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[actions] update 13 packages (#99)
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Co-authored-by: zkamvar <[email protected]>
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@carpentries-bot @zkamvar
carpentries-bot and zkamvar authored Oct 1, 2024
1 parent 9e5bd4f commit d93acd0
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Showing 2 changed files with 125 additions and 39 deletions.
105 changes: 96 additions & 9 deletions renv/activate.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
}
Expand Down Expand Up @@ -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)

}

Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -470,23 +549,31 @@ 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")
if (!identical(enabled, "TRUE"))
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)
Expand Down
59 changes: 29 additions & 30 deletions renv/profiles/lesson-requirements/renv.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -704,15 +704,15 @@
},
"abind": {
"Package": "abind",
"Version": "1.4-5",
"Version": "1.4-8",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"methods",
"utils"
],
"Hash": "4f57884290cc75ab22f4af9e9d4ca862"
"Hash": "2288423bb0f20a457800d7fc47f6aa54"
},
"askpass": {
"Package": "askpass",
Expand Down Expand Up @@ -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": [
Expand All @@ -797,7 +797,7 @@
"stats",
"utils"
],
"Hash": "9fe98599ca456d6552421db0d6772d8f"
"Hash": "e84984bf5f12a18628d9a02322128dfd"
},
"bitops": {
"Package": "bitops",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -1186,7 +1185,7 @@
},
"httr2": {
"Package": "httr2",
"Version": "1.0.3",
"Version": "1.0.5",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
Expand All @@ -1203,7 +1202,7 @@
"vctrs",
"withr"
],
"Hash": "10d93e97faad6b629301bb3a2fd23378"
"Hash": "d84e4c33206aaace37714901ac2b00c3"
},
"jquerylib": {
"Package": "jquerylib",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down

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