Try simpler Dockerfile approach

.Rprofile

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

.dockerignore

@@ -1 +0,0 @@
-renv

Dockerfile

@@ -2,17 +2,13 @@ FROM rocker/shiny-verse:latest
 
 WORKDIR /code
 
-# Cache doesn't help for single-use containers (and huggingface
-# spaces don't let us write to renv's default cache path)
-ENV RENV_CONFIG_CACHE_ENABLED=FALSE
+RUN install2.r --ncpus 2 --error \
+    ggExtra \
+    bslib
 
-RUN R --quiet -e "install.packages('renv'); renv::init()"
-
-COPY ./renv.lock /code/renv.lock
-
-RUN R --quiet -e "renv::restore()"
-RUN R --quiet -e "renv::install('rstudio/httpuv@ping')"
-RUN ls
+# RUN installGithub.r \
+#     rstudio/shiny \
+#     rstudio/httpuv@ping
 
 COPY . .
 

prepare.R

@@ -1,24 +0,0 @@
-capitalize <- function(str) {
-  sub("^.", toupper(substr(str, 1, 1)), str)
-}
-
-renamer <- function(name) {
-  parts <- strsplit(name, "_", fixed = TRUE)[[1]]
-  units <- NULL
-  
-  if (length(parts) > 1 && tail(parts, 1) %in% c("mm", "g")) {
-    units <- paste0(" (", tail(parts, 1), ")")
-    parts <- head(parts, -1)
-  }
-  
-  parts <- vapply(parts, capitalize, character(1))
-  paste0(paste(parts, collapse = " "), units)
-}
-
-rename_all <- function(names) {
-  vapply(names, renamer, character(1))
-}
-
-palmerpenguins::penguins |>
-  dplyr::rename_with(rename_all) |>
-  readr::write_csv("penguins.csv")

renv.lock

@@ -1,1181 +0,0 @@
-{
-  "R": {
-    "Version": "4.2.3",
-    "Repositories": [
-      {
-        "Name": "CRAN",
-        "URL": "https://cloud.r-project.org"
-      }
-    ]
-  },
-  "Packages": {
-    "MASS": {
-      "Package": "MASS",
-      "Version": "7.3-58.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "9586b552d57f5516fe4d25398c1bacd6"
-    },
-    "Matrix": {
-      "Package": "Matrix",
-      "Version": "1.5-1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "539dc0c0c05636812f1080f473d2c177"
-    },
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
-    },
-    "RColorBrewer": {
-      "Package": "RColorBrewer",
-      "Version": "1.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
-    },
-    "Rcpp": {
-      "Package": "Rcpp",
-      "Version": "1.0.10",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "methods",
-        "utils"
-      ],
-      "Hash": "e749cae40fa9ef469b6050959517453c"
-    },
-    "askpass": {
-      "Package": "askpass",
-      "Version": "1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "sys"
-      ],
-      "Hash": "e8a22846fff485f0be3770c2da758713"
-    },
-    "base64enc": {
-      "Package": "base64enc",
-      "Version": "0.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "543776ae6848fde2f48ff3816d0628bc"
-    },
-    "bit": {
-      "Package": "bit",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "d242abec29412ce988848d0294b208fd"
-    },
-    "bit64": {
-      "Package": "bit64",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bit",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "9fe98599ca456d6552421db0d6772d8f"
-    },
-    "bslib": {
-      "Package": "bslib",
-      "Version": "0.4.2.9000",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteRepo": "bslib",
-      "RemoteUsername": "rstudio",
-      "RemotePkgRef": "rstudio/bslib",
-      "RemoteRef": "HEAD",
-      "RemoteSha": "4c3073a4bb4d135e21086253592ec857b99daed1",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "cachem",
-        "grDevices",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "memoise",
-        "mime",
-        "rlang",
-        "sass"
-      ],
-      "Hash": "007572b82ef9ce87e65a09e4145de631"
-    },
-    "cachem": {
-      "Package": "cachem",
-      "Version": "1.0.7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "fastmap",
-        "rlang"
-      ],
-      "Hash": "cda74447c42f529de601fe4d4050daef"
-    },
-    "cli": {
-      "Package": "cli",
-      "Version": "3.6.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "89e6d8219950eac806ae0c489052048a"
-    },
-    "clipr": {
-      "Package": "clipr",
-      "Version": "0.8.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
-    },
-    "colorspace": {
-      "Package": "colorspace",
-      "Version": "2.1-0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "stats"
-      ],
-      "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
-    },
-    "colourpicker": {
-      "Package": "colourpicker",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "ggplot2",
-        "htmltools",
-        "htmlwidgets",
-        "jsonlite",
-        "miniUI",
-        "shiny",
-        "shinyjs",
-        "utils"
-      ],
-      "Hash": "ca4d99d106687d68392ffe270081bfc0"
-    },
-    "commonmark": {
-      "Package": "commonmark",
-      "Version": "1.9.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "d691c61bff84bd63c383874d2d0c3307"
-    },
-    "cpp11": {
-      "Package": "cpp11",
-      "Version": "0.4.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "ed588261931ee3be2c700d22e94a29ab"
-    },
-    "crayon": {
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-      "Version": "1.5.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
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-        "methods",
-        "utils"
-      ],
-      "Hash": "e8a1e41acf02548751f45c718d55aa6a"
-    },
-    "curl": {
-      "Package": "curl",
-      "Version": "5.0.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "RemoteType": "standard",
-      "RemotePkgRef": "curl",
-      "RemoteRef": "curl",
-      "RemoteRepos": "https://cloud.r-project.org",
-      "RemotePkgPlatform": "source",
-      "RemoteSha": "5.0.0",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "e4f97056611e8e6b8b852d13b7400cf1"
-    },
-    "digest": {
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-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
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-      ],
-      "Hash": "8b708f296afd9ae69f450f9640be8990"
-    },
-    "dplyr": {
-      "Package": "dplyr",
-      "Version": "1.1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "cli",
-        "generics",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "methods",
-        "pillar",
-        "rlang",
-        "tibble",
-        "tidyselect",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "eb5742d256a0d9306d85ea68756d8187"
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-        "scales",
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-      "RemotePkgRef": "palmerpenguins",
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-      "RemoteRepos": "https://cloud.r-project.org",
-      "RemotePkgPlatform": "source",
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-      "Requirements": [
-        "R"
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-      "Hash": "6c6861efbc13c1d543749e9c7be4a592"
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-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "cli",
-        "fansi",
-        "glue",
-        "lifecycle",
-        "rlang",
-        "utf8",
-        "utils",
-        "vctrs"
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-      "Hash": "15da5a8412f317beeee6175fbc76f4bb"
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-      "Source": "Repository",
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-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R6",
-        "Rcpp",
-        "later",
-        "magrittr",
-        "rlang",
-        "stats"
-      ],
-      "Hash": "4ab2c43adb4d4699cf3690acd378d75d"
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-        "httpuv",
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-        "R",
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-        "R",
-        "bit64",
-        "cli",
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-        "crayon",
-        "glue",
-        "hms",
-        "lifecycle",
-        "methods",
-        "progress",
-        "rlang",
-        "stats",
-        "tibble",
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-        "vctrs",
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-      "Repository": "CRAN",
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-        "R",
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-      "Package": "xfun",
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-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "stats",
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-      "Hash": "1ed71215d45e85562d3b1b29a068ccec"
-    },
-    "xtable": {
-      "Package": "xtable",
-      "Version": "1.8-4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "stats",
-        "utils"
-      ],
-      "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
-    },
-    "yaml": {
-      "Package": "yaml",
-      "Version": "2.3.7",
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-      "Repository": "CRAN",
-      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
-    }
-  }
-}

renv/.gitignore

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

renv/activate.R

@@ -1,1032 +0,0 @@
-
-local({
-
-  # the requested version of renv
-  version <- "0.17.3"
-
-  # the project directory
-  project <- getwd()
-
-  # 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)
-
-    # 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
-
-  })
-
-  if (!enabled)
-    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.environment(x) || length(x)) x else y
-  }
-  
-  `%??%` <- function(x, y) {
-    if (is.null(x)) y else x
-  }
-  
-  bootstrap <- function(version, library) {
-  
-    # attempt to download renv
-    tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
-    if (inherits(tarball, "error"))
-      stop("failed to download renv ", version)
-  
-    # now attempt to install
-    status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity)
-    if (inherits(status, "error"))
-      stop("failed to install renv ", version)
-  
-  }
-  
-  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)
-  
-    # if we're testing, re-use the test repositories
-    if (renv_bootstrap_tests_running()) {
-      repos <- getOption("renv.tests.repos")
-      if (!is.null(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) {
-  
-    # if the renv version number has 4 components, assume it must
-    # be retrieved via github
-    nv <- numeric_version(version)
-    components <- unclass(nv)[[1]]
-  
-    # if this appears to be a development version of 'renv', we'll
-    # try to restore from github
-    dev <- length(components) == 4L
-  
-    # begin collecting different methods for finding renv
-    methods <- c(
-      renv_bootstrap_download_tarball,
-      if (dev)
-        renv_bootstrap_download_github
-      else c(
-        renv_bootstrap_download_cran_latest,
-        renv_bootstrap_download_cran_archive
-      )
-    )
-  
-    for (method in methods) {
-      path <- tryCatch(method(version), error = identity)
-      if (is.character(path) && file.exists(path))
-        return(path)
-    }
-  
-    stop("failed to download renv ", version)
-  
-  }
-  
-  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$repos
-  
-    message("* Downloading renv ", version, " ... ", appendLF = FALSE)
-  
-    baseurl <- utils::contrib.url(repos = repos, type = type)
-    ext <- if (identical(type, "source"))
-      ".tar.gz"
-    else if (Sys.info()[["sysname"]] == "Windows")
-      ".zip"
-    else
-      ".tgz"
-    name <- sprintf("renv_%s%s", version, ext)
-    url <- paste(baseurl, name, sep = "/")
-  
-    destfile <- file.path(tempdir(), name)
-    status <- tryCatch(
-      renv_bootstrap_download_impl(url, destfile),
-      condition = identity
-    )
-  
-    if (inherits(status, "condition")) {
-      message("FAILED")
-      return(FALSE)
-    }
-  
-    # report success and return
-    message("OK (downloaded ", type, ")")
-    destfile
-  
-  }
-  
-  renv_bootstrap_download_cran_latest_find <- function(version) {
-  
-    # check whether binaries are supported on this system
-    binary <-
-      getOption("renv.bootstrap.binary", default = TRUE) &&
-      !identical(.Platform$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)
-  
-    message("* Downloading renv ", version, " ... ", appendLF = FALSE)
-  
-    for (url in urls) {
-  
-      status <- tryCatch(
-        renv_bootstrap_download_impl(url, destfile),
-        condition = identity
-      )
-  
-      if (identical(status, 0L)) {
-        message("OK")
-        return(destfile)
-      }
-  
-    }
-  
-    message("FAILED")
-    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()
-  
-    }
-  
-    fmt <- "* Bootstrapping with tarball at path '%s'."
-    msg <- sprintf(fmt, tarball)
-    message(msg)
-  
-    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)
-    }
-  
-    message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE)
-  
-    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)) {
-      message("FAILED")
-      return(FALSE)
-    }
-  
-    message("OK")
-    return(destfile)
-  
-  }
-  
-  renv_bootstrap_install <- function(version, tarball, library) {
-  
-    # attempt to install it into project library
-    message("* Installing renv ", version, " ... ", appendLF = FALSE)
-    dir.create(library, showWarnings = FALSE, recursive = TRUE)
-  
-    # 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))
-    )
-  
-    output <- system2(r, args, stdout = TRUE, stderr = TRUE)
-    message("Done!")
-  
-    # check for successful install
-    status <- attr(output, "status")
-    if (is.numeric(status) && !identical(status, 0L)) {
-      header <- "Error installing renv:"
-      lines <- paste(rep.int("=", nchar(header)), collapse = "")
-      text <- c(header, lines, output)
-      writeLines(text, con = stderr())
-    }
-  
-    status
-  
-  }
-  
-  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 (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) {
-  
-    loadedversion <- utils::packageDescription("renv", fields = "Version")
-    if (version == loadedversion)
-      return(TRUE)
-  
-    # assume four-component versions are from GitHub;
-    # three-component versions are from CRAN
-    components <- strsplit(loadedversion, "[.-]")[[1]]
-    remote <- if (length(components) == 4L)
-      paste("rstudio/renv", loadedversion, sep = "@")
-    else
-      paste("renv", loadedversion, sep = "@")
-  
-    fmt <- paste(
-      "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.",
-      sep = "\n"
-    )
-  
-    msg <- sprintf(fmt, loadedversion, version, remote)
-    warning(msg, call. = FALSE)
-  
-    FALSE
-  
-  }
-  
-  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 = warning)
-  
-    # 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_json_read <- function(file = NULL, text = NULL) {
-  
-    jlerr <- NULL
-  
-    # if jsonlite is loaded, use that instead
-    if ("jsonlite" %in% loadedNamespaces()) {
-  
-      json <- catch(renv_json_read_jsonlite(file, text))
-      if (!inherits(json, "error"))
-        return(json)
-  
-      jlerr <- json
-  
-    }
-  
-    # otherwise, fall back to the default JSON reader
-    json <- catch(renv_json_read_default(file, text))
-    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 %||% read(file), 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 %||% read(file), 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_remap(json, map)
-  
-    # evaluate
-    eval(remapped, envir = baseenv())
-  
-  }
-  
-  renv_json_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_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)
-
-  # attempt to load
-  if (renv_bootstrap_load(project, libpath, version))
-    return(TRUE)
-
-  # load failed; inform user we're about to bootstrap
-  prefix <- paste("# Bootstrapping renv", version)
-  postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "")
-  header <- paste(prefix, postfix)
-  message(header)
-
-  # 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)) {
-    message("* Successfully installed and loaded renv ", version, ".")
-    return(renv::load())
-  }
-
-  # 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/settings.json

@@ -1,17 +0,0 @@
-{
-  "bioconductor.version": null,
-  "external.libraries": [],
-  "ignored.packages": [],
-  "package.dependency.fields": [
-    "Imports",
-    "Depends",
-    "LinkingTo"
-  ],
-  "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
-}