updating Dockerfile

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

Dockerfile

@@ -1,9 +1,33 @@
 FROM rocker/shiny:latest
 
-RUN R -e "install.packages(c('leaflet', 'sf', 'dplyr', 'ggplot2', 'arrow', 'scales', 'viridisLite', 'bslib'), repos='https://cran.rstudio.com/')"
+# system dependencies
+RUN apt-get update && apt-get install -y \
+    libgdal-dev \
+    libgeos-dev \
+    libproj-dev \
+    libssl-dev \
+    libcurl4-openssl-dev \
+    libxml2-dev \
+    && rm -rf /var/lib/apt/lists/*
 
-COPY . /srv/shiny-server/
+# R packages — add everything your app uses
+RUN R -e "install.packages(c(
+  'shiny', 'dplyr', 'readr', 'ggplot2',
+  'leaflet', 'sf', 'viridisLite', 'scales',
+  'zoo', 'shinydashboard'
+), repos='https://cran.rstudio.com/')"
 
-EXPOSE 3838
+# copy app files
+COPY app.R /srv/shiny-server/
+COPY brt_projections_by_rock/ /srv/shiny-server/brt_projections_by_rock/
+COPY shp/ /srv/shiny-server/shp/
 
-CMD ["/usr/bin/shiny-server"]
+# Hugging Face runs as non-root user 1000 — needs write permission
+RUN chown -R 1000:1000 /srv/shiny-server/ \
+    && chmod -R 755 /srv/shiny-server/
+
+# Hugging Face expects port 7860
+EXPOSE 7860
+
+# override default shiny port to 7860
+CMD ["R", "-e", "shiny::runApp('/srv/shiny-server/app.R', host='0.0.0.0', port=7860)"]

renv/.gitignore

@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/

renv/activate.R

@@ -0,0 +1,1438 @@
+
+local({
+
+  # the requested version of renv
+  version <- "1.2.0"
+  attr(version, "md5") <- "b7d230b07507f361d3bcf794d157a188"
+  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
+    # 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   
+  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;;x-r-help:\\1\a?\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # runnable code
+    pattern <- "`(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;x-r-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
+  }
+  
+  catf <- function(fmt, ..., appendLF = TRUE) {
+  
+    quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
+    if (quiet)
+      return(invisible())
+  
+    # also check for config environment variables that should suppress messages
+    # https://github.com/rstudio/renv/issues/2214
+    enabled <- Sys.getenv("RENV_CONFIG_STARTUP_QUIET", unset = NA)
+    if (!is.na(enabled) && tolower(enabled) %in% c("true", "1"))
+      return(invisible())
+  
+    enabled <- Sys.getenv("RENV_CONFIG_SYNCHRONIZED_CHECK", unset = NA)
+    if (!is.na(enabled) && tolower(enabled) %in% c("false", "0"))
+      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
+    text <- paste(substring(lines, common), collapse = "\n")
+  
+    # substitute in ANSI links for executable renv code
+    ansify(text)
+  
+  }
+  
+  bootstrap <- function(version, library) {
+  
+    friendly <- renv_bootstrap_version_friendly(version)
+    section <- header(sprintf("Bootstrapping renv %s", friendly))
+    catf(section)
+  
+    # ensure the target library path exists; required for file.copy(..., recursive = TRUE)
+    dir.create(library, showWarnings = FALSE, recursive = TRUE)
+  
+    # try to install renv from cache
+    md5 <- attr(version, "md5", exact = TRUE)
+    if (length(md5)) {
+      pkgpath <- renv_bootstrap_find(version)
+      if (length(pkgpath) && file.exists(pkgpath)) {
+        ok <- file.copy(pkgpath, library, recursive = TRUE)
+        if (isTRUE(ok))
+          return(invisible())
+      }
+    }
+  
+    # 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)) {
+  
+      # split on ';' if present
+      parts <- strsplit(repos, ";", fixed = TRUE)[[1L]]
+  
+      # split into named repositories if present
+      idx <- regexpr("=", parts, fixed = TRUE)
+      keys <- substring(parts, 1L, idx - 1L)
+      vals <- substring(parts, idx + 1L)
+      names(vals) <- keys
+  
+      # if we have a single unnamed repository, call it CRAN
+      if (length(vals) == 1L && identical(keys, ""))
+        names(vals) <- "CRAN"
+  
+      return(vals)
+  
+    }
+  
+    # 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$Repositories
+    if (length(repos) == 0)
+      return(NULL)
+  
+    keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
+    vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
+    names(vals) <- keys
+  
+    return(vals)
+  
+  }
+  
+  renv_bootstrap_download <- function(version) {
+  
+    sha <- attr(version, "sha", exact = TRUE)
+  
+    methods <- if (!is.null(sha)) {
+  
+      # attempting to bootstrap a development version of renv
+      c(
+        function() renv_bootstrap_download_tarball(sha),
+        function() renv_bootstrap_download_github(sha)
+      )
+  
+    } else {
+  
+      # attempting to bootstrap a release version of renv
+      c(
+        function() renv_bootstrap_download_tarball(version),
+        function() renv_bootstrap_download_cran_latest(version),
+        function() renv_bootstrap_download_cran_archive(version)
+      )
+  
+    }
+  
+    for (method in methods) {
+      path <- tryCatch(method(), error = identity)
+      if (is.character(path) && file.exists(path))
+        return(path)
+    }
+  
+    stop("All download methods failed")
+  
+  }
+  
+  renv_bootstrap_download_impl <- function(url, destfile) {
+  
+    mode <- "wb"
+  
+    # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+    fixup <-
+      Sys.info()[["sysname"]] == "Windows" &&
+      substring(url, 1L, 5L) == "file:"
+  
+    if (fixup)
+      mode <- "w+b"
+  
+    args <- list(
+      url      = url,
+      destfile = destfile,
+      mode     = mode,
+      quiet    = TRUE
+    )
+  
+    if ("headers" %in% names(formals(utils::download.file))) {
+      headers <- renv_bootstrap_download_custom_headers(url)
+      if (length(headers) && is.character(headers))
+        args$headers <- headers
+    }
+  
+    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$pkgType, "source") &&
+      !identical(getOption("pkgType"), "source") &&
+      Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
+  
+    types <- c(if (binary) "binary", "source")
+  
+    # iterate over types + repositories
+    for (type in types) {
+      for (repos in renv_bootstrap_repos()) {
+  
+        # build arguments for utils::available.packages() call
+        args <- list(type = type, repos = repos)
+  
+        # add custom headers if available -- note that
+        # utils::available.packages() will pass this to download.file()
+        if ("headers" %in% names(formals(utils::download.file))) {
+          headers <- renv_bootstrap_download_custom_headers(repos)
+          if (length(headers) && is.character(headers))
+            args$headers <- headers
+        }
+  
+        # retrieve package database
+        db <- tryCatch(
+          as.data.frame(
+            do.call(utils::available.packages, args),
+            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_find <- function(version) {
+  
+    path <- renv_bootstrap_find_cache(version)
+    if (length(path) && file.exists(path)) {
+      catf("- Using renv %s from global package cache", version)
+      return(path)
+    }
+  
+  }
+  
+  renv_bootstrap_find_cache <- function(version) {
+  
+    md5 <- attr(version, "md5", exact = TRUE)
+    if (is.null(md5))
+      return()
+  
+    # infer path to renv cache
+    cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "")
+    if (!nzchar(cache)) {
+      root <- Sys.getenv("RENV_PATHS_ROOT", unset = NA)
+      if (!is.na(root))
+        cache <- file.path(root, "cache")
+    }
+  
+    if (!nzchar(cache)) {
+      tools <- asNamespace("tools")
+      if (is.function(tools$R_user_dir)) {
+        root <- tools$R_user_dir("renv", "cache")
+        cache <- file.path(root, "cache")
+      }
+    }
+  
+    # start completing path to cache
+    file.path(
+      cache,
+      renv_bootstrap_cache_version(),
+      renv_bootstrap_platform_prefix(),
+      "renv",
+      version,
+      md5,
+      "renv"
+    )
+  
+  }
+  
+  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_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
+    token <- renv_bootstrap_github_token()
+    if (is.null(token))
+      token <- ""
+  
+    if (nzchar(Sys.which("curl")) && nzchar(token)) {
+      fmt <- "--location --fail --header \"Authorization: token %s\""
+      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(token)) {
+      fmt <- "--header=\"Authorization: token %s\""
+      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)
+    }
+  
+    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_default <- function() {
+  
+    # read version component
+    version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v")
+  
+    # expand placeholders
+    placeholders <- list(
+      list("%v", format(getRversion()[1, 1:2])),
+      list("%V", format(getRversion()[1, 1:3]))
+    )
+  
+    for (placeholder in placeholders)
+      version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE)
+  
+    # 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)
+      version <- paste(version, R.version[["svn rev"]], sep = "-r")
+  
+    version
+  
+  }
+  
+  renv_bootstrap_platform_prefix <- function() {
+  
+    # construct version prefix
+    version <- renv_bootstrap_platform_prefix_default()
+  
+    # build list of path components
+    components <- c(version, 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"]]
+    if (!is.character(expected))
+      return(FALSE)
+  
+    pattern <- sprintf("^\\Q%s\\E", version)
+    grepl(pattern, expected, perl = TRUE)
+  
+  }
+  
+  renv_bootstrap_validate_version_release <- function(version, description) {
+    expected <- description[["Version"]]
+    is.character(expected) && identical(c(expected), c(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(project, libpath, version)
+  }
+  
+  renv_bootstrap_run <- function(project, libpath, version) {
+    tryCatch(
+      renv_bootstrap_run_impl(project, libpath, version),
+      error = function(e) {
+        msg <- paste(
+          "failed to bootstrap renv: the project will not be loaded.",
+          paste("Reason:", conditionMessage(e)),
+          "Use `renv::activate()` to re-initialize the project.",
+          sep = "\n"
+        )
+        warning(msg, call. = FALSE)
+      }
+    )
+  }
+  
+  renv_bootstrap_run_impl <- function(project, libpath, version) {
+  
+    # 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 = project))
+    }
+  
+    # 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_bootstrap_cache_version <- function() {
+    # NOTE: users should normally not override the cache version;
+    # this is provided just to make testing easier
+    Sys.getenv("RENV_CACHE_VERSION", unset = "v5")
+  }
+  
+  renv_bootstrap_cache_version_previous <- function() {
+    version <- renv_bootstrap_cache_version()
+    number <- as.integer(substring(version, 2L))
+    paste("v", number - 1L, sep = "")
+  }
+  
+  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_patterns <- function() {
+  
+    list(
+  
+      # objects
+      list("{", "\t\n\tobject(\t\n\t", TRUE),
+      list("}", "\t\n\t)\t\n\t",       TRUE),
+  
+      # arrays
+      list("[", "\t\n\tarray(\t\n\t", TRUE),
+      list("]", "\n\t\n)\n\t\n",      TRUE),
+  
+      # maps
+      list(":", "\t\n\t=\t\n\t", TRUE),
+  
+      # newlines
+      list("\\u000a", "\n", FALSE)
+  
+    )
+  
+  }
+  
+  renv_json_read_envir <- function() {
+  
+    envir <- new.env(parent = emptyenv())
+  
+    envir[["+"]] <- `+`
+    envir[["-"]] <- `-`
+  
+    envir[["object"]] <- function(...) {
+      result <- list(...)
+      names(result) <- as.character(names(result))
+      result
+    }
+  
+    envir[["array"]] <- list
+  
+    envir[["true"]]  <- TRUE
+    envir[["false"]] <- FALSE
+    envir[["null"]]  <- NULL
+  
+    envir
+  
+  }
+  
+  renv_json_read_remap <- function(object, patterns) {
+  
+    # repair names if necessary
+    if (!is.null(names(object))) {
+  
+      nms <- names(object)
+      for (pattern in patterns)
+        nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE)
+      names(object) <- nms
+  
+    }
+  
+    # repair strings if necessary
+    if (is.character(object)) {
+      for (pattern in patterns)
+        object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE)
+    }
+  
+    # recurse for other objects
+    if (is.recursive(object))
+      for (i in seq_along(object))
+        object[i] <- list(renv_json_read_remap(object[[i]], patterns))
+  
+    # return remapped object
+    object
+  
+  }
+  
+  renv_json_read_default <- function(file = NULL, text = NULL) {
+  
+    # read json text
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+  
+    # convert into something the R parser will understand
+    patterns <- renv_json_read_patterns()
+    transformed <- text
+    for (pattern in patterns)
+      transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE)
+  
+    # parse it
+    rfile <- tempfile("renv-json-", fileext = ".R")
+    on.exit(unlink(rfile), add = TRUE)
+    writeLines(transformed, con = rfile)
+    json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]]
+  
+    # evaluate in safe environment
+    result <- eval(json, envir = renv_json_read_envir())
+  
+    # fix up strings if necessary -- do so only with reversible patterns
+    patterns <- Filter(function(pattern) pattern[[3L]], patterns)
+    renv_json_read_remap(result, patterns)
+  
+  }
+  
+
+  # 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()
+
+})

renv/settings.json

@@ -0,0 +1,20 @@
+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.dev": false,
+  "snapshot.type": "implicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}