diff --git a/.Rprofile b/.Rprofile
deleted file mode 100644
index 81b960f5c6a8ee40840badd620f8af9743787730..0000000000000000000000000000000000000000
--- a/.Rprofile
+++ /dev/null
@@ -1 +0,0 @@
-source("renv/activate.R")
diff --git a/renv.lock b/renv.lock
deleted file mode 100644
index 6bca5370ae38f174346aba6852fb499ac6b21946..0000000000000000000000000000000000000000
--- a/renv.lock
+++ /dev/null
@@ -1,1844 +0,0 @@
-{
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- "URL": "https://ftp.gwdg.de/pub/misc/cran"
- }
- ]
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- "Hash": "47e968dfe563c1b22c2e20a067ec21d5"
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- "Version": "1.6.5",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "bit64",
- "cli",
- "cpp11",
- "crayon",
- "glue",
- "hms",
- "lifecycle",
- "methods",
- "progress",
- "rlang",
- "stats",
- "tibble",
- "tidyselect",
- "tzdb",
- "vctrs",
- "withr"
- ],
- "Hash": "390f9315bc0025be03012054103d227c"
- },
- "withr": {
- "Package": "withr",
- "Version": "3.0.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "grDevices",
- "graphics"
- ],
- "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
- },
- "xfun": {
- "Package": "xfun",
- "Version": "0.44",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "grDevices",
- "stats",
- "tools"
- ],
- "Hash": "317a0538d32f4a009658bcedb7923f4b"
- },
- "xml2": {
- "Package": "xml2",
- "Version": "1.3.6",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "cli",
- "methods",
- "rlang"
- ],
- "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61"
- },
- "xtable": {
- "Package": "xtable",
- "Version": "1.8-4",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "R",
- "stats",
- "utils"
- ],
- "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
- },
- "yaml": {
- "Package": "yaml",
- "Version": "2.3.8",
- "Source": "Repository",
- "Repository": "CRAN",
- "Hash": "29240487a071f535f5e5d5a323b7afbd"
- },
- "zip": {
- "Package": "zip",
- "Version": "2.3.1",
- "Source": "Repository",
- "Repository": "CRAN",
- "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab"
- }
- }
-}
diff --git a/renv/.gitignore b/renv/.gitignore
deleted file mode 100644
index 0ec0cbba2d7755cbd91956afaa585449906a1e16..0000000000000000000000000000000000000000
--- a/renv/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-library/
-local/
-cellar/
-lock/
-python/
-sandbox/
-staging/
diff --git a/renv/activate.R b/renv/activate.R
deleted file mode 100644
index d13f9932a16a92986a514d8cb439662d85db3add..0000000000000000000000000000000000000000
--- a/renv/activate.R
+++ /dev/null
@@ -1,1220 +0,0 @@
-
-local({
-
- # the requested version of renv
- version <- "1.0.7"
- attr(version, "sha") <- NULL
-
- # the project directory
- project <- Sys.getenv("RENV_PROJECT")
- if (!nzchar(project))
- project <- getwd()
-
- # use start-up diagnostics if enabled
- diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
- if (diagnostics) {
- start <- Sys.time()
- profile <- tempfile("renv-startup-", fileext = ".Rprof")
- utils::Rprof(profile)
- on.exit({
- utils::Rprof(NULL)
- elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
- writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
- writeLines(sprintf("- Profile: %s", profile))
- print(utils::summaryRprof(profile))
- }, add = TRUE)
- }
-
- # figure out whether the autoloader is enabled
- enabled <- local({
-
- # first, check config option
- override <- getOption("renv.config.autoloader.enabled")
- if (!is.null(override))
- return(override)
-
- # if we're being run in a context where R_LIBS is already set,
- # don't load -- presumably we're being run as a sub-process and
- # the parent process has already set up library paths for us
- rcmd <- Sys.getenv("R_CMD", unset = NA)
- rlibs <- Sys.getenv("R_LIBS", unset = NA)
- if (!is.na(rlibs) && !is.na(rcmd))
- return(FALSE)
-
- # next, check environment variables
- # TODO: prefer using the configuration one in the future
- envvars <- c(
- "RENV_CONFIG_AUTOLOADER_ENABLED",
- "RENV_AUTOLOADER_ENABLED",
- "RENV_ACTIVATE_PROJECT"
- )
-
- for (envvar in envvars) {
- envval <- Sys.getenv(envvar, unset = NA)
- if (!is.na(envval))
- return(tolower(envval) %in% c("true", "t", "1"))
- }
-
- # enable by default
- TRUE
-
- })
-
- # bail if we're not enabled
- if (!enabled) {
-
- # if we're not enabled, we might still need to manually load
- # the user profile here
- profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
- if (file.exists(profile)) {
- cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
- if (tolower(cfg) %in% c("true", "t", "1"))
- sys.source(profile, envir = globalenv())
- }
-
- return(FALSE)
-
- }
-
- # avoid recursion
- if (identical(getOption("renv.autoloader.running"), TRUE)) {
- warning("ignoring recursive attempt to run renv autoloader")
- return(invisible(TRUE))
- }
-
- # signal that we're loading renv during R startup
- options(renv.autoloader.running = TRUE)
- on.exit(options(renv.autoloader.running = NULL), add = TRUE)
-
- # signal that we've consented to use renv
- options(renv.consent = TRUE)
-
- # load the 'utils' package eagerly -- this ensures that renv shims, which
- # mask 'utils' packages, will come first on the search path
- library(utils, lib.loc = .Library)
-
- # unload renv if it's already been loaded
- if ("renv" %in% loadedNamespaces())
- unloadNamespace("renv")
-
- # load bootstrap tools
- `%||%` <- function(x, y) {
- if (is.null(x)) y else x
- }
-
- catf <- function(fmt, ..., appendLF = TRUE) {
-
- quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
- if (quiet)
- return(invisible())
-
- msg <- sprintf(fmt, ...)
- cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
-
- invisible(msg)
-
- }
-
- header <- function(label,
- ...,
- prefix = "#",
- suffix = "-",
- n = min(getOption("width"), 78))
- {
- label <- sprintf(label, ...)
- n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
- if (n <= 0)
- return(paste(prefix, label))
-
- tail <- paste(rep.int(suffix, n), collapse = "")
- paste0(prefix, " ", label, " ", tail)
-
- }
-
- heredoc <- function(text, leave = 0) {
-
- # remove leading, trailing whitespace
- trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
-
- # split into lines
- lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
-
- # compute common indent
- indent <- regexpr("[^[:space:]]", lines)
- common <- min(setdiff(indent, -1L)) - leave
- paste(substring(lines, common), collapse = "\n")
-
- }
-
- startswith <- function(string, prefix) {
- substring(string, 1, nchar(prefix)) == prefix
- }
-
- bootstrap <- function(version, library) {
-
- friendly <- renv_bootstrap_version_friendly(version)
- section <- header(sprintf("Bootstrapping renv %s", friendly))
- catf(section)
-
- # attempt to download renv
- catf("- Downloading renv ... ", appendLF = FALSE)
- withCallingHandlers(
- tarball <- renv_bootstrap_download(version),
- error = function(err) {
- catf("FAILED")
- stop("failed to download:\n", conditionMessage(err))
- }
- )
- catf("OK")
- on.exit(unlink(tarball), add = TRUE)
-
- # now attempt to install
- catf("- Installing renv ... ", appendLF = FALSE)
- withCallingHandlers(
- status <- renv_bootstrap_install(version, tarball, library),
- error = function(err) {
- catf("FAILED")
- stop("failed to install:\n", conditionMessage(err))
- }
- )
- catf("OK")
-
- # add empty line to break up bootstrapping from normal output
- catf("")
-
- return(invisible())
- }
-
- renv_bootstrap_tests_running <- function() {
- getOption("renv.tests.running", default = FALSE)
- }
-
- renv_bootstrap_repos <- function() {
-
- # get CRAN repository
- cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
-
- # check for repos override
- repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
- if (!is.na(repos)) {
-
- # check for RSPM; if set, use a fallback repository for renv
- rspm <- Sys.getenv("RSPM", unset = NA)
- if (identical(rspm, repos))
- repos <- c(RSPM = rspm, CRAN = cran)
-
- return(repos)
-
- }
-
- # check for lockfile repositories
- repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
- if (!inherits(repos, "error") && length(repos))
- return(repos)
-
- # retrieve current repos
- repos <- getOption("repos")
-
- # ensure @CRAN@ entries are resolved
- repos[repos == "@CRAN@"] <- cran
-
- # 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$Repositories
- if (length(repos) == 0)
- return(NULL)
-
- keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
- vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
- names(vals) <- keys
-
- return(vals)
-
- }
-
- renv_bootstrap_download <- function(version) {
-
- sha <- attr(version, "sha", exact = TRUE)
-
- methods <- if (!is.null(sha)) {
-
- # attempting to bootstrap a development version of renv
- c(
- function() renv_bootstrap_download_tarball(sha),
- function() renv_bootstrap_download_github(sha)
- )
-
- } else {
-
- # attempting to bootstrap a release version of renv
- c(
- function() renv_bootstrap_download_tarball(version),
- function() renv_bootstrap_download_cran_latest(version),
- function() renv_bootstrap_download_cran_archive(version)
- )
-
- }
-
- for (method in methods) {
- path <- tryCatch(method(), error = identity)
- if (is.character(path) && file.exists(path))
- return(path)
- }
-
- stop("All download methods failed")
-
- }
-
- renv_bootstrap_download_impl <- function(url, destfile) {
-
- mode <- "wb"
-
- # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
- fixup <-
- Sys.info()[["sysname"]] == "Windows" &&
- substring(url, 1L, 5L) == "file:"
-
- if (fixup)
- mode <- "w+b"
-
- args <- list(
- url = url,
- destfile = destfile,
- mode = mode,
- quiet = TRUE
- )
-
- if ("headers" %in% names(formals(utils::download.file)))
- args$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
-
- baseurl <- utils::contrib.url(repos = repos, type = type)
- ext <- if (identical(type, "source"))
- ".tar.gz"
- else if (Sys.info()[["sysname"]] == "Windows")
- ".zip"
- else
- ".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"))
- return(FALSE)
-
- # report success and return
- 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$pkgType, "source") &&
- !identical(getOption("pkgType"), "source") &&
- Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
-
- types <- c(if (binary) "binary", "source")
-
- # iterate over types + repositories
- for (type in types) {
- for (repos in renv_bootstrap_repos()) {
-
- # retrieve package database
- db <- tryCatch(
- as.data.frame(
- utils::available.packages(type = type, repos = repos),
- stringsAsFactors = FALSE
- ),
- error = identity
- )
-
- if (inherits(db, "error"))
- next
-
- # check for compatible entry
- entry <- db[db$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)
-
- for (url in urls) {
-
- status <- tryCatch(
- renv_bootstrap_download_impl(url, destfile),
- condition = identity
- )
-
- if (identical(status, 0L))
- return(destfile)
-
- }
-
- 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
- if (dir.exists(tarball)) {
- 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()
-
- }
-
- catf("- Using local tarball '%s'.", tarball)
- 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)) {
- fmt <- "--location --fail --header \"Authorization: token %s\""
- extra <- sprintf(fmt, pat)
- 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)) {
- fmt <- "--header=\"Authorization: token %s\""
- extra <- sprintf(fmt, pat)
- 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)
- }
-
- 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))
- return(FALSE)
-
- renv_bootstrap_download_augment(destfile)
-
- return(destfile)
-
- }
-
- # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
- # can use renv::install() to fully capture metadata.
- renv_bootstrap_download_augment <- function(destfile) {
- sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
- if (is.null(sha)) {
- return()
- }
-
- # Untar
- tempdir <- tempfile("renv-github-")
- on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
- untar(destfile, exdir = tempdir)
- pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
-
- # Modify description
- desc_path <- file.path(pkgdir, "DESCRIPTION")
- desc_lines <- readLines(desc_path)
- remotes_fields <- c(
- "RemoteType: github",
- "RemoteHost: api.github.com",
- "RemoteRepo: renv",
- "RemoteUsername: rstudio",
- "RemotePkgRef: rstudio/renv",
- paste("RemoteRef: ", sha),
- paste("RemoteSha: ", sha)
- )
- writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
-
- # Re-tar
- local({
- old <- setwd(tempdir)
- on.exit(setwd(old), add = TRUE)
-
- tar(destfile, compression = "gzip")
- })
- invisible()
- }
-
- # Extract the commit hash from a git archive. Git archives include the SHA1
- # hash as the comment field of the tarball pax extended header
- # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
- # For GitHub archives this should be the first header after the default one
- # (512 byte) header.
- renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
-
- # open the bundle for reading
- # We use gzcon for everything because (from ?gzcon)
- # > Reading from a connection which does not supply a 'gzip' magic
- # > header is equivalent to reading from the original connection
- conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
- on.exit(close(conn))
-
- # The default pax header is 512 bytes long and the first pax extended header
- # with the comment should be 51 bytes long
- # `52 comment=` (11 chars) + 40 byte SHA1 hash
- len <- 0x200 + 0x33
- res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
-
- if (grepl("^52 comment=", res)) {
- sub("52 comment=", "", res)
- } else {
- NULL
- }
- }
-
- renv_bootstrap_install <- function(version, tarball, library) {
-
- # attempt to install it into project library
- dir.create(library, showWarnings = FALSE, recursive = TRUE)
- output <- renv_bootstrap_install_impl(library, tarball)
-
- # check for successful install
- status <- attr(output, "status")
- if (is.null(status) || identical(status, 0L))
- return(status)
-
- # an error occurred; report it
- header <- "installation of renv failed"
- lines <- paste(rep.int("=", nchar(header)), collapse = "")
- text <- paste(c(header, lines, output), collapse = "\n")
- stop(text)
-
- }
-
- renv_bootstrap_install_impl <- function(library, tarball) {
-
- # 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))
- )
-
- system2(R, args, stdout = TRUE, stderr = TRUE)
-
- }
-
- 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 (is.na(auto) && getRversion() >= "4.4.0")
- auto <- "TRUE"
-
- 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,
- sep = "=",
- quote = c("\"", "'"),
- col.names = c("Key", "Value"),
- 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")) {
- if (field %in% names(vars) && nzchar(vars[[field]])) {
- id <- vars[[field]]
- break
- }
- }
-
- # read version
- version <- "unknown"
- for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
- if (field %in% names(vars) && nzchar(vars[[field]])) {
- version <- vars[[field]]
- 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"
- else if (grepl("redhat", contents, ignore.case = TRUE))
- "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, description = NULL) {
-
- # resolve description file
- #
- # avoid passing lib.loc to `packageDescription()` below, since R will
- # use the loaded version of the package by default anyhow. note that
- # this function should only be called after 'renv' is loaded
- # https://github.com/rstudio/renv/issues/1625
- description <- description %||% packageDescription("renv")
-
- # check whether requested version 'version' matches loaded version of renv
- sha <- attr(version, "sha", exact = TRUE)
- valid <- if (!is.null(sha))
- renv_bootstrap_validate_version_dev(sha, description)
- else
- renv_bootstrap_validate_version_release(version, description)
-
- if (valid)
- return(TRUE)
-
- # the loaded version of renv doesn't match the requested version;
- # give the user instructions on how to proceed
- dev <- identical(description[["RemoteType"]], "github")
- remote <- if (dev)
- paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
- else
- paste("renv", description[["Version"]], sep = "@")
-
- # display both loaded version + sha if available
- friendly <- renv_bootstrap_version_friendly(
- version = description[["Version"]],
- sha = if (dev) description[["RemoteSha"]]
- )
-
- fmt <- heredoc("
- 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.
- ")
- catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
-
- FALSE
-
- }
-
- renv_bootstrap_validate_version_dev <- function(version, description) {
- expected <- description[["RemoteSha"]]
- is.character(expected) && startswith(expected, version)
- }
-
- renv_bootstrap_validate_version_release <- function(version, description) {
- expected <- description[["Version"]]
- is.character(expected) && identical(expected, version)
- }
-
- 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)
-
- # execute renv load hooks, if any
- hooks <- getHook("renv::autoload")
- for (hook in hooks)
- if (is.function(hook))
- tryCatch(hook(), error = warnify)
-
- # 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))
- Sys.unsetenv("RENV_PROFILE")
- 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
- prefix <- if (profile) renv_bootstrap_profile_prefix()
- 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) {
- root <- Sys.getenv(envvar, unset = NA)
- 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")
- else if (Sys.info()[["sysname"]] == "Darwin")
- "~/Library/Caches/org.R-project.R/R/renv"
- else
- "~/.cache/R/renv"
-
- }
-
- renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
- sha <- sha %||% attr(version, "sha", exact = TRUE)
- parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
- paste(parts, collapse = "")
- }
-
- renv_bootstrap_exec <- function(project, libpath, version) {
- if (!renv_bootstrap_load(project, libpath, version))
- renv_bootstrap_run(version, libpath)
- }
-
- renv_bootstrap_run <- function(version, libpath) {
-
- # perform bootstrap
- bootstrap(version, libpath)
-
- # exit early if we're just testing bootstrap
- if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
- return(TRUE)
-
- # try again to load
- if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
- return(renv::load(project = getwd()))
- }
-
- # failed to download or load renv; warn the user
- msg <- c(
- "Failed to find an renv installation: the project will not be loaded.",
- "Use `renv::activate()` to re-initialize the project."
- )
-
- warning(paste(msg, collapse = "\n"), call. = FALSE)
-
- }
-
- renv_json_read <- function(file = NULL, text = NULL) {
-
- jlerr <- NULL
-
- # if jsonlite is loaded, use that instead
- if ("jsonlite" %in% loadedNamespaces()) {
-
- json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
- if (!inherits(json, "error"))
- return(json)
-
- jlerr <- json
-
- }
-
- # otherwise, fall back to the default JSON reader
- json <- tryCatch(renv_json_read_default(file, text), error = identity)
- if (!inherits(json, "error"))
- return(json)
-
- # report an error
- if (!is.null(jlerr))
- stop(jlerr)
- else
- stop(json)
-
- }
-
- renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
- text <- paste(text %||% readLines(file, warn = FALSE), 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 %||% readLines(file, warn = FALSE), 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)
- transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
- 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_read_remap(json, map)
-
- # evaluate
- eval(remapped, envir = baseenv())
-
- }
-
- renv_json_read_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)
- if (text == "true")
- return(TRUE)
- else if (text == "false")
- return(FALSE)
- else if (text == "null")
- return(NULL)
- }
-
- # recurse
- if (is.recursive(json)) {
- for (i in seq_along(json)) {
- json[i] <- list(renv_json_read_remap(json[[i]], map))
- }
- }
-
- json
-
- }
-
- # load the renv profile, if any
- renv_bootstrap_profile_load(project)
-
- # construct path to library root
- root <- renv_bootstrap_library_root(project)
-
- # construct library prefix for platform
- prefix <- renv_bootstrap_platform_prefix()
-
- # construct full libpath
- libpath <- file.path(root, prefix)
-
- # run bootstrap code
- renv_bootstrap_exec(project, libpath, version)
-
- invisible()
-
-})
diff --git a/renv/settings.json b/renv/settings.json
deleted file mode 100644
index ffdbb3200f779343ad1aa1a2fb6c74a02fd9b365..0000000000000000000000000000000000000000
--- a/renv/settings.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "bioconductor.version": null,
- "external.libraries": [],
- "ignored.packages": [],
- "package.dependency.fields": [
- "Imports",
- "Depends",
- "LinkingTo"
- ],
- "ppm.enabled": null,
- "ppm.ignored.urls": [],
- "r.version": null,
- "snapshot.type": "implicit",
- "use.cache": true,
- "vcs.ignore.cellar": true,
- "vcs.ignore.library": true,
- "vcs.ignore.local": true,
- "vcs.manage.ignores": true
-}
diff --git a/workflows/R-renv-docker/Dockerfile b/workflows/R-renv-docker/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..81d77b937131578874af867dfb955fd61788b815
--- /dev/null
+++ b/workflows/R-renv-docker/Dockerfile
@@ -0,0 +1,10 @@
+## Use pre-built base image coming with R and required system libraries
+
+FROM rstudio/r-base:4.3-jammy
+
+## Install package `renv` to Docker image
+RUN R -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))"
+
+## pull in a manifest file and restore it
+COPY renv.lock ./
+RUN R -e 'renv::restore()'
\ No newline at end of file
diff --git a/workflows/R-renv-docker/README.md b/workflows/R-renv-docker/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..358084d201271231cc81aa9ac7db454955003da6
--- /dev/null
+++ b/workflows/R-renv-docker/README.md
@@ -0,0 +1,5 @@
+
+
+## Build docker image
+
+docker build --pull --rm -f "workflows/_R-docker/Dockerfile" -t rdocker-test:latest "workflows/_R-docker"
diff --git a/workflows/R-renv-docker/renv.rmd b/workflows/R-renv-docker/renv.rmd
new file mode 100644
index 0000000000000000000000000000000000000000..63f67b5f04f23f45f0cff16029dd478c9c8c71fd
--- /dev/null
+++ b/workflows/R-renv-docker/renv.rmd
@@ -0,0 +1,25 @@
+---
+title: "Using renv and docker"
+author: "Dominik Brilhaus"
+date: 2024-08-05
+output: html_document
+---
+
+
+```{r}
+install.packages("renv")
+
+renv::init(bare = TRUE)
+renv::status()
+renv::dependencies()
+
+renv::snapshot()
+
+```
+```{r}
+if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
+BiocManager::install(version = "3.19")
+```
+
+