first commit

.Rprofile

+source("renv/activate.R")

.batchtools.conf.R

+cluster.functions <- makeClusterFunctionsSlurm(template = "batchtools.slurm.tmpl")

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

_targets.R

+library(targets)
+library(future)
+library(future.batchtools)
+library(tidyverse)
+
+# Example from https://github.com/ropensci/targets/discussions/432
+
+plan(strategy = batchtools_slurm, template = "batchtools.slurm.tmpl")
+tar_option_set(resources = list(ncpus = 2, walltime = 60))
+
+list(
+  tar_target(the_data, tibble(mtcars)),
+  tar_target(model_it, lm(mpg ~ cyl, data = the_data)),
+  tar_target(figure, ggplot(data = the_data) + geom_point(aes(x = cyl, y = mpg)))
+)

batchtools.slurm.tmpl

+#!/bin/bash
+
+## Job Resource Interface Definition
+##
+## ntasks [integer(1)]:       Number of required tasks,
+##                            Set larger than 1 if you want to further parallelize
+##                            with MPI within your job.
+## cpus-per-task [integer(1)]: Number of required cpus per task,
+##                            Set larger than 1 if you want to further parallelize
+##                            with multicore/parallel within each task.
+## walltime [integer(1)]:     Set a limit on the total run time of the job allocation.
+##                            Must be at least 60 seconds.
+## memory   [integer(1)]:     Memory in megabytes required per node.
+##
+## Default resources can be set in your .batchtools.conf.R by defining the variable
+## 'default.resources' as a named list.
+
+cd /home/users/aginolhac/targets_test
+
+<%
+# relative paths are not handled well by Slurm
+log.file = fs::path_expand(log.file)
+-%>
+
+#SBATCH --job-name=<%= job.name %>
+#SBATCH --output=<%= log.file %>
+#SBATCH --error=<%= log.file %>
+#SBATCH --time=<%= ceiling(resources$walltime / 60) %>
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=<%= resources$ncpus %>
+#SBATCH --mem=<%= resources$memory %>
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=<%= resources$user_email %>
+#SBATCH --verbose
+<%= if (!is.null(resources$partition)) sprintf(paste0("#SBATCH --partition='", resources$partition, "'")) %>
+<%= if (array.jobs) sprintf("#SBATCH --array=1-%i", nrow(jobs)) else "" %>
+
+
+## Export value of DEBUGME environemnt var to slave
+export DEBUGME=<%= Sys.getenv("DEBUGME") %>
+
+## Run R:
+## we merge R output with stdout from SLURM, which gets then logged via --output option
+Rscript -e 'batchtools::doJobCollection("<%= uri %>")'

renv/.gitignore

+library/
+local/
+lock/
+python/
+staging/

renv/activate.R

+
+local({
+
+  # the requested version of renv
+  version <- "0.13.2"
+
+  # the project directory
+  project <- getwd()
+
+  # avoid recursion
+  if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA)))
+    return(invisible(TRUE))
+
+  # signal that we're loading renv during R startup
+  Sys.setenv("RENV_R_INITIALIZING" = "true")
+  on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), 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)
+
+  # check to see if renv has already been loaded
+  if ("renv" %in% loadedNamespaces()) {
+
+    # if renv has already been loaded, and it's the requested version of renv,
+    # nothing to do
+    spec <- .getNamespaceInfo(.getNamespace("renv"), "spec")
+    if (identical(spec[["version"]], version))
+      return(invisible(TRUE))
+
+    # otherwise, unload and attempt to load the correct version of renv
+    unloadNamespace("renv")
+
+  }
+
+  # load bootstrap tools   
+  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() {
+  
+    # check for repos override
+    repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+    if (!is.na(repos))
+      return(repos)
+  
+    # if we're testing, re-use the test repositories
+    if (renv_bootstrap_tests_running())
+      return(getOption("renv.tests.repos"))
+  
+    # retrieve current repos
+    repos <- getOption("repos")
+  
+    # ensure @CRAN@ entries are resolved
+    repos[repos == "@CRAN@"] <- getOption(
+      "renv.repos.cran",
+      "https://cloud.r-project.org"
+    )
+  
+    # 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_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]]
+  
+    methods <- if (length(components) == 4L) {
+      list(
+        renv_bootstrap_download_github
+      )
+    } else {
+      list(
+        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"
+  
+    utils::download.file(
+      url      = url,
+      destfile = destfile,
+      mode     = mode,
+      quiet    = TRUE
+    )
+  
+  }
+  
+  renv_bootstrap_download_cran_latest <- function(version) {
+  
+    spec <- renv_bootstrap_download_cran_latest_find(version)
+  
+    message("* Downloading renv ", version, " ... ", appendLF = FALSE)
+  
+    type  <- spec$type
+    repos <- spec$repos
+  
+    info <- tryCatch(
+      utils::download.packages(
+        pkgs    = "renv",
+        destdir = tempdir(),
+        repos   = repos,
+        type    = type,
+        quiet   = TRUE
+      ),
+      condition = identity
+    )
+  
+    if (inherits(info, "condition")) {
+      message("FAILED")
+      return(FALSE)
+    }
+  
+    # report success and return
+    message("OK (downloaded ", type, ")")
+    info[1, 2]
+  
+  }
+  
+  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_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", "-l", shQuote(library), shQuote(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) {
+  
+    path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+    if (!is.na(path))
+      return(path)
+  
+    path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+    if (!is.na(path)) {
+      name <- renv_bootstrap_library_root_name(project)
+      return(file.path(path, name))
+    }
+  
+    prefix <- renv_bootstrap_profile_prefix()
+    paste(c(project, prefix, "renv/library"), collapse = "/")
+  
+  }
+  
+  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)