- min(setdiff(indent, -1L)) - leave - paste(substring(lines, common), collapse = "\n") + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) } @@ -306,7 +369,11 @@ local({ ) if ("headers" %in% names(formals(utils::download.file))) - args$headers <- renv_bootstrap_download_custom_headers(url) + { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } do.call(utils::download.file, args) @@ -385,10 +452,22 @@ local({ for (type in types) { for (repos in renv_bootstrap_repos()) { + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) + { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + # retrieve package database db <- tryCatch( as.data.frame( - utils::available.packages(type = type, repos = repos), + do.call(utils::available.packages, args), stringsAsFactors = FALSE ), error = identity @@ -470,6 +549,14 @@ local({ } + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + renv_bootstrap_download_github <- function(version) { enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") @@ -477,16 +564,16 @@ local({ return(FALSE) # prepare download options - pat <- Sys.getenv("GITHUB_PAT") - if (nzchar(Sys.which("curl")) && nzchar(pat)) { + token <- renv_bootstrap_github_token() + if (nzchar(Sys.which("curl")) && nzchar(token)) { fmt <- "--location --fail --header \"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + extra <- sprintf(fmt, token) saved <- options("download.file.method", "download.file.extra") options(download.file.method = "curl", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) - } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { fmt <- "--header=\"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + extra <- sprintf(fmt, token) saved <- options("download.file.method", "download.file.extra") options(download.file.method = "wget", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index f7c2c129..6f9fa770 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -704,7 +704,7 @@ }, "abind": { "Package": "abind", - "Version": "1.4-5", + "Version": "1.4-8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -712,7 +712,7 @@ "methods", "utils" ], - "Hash": "4f57884290cc75ab22f4af9e9d4ca862" + "Hash": "2288423bb0f20a457800d7fc47f6aa54" }, "askpass": { "Package": "askpass", @@ -777,17 +777,17 @@ }, "bit": { "Package": "bit", - "Version": "4.0.5", + "Version": "4.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "d242abec29412ce988848d0294b208fd" + "Hash": "5dc7b2677d65d0e874fc4aaf0e879987" }, "bit64": { "Package": "bit64", - "Version": "4.0.5", + "Version": "4.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -797,7 +797,7 @@ "stats", "utils" ], - "Hash": "9fe98599ca456d6552421db0d6772d8f" + "Hash": "e84984bf5f12a18628d9a02322128dfd" }, "bitops": { "Package": "bitops", @@ -913,13 +913,13 @@ }, "curl": { "Package": "curl", - "Version": "5.2.2", + "Version": "5.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "8f27335f2bcff4d6035edcc82d7d46de" + "Hash": "d91263322a58af798f6cf3b13fd56dde" }, "dbplyr": { "Package": "dbplyr", @@ -1012,14 +1012,13 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.24.0", + "Version": "1.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "R", - "methods" + "R" ], - "Hash": "a1066cbc05caee9a4bf6d90f194ff4da" + "Hash": "6b567375113ceb7d9f800de4dd42218e" }, "fansi": { "Package": "fansi", @@ -1119,14 +1118,14 @@ }, "glue": { "Package": "glue", - "Version": "1.7.0", + "Version": "1.8.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "e0b3a53876554bd45879e596cdb10a52" + "Hash": "5899f1eaa825580172bb56c08266f37c" }, "highr": { "Package": "highr", @@ -1186,7 +1185,7 @@ }, "httr2": { "Package": "httr2", - "Version": "1.0.3", + "Version": "1.0.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1203,7 +1202,7 @@ "vctrs", "withr" ], - "Hash": "10d93e97faad6b629301bb3a2fd23378" + "Hash": "d84e4c33206aaace37714901ac2b00c3" }, "jquerylib": { "Package": "jquerylib", @@ -1217,13 +1216,13 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.8", + "Version": "1.8.9", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "e1b9c55281c5adc4dd113652d9e26768" + "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" }, "knitr": { "Package": "knitr", @@ -1315,13 +1314,13 @@ }, "matrixStats": { "Package": "matrixStats", - "Version": "1.3.0", + "Version": "1.4.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "4b3ea27a19d669c0405b38134d89a9d1" + "Hash": "8885ffb1f46e820dede6b2ca9442abca" }, "memoise": { "Package": "memoise", @@ -1346,13 +1345,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.2.1", + "Version": "2.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "c62edf62de70cadf40553e10c739049d" + "Hash": "d413e0fef796c9401a4419485f709ca1" }, "org.Hs.eg.db": { "Package": "org.Hs.eg.db", @@ -1471,13 +1470,13 @@ }, "renv": { "Package": "renv", - "Version": "1.0.7", + "Version": "1.0.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "397b7b2a265bc5a7a06852524dabae20" + "Hash": "ef233f0e9064fc88c898b340c9add5c2" }, "restfulr": { "Package": "restfulr", @@ -1497,13 +1496,13 @@ }, "rjson": { "Package": "rjson", - "Version": "0.2.22", + "Version": "0.2.23", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "ff387cabd34002e7e50d2becacb0be76" + "Hash": "7a04e9eff95857dbf557b4e5f0b3d1a8" }, "rlang": { "Package": "rlang", @@ -1699,13 +1698,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.52", + "Version": "0.53", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "cfbad971a71f0e27cec22e544a08bc3b" + "Hash": "9db859e8aabbb474293dde3097839420" }, "utf8": { "Package": "utf8",