From f52960eae8f504d8467d71fa2c8515e018fb648a Mon Sep 17 00:00:00 2001 From: "The Carpentries Apprentice (beta)" <64428345+carpentries-bot@users.noreply.github.com> Date: Tue, 8 Oct 2024 11:39:38 +0100 Subject: [PATCH] [actions] update 22 packages (#39) Co-authored-by: Athanasiamo --- renv/activate.R | 105 ++++++++++++++++++-- renv/profiles/lesson-requirements/renv.lock | 89 +++++++++-------- 2 files changed, 142 insertions(+), 52 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 e5f2af72..153852dc 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -112,19 +112,19 @@ }, "bit": { "Package": "bit", - "Version": "4.0.5", + "Version": "4.5.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "d242abec29412ce988848d0294b208fd" + "Hash": "5dc7b2677d65d0e874fc4aaf0e879987" }, "bit64": { "Package": "bit64", - "Version": "4.0.5", + "Version": "4.5.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "bit", @@ -132,7 +132,7 @@ "stats", "utils" ], - "Hash": "9fe98599ca456d6552421db0d6772d8f" + "Hash": "e84984bf5f12a18628d9a02322128dfd" }, "blob": { "Package": "blob", @@ -148,7 +148,7 @@ }, "broom": { "Package": "broom", - "Version": "1.0.6", + "Version": "1.0.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -164,7 +164,7 @@ "tibble", "tidyr" ], - "Hash": "a4652c36d1f8abfc3ddf4774f768c934" + "Hash": "8fcc818f3b9887aebaf206f141437cc9" }, "bslib": { "Package": "bslib", @@ -274,13 +274,13 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.4.7", + "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "5a295d7d963cc5035284dcdbaf334f4e" + "Hash": "91570bba75d0c9d3f1040c835cee8fba" }, "crayon": { "Package": "crayon", @@ -296,24 +296,24 @@ }, "curl": { "Package": "curl", - "Version": "5.2.1", + "Version": "5.2.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "411ca2c03b1ce5f548345d2fc2685f7a" + "Hash": "d91263322a58af798f6cf3b13fd56dde" }, "data.table": { "Package": "data.table", - "Version": "1.15.4", + "Version": "1.16.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e" + "Hash": "fb24e05d4a91d8b1c7ff8e284bde834a" }, "dbplyr": { "Package": "dbplyr", @@ -345,14 +345,14 @@ }, "digest": { "Package": "digest", - "Version": "0.6.36", + "Version": "0.6.37", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "fd6824ad91ede64151e93af67df6376b" + "Hash": "33698c4b3127fc9f506654607fb73676" }, "dplyr": { "Package": "dplyr", @@ -398,14 +398,13 @@ }, "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", @@ -532,14 +531,14 @@ }, "glue": { "Package": "glue", - "Version": "1.7.0", + "Version": "1.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "e0b3a53876554bd45879e596cdb10a52" + "Hash": "5899f1eaa825580172bb56c08266f37c" }, "googledrive": { "Package": "googledrive", @@ -720,13 +719,13 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.8", + "Version": "1.8.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "e1b9c55281c5adc4dd113652d9e26768" + "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" }, "knitr": { "Package": "knitr", @@ -875,7 +874,7 @@ }, "nlme": { "Package": "nlme", - "Version": "3.1-165", + "Version": "3.1-166", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -885,17 +884,17 @@ "stats", "utils" ], - "Hash": "2769a88be217841b1f33ed469675c3cc" + "Hash": "ccbb8846be320b627e6aa2b4616a2ded" }, "openssl": { "Package": "openssl", - "Version": "2.2.0", + "Version": "2.2.2", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e" + "Hash": "d413e0fef796c9401a4419485f709ca1" }, "palmerpenguins": { "Package": "palmerpenguins", @@ -973,14 +972,14 @@ }, "ps": { "Package": "ps", - "Version": "1.7.7", + "Version": "1.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "878b467580097e9c383acbb16adab57a" + "Hash": "4b9c8485b0c7eecdf0a9ba5132a45576" }, "purrr": { "Package": "purrr", @@ -999,14 +998,17 @@ }, "ragg": { "Package": "ragg", - "Version": "1.3.2", + "Version": "1.3.3", "Source": "Repository", - "Repository": "RSPM", + "Repository": "https://carpentries.r-universe.dev", + "RemoteUrl": "https://github.com/r-lib/ragg", + "RemoteRef": "v1.3.3", + "RemoteSha": "6f2279ae8cd0e0d7e9d0e1ede2b742666f9f1d49", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "e3087db406e079a8a2fd87f413918ed3" + "Hash": "0595fe5e47357111f29ad19101c7d271" }, "rappdirs": { "Package": "rappdirs", @@ -1075,13 +1077,13 @@ }, "renv": { "Package": "renv", - "Version": "1.0.7", + "Version": "1.0.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "397b7b2a265bc5a7a06852524dabae20" + "Hash": "ef233f0e9064fc88c898b340c9add5c2" }, "reprex": { "Package": "reprex", @@ -1118,7 +1120,7 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.27", + "Version": "2.28", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1137,7 +1139,7 @@ "xfun", "yaml" ], - "Hash": "27f9502e1cdbfa195f94e03b0f517484" + "Hash": "062470668513dcda416927085ee9bdc7" }, "rstudioapi": { "Package": "rstudioapi", @@ -1385,13 +1387,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.52", + "Version": "0.53", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "cfbad971a71f0e27cec22e544a08bc3b" + "Hash": "9db859e8aabbb474293dde3097839420" }, "tzdb": { "Package": "tzdb", @@ -1488,15 +1490,16 @@ }, "xfun": { "Package": "xfun", - "Version": "0.46", + "Version": "0.47", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "grDevices", "stats", "tools" ], - "Hash": "00ce32f398db0415dde61abfef11300c" + "Hash": "36ab21660e2d095fef0d83f689e0477c" }, "xml2": { "Package": "xml2",