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Merge pull request #16 from LibraryCarpentry/update/packages
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Update 5 packages
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@jt14den
jt14den authored Nov 12, 2024
2 parents db6da0d + 3cbc597 commit 052f4e1
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Showing 2 changed files with 112 additions and 28 deletions.
105 changes: 95 additions & 10 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 <- "1.0.11"
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 @@ -305,8 +368,11 @@ local({
quiet = TRUE
)

if ("headers" %in% names(formals(utils::download.file)))
args$headers <- renv_bootstrap_download_custom_headers(url)
if ("headers" %in% names(formals(utils::download.file))) {
headers <- renv_bootstrap_download_custom_headers(url)
if (length(headers) && is.character(headers))
args$headers <- headers
}

do.call(utils::download.file, args)

Expand Down Expand Up @@ -385,10 +451,21 @@ 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(repos)
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 +547,31 @@ 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
35 changes: 17 additions & 18 deletions renv/profiles/lesson-requirements/renv.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -94,14 +94,13 @@
},
"evaluate": {
"Package": "evaluate",
"Version": "0.24.0",
"Version": "1.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"methods"
"R"
],
"Hash": "a1066cbc05caee9a4bf6d90f194ff4da"
"Hash": "3fd29944b231036ad67c3edb32e02201"
},
"fastmap": {
"Package": "fastmap",
Expand All @@ -124,25 +123,25 @@
},
"fs": {
"Package": "fs",
"Version": "1.6.4",
"Version": "1.6.5",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"methods"
],
"Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
"Hash": "7f48af39fa27711ea5fbd183b399920d"
},
"glue": {
"Package": "glue",
"Version": "1.7.0",
"Version": "1.8.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"methods"
],
"Hash": "e0b3a53876554bd45879e596cdb10a52"
"Hash": "5899f1eaa825580172bb56c08266f37c"
},
"highr": {
"Package": "highr",
Expand Down Expand Up @@ -183,13 +182,13 @@
},
"jsonlite": {
"Package": "jsonlite",
"Version": "1.8.8",
"Version": "1.8.9",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"methods"
],
"Hash": "e1b9c55281c5adc4dd113652d9e26768"
"Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b"
},
"knitr": {
"Package": "knitr",
Expand Down Expand Up @@ -253,13 +252,13 @@
},
"renv": {
"Package": "renv",
"Version": "1.0.7",
"Version": "1.0.11",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"utils"
],
"Hash": "397b7b2a265bc5a7a06852524dabae20"
"Hash": "47623f66b4e80b3b0587bc5d7b309888"
},
"rlang": {
"Package": "rlang",
Expand All @@ -274,7 +273,7 @@
},
"rmarkdown": {
"Package": "rmarkdown",
"Version": "2.28",
"Version": "2.29",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
Expand All @@ -293,7 +292,7 @@
"xfun",
"yaml"
],
"Hash": "062470668513dcda416927085ee9bdc7"
"Hash": "df99277f63d01c34e95e3d2f06a79736"
},
"sass": {
"Package": "sass",
Expand All @@ -311,17 +310,17 @@
},
"tinytex": {
"Package": "tinytex",
"Version": "0.52",
"Version": "0.54",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"xfun"
],
"Hash": "cfbad971a71f0e27cec22e544a08bc3b"
"Hash": "3ec7e3ddcacc2d34a9046941222bf94d"
},
"xfun": {
"Package": "xfun",
"Version": "0.47",
"Version": "0.49",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
Expand All @@ -330,7 +329,7 @@
"stats",
"tools"
],
"Hash": "36ab21660e2d095fef0d83f689e0477c"
"Hash": "8687398773806cfff9401a2feca96298"
},
"yaml": {
"Package": "yaml",
Expand Down

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