Try huggingface deployment

.Rprofile

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

.dockerignore

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

Dockerfile

@@ -0,0 +1,14 @@
+FROM rocker/shiny-verse:latest
+
+WORKDIR /code
+
+RUN R --quiet -e "install.packages('renv'); renv::init()"
+
+COPY ./renv.lock /code/renv.lock
+
+RUN R --quiet -e "renv::restore()"
+RUN ls
+
+COPY . .
+
+CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=7860)"]

renv.lock

@@ -0,0 +1,989 @@
+{
+  "R": {
+    "Version": "4.2.3",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cloud.r-project.org"
+      }
+    ]
+  },
+  "Packages": {
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+      "Repository": "CRAN",
+      "Requirements": [
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+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "9586b552d57f5516fe4d25398c1bacd6"
+    },
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+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "graphics",
+        "grid",
+        "lattice",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "539dc0c0c05636812f1080f473d2c177"
+    },
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+      "Version": "2.5.1",
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+      "Requirements": [
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+      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+    },
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+      "RemoteUsername": "rstudio",
+      "RemotePkgRef": "rstudio/bslib",
+      "RemoteRef": "HEAD",
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+        "htmltools",
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+        "memoise",
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+        "sass"
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+      "Hash": "fe178fc15af80952f546aafedf655b36"
+    },
+    "rstudioapi": {
+      "Package": "rstudioapi",
+      "Version": "0.14",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "690bd2acc42a9166ce34845884459320"
+    },
+    "sass": {
+      "Package": "sass",
+      "Version": "0.4.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R6",
+        "fs",
+        "htmltools",
+        "rappdirs",
+        "rlang"
+      ],
+      "Hash": "2bb4371a4c80115518261866eab6ab11"
+    },
+    "scales": {
+      "Package": "scales",
+      "Version": "1.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "RColorBrewer",
+        "farver",
+        "labeling",
+        "lifecycle",
+        "munsell",
+        "rlang",
+        "viridisLite"
+      ],
+      "Hash": "906cb23d2f1c5680b8ce439b44c6fa63"
+    },
+    "shiny": {
+      "Package": "shiny",
+      "Version": "1.7.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "bslib",
+        "cachem",
+        "commonmark",
+        "crayon",
+        "ellipsis",
+        "fastmap",
+        "fontawesome",
+        "glue",
+        "grDevices",
+        "htmltools",
+        "httpuv",
+        "jsonlite",
+        "later",
+        "lifecycle",
+        "methods",
+        "mime",
+        "promises",
+        "rlang",
+        "sourcetools",
+        "tools",
+        "utils",
+        "withr",
+        "xtable"
+      ],
+      "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5"
+    },
+    "sourcetools": {
+      "Package": "sourcetools",
+      "Version": "0.1.7-1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5f5a7629f956619d519205ec475fe647"
+    },
+    "sys": {
+      "Package": "sys",
+      "Version": "3.4.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "34c16f1ef796057bfa06d3f4ff818a5d"
+    },
+    "tibble": {
+      "Package": "tibble",
+      "Version": "3.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "fansi",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "pillar",
+        "pkgconfig",
+        "rlang",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
+    },
+    "tidyselect": {
+      "Package": "tidyselect",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "rlang",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "79540e5fcd9e0435af547d885f184fd5"
+    },
+    "tzdb": {
+      "Package": "tzdb",
+      "Version": "0.3.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cpp11"
+      ],
+      "Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e"
+    },
+    "utf8": {
+      "Package": "utf8",
+      "Version": "1.2.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "1fe17157424bb09c48a8b3b550c753bc"
+    },
+    "vctrs": {
+      "Package": "vctrs",
+      "Version": "0.6.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "rlang"
+      ],
+      "Hash": "06eceb3a5d716fd0654cc23ca3d71a99"
+    },
+    "viridisLite": {
+      "Package": "viridisLite",
+      "Version": "0.4.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "62f4b5da3e08d8e5bcba6cac15603f70"
+    },
+    "vroom": {
+      "Package": "vroom",
+      "Version": "1.6.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bit64",
+        "cli",
+        "cpp11",
+        "crayon",
+        "glue",
+        "hms",
+        "lifecycle",
+        "methods",
+        "progress",
+        "rlang",
+        "stats",
+        "tibble",
+        "tidyselect",
+        "tzdb",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "7015a74373b83ffaef64023f4a0f5033"
+    },
+    "withr": {
+      "Package": "withr",
+      "Version": "2.5.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "stats"
+      ],
+      "Hash": "c0e49a9760983e81e55cdd9be92e7182"
+    },
+    "xtable": {
+      "Package": "xtable",
+      "Version": "1.8-4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats",
+        "utils"
+      ],
+      "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+    }
+  }
+}

renv/.gitignore

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

renv/activate.R

@@ -0,0 +1,1032 @@
+
+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

@@ -0,0 +1,17 @@
+{
+  "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
+}