renv

README.Rmd

@@ -15,7 +15,6 @@ knitr::opts_chunk$set(
 
 # balselr
 
-This package is under construction. If you want to run NCD1 or NCD2, please use this [other repo](https://github.com/bbitarello/NCD-Statistics) for now. 
 
 <!-- badges: start -->
 ![](images/balselr2.png){width=40% height=40%}

README.md

@@ -3,10 +3,6 @@
 
 # balselr
 
-This package is under construction. If you want to run NCD1 or NCD2,
-please use this [other
-repo](https://github.com/bbitarello/NCD-Statistics) for now.
-
 <!-- badges: start -->
 
 <img src="images/balselr2.png" style="width:40.0%;height:40.0%" />

renv.lock

@@ -534,13 +534,8 @@
  },
  "renv": {
  "Package": "renv",
- "Version": "1.0.0",
- "Source": "Repository",
- "Repository": "CRAN",
- "Requirements": [
- "utils"
- ],
- "Hash": "c321cd99d56443dbffd1c9e673c0c1a2"
+ "Version": "1.0.4",
+ "Source": "Repository"
  },
  "rlang": {
  "Package": "rlang",

renv/activate.R

@@ -2,12 +2,27 @@
 local({
 
  # the requested version of renv
- version <- "1.0.0"
+ version <- "1.0.4"
  attr(version, "sha") <- NULL
 
  # the project directory
  project <- getwd()
 
+ # use start-up diagnostics if enabled
+ diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+ if (diagnostics) {
+ start <- Sys.time()
+ profile <- tempfile("renv-startup-", fileext = ".Rprof")
+ utils::Rprof(profile)
+ on.exit({
+ utils::Rprof(NULL)
+ elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+ writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+ writeLines(sprintf("- Profile: %s", profile))
+ print(utils::summaryRprof(profile))
+ }, add = TRUE)
+ }
+
  # figure out whether the autoloader is enabled
  enabled <- local({
 
@@ -16,6 +31,14 @@ local({
  if (!is.null(override))
  return(override)
 
+ # if we're being run in a context where R_LIBS is already set,
+ # don't load -- presumably we're being run as a sub-process and
+ # the parent process has already set up library paths for us
+ rcmd <- Sys.getenv("R_CMD", unset = NA)
+ rlibs <- Sys.getenv("R_LIBS", unset = NA)
+ if (!is.na(rlibs) && !is.na(rcmd))
+ return(FALSE)
+
  # next, check environment variables
  # TODO: prefer using the configuration one in the future
  envvars <- c(
@@ -35,9 +58,22 @@ local({
 
  })
 
- if (!enabled)
+ # bail if we're not enabled
+ if (!enabled) {
+
+ # if we're not enabled, we might still need to manually load
+ # the user profile here
+ profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+ if (file.exists(profile)) {
+ cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+ if (tolower(cfg) %in% c("true", "t", "1"))
+ sys.source(profile, envir = globalenv())
+ }
+
  return(FALSE)
 
+ }
+
  # avoid recursion
  if (identical(getOption("renv.autoloader.running"), TRUE)) {
  warning("ignoring recursive attempt to run renv autoloader")
@@ -504,7 +540,7 @@ local({
 
  # open the bundle for reading
  # We use gzcon for everything because (from ?gzcon)
- # > Reading from a connection which does not supply a ‘gzip’ magic
+ # > Reading from a connection which does not supply a 'gzip' magic
  # > header is equivalent to reading from the original connection
  conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
  on.exit(close(conn))
@@ -767,10 +803,12 @@ local({
  renv_bootstrap_validate_version <- function(version, description = NULL) {
 
  # resolve description file
- description <- description %||% {
- path <- getNamespaceInfo("renv", "path")
- packageDescription("renv", lib.loc = dirname(path))
- }
+ #
+ # avoid passing lib.loc to `packageDescription()` below, since R will
+ # use the loaded version of the package by default anyhow. note that
+ # this function should only be called after 'renv' is loaded
+ # https://github.com/rstudio/renv/issues/1625
+ description <- description %||% packageDescription("renv")
 
  # check whether requested version 'version' matches loaded version of renv
  sha <- attr(version, "sha", exact = TRUE)
@@ -841,7 +879,7 @@ local({
  hooks <- getHook("renv::autoload")
  for (hook in hooks)
  if (is.function(hook))
- tryCatch(hook(), error = warning)
+ tryCatch(hook(), error = warnify)
 
  # load the project
  renv::load(project)
@@ -982,10 +1020,15 @@ local({
 
  }
 
- renv_bootstrap_version_friendly <- function(version, sha = NULL) {
+ renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
  sha <- sha %||% attr(version, "sha", exact = TRUE)
- parts <- c(version, sprintf("[sha: %s]", substring(sha, 1L, 7L)))
- paste(parts, collapse = " ")
+ parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+ paste(parts, collapse = "")
+ }
+
+ renv_bootstrap_exec <- function(project, libpath, version) {
+ if (!renv_bootstrap_load(project, libpath, version))
+ renv_bootstrap_run(version, libpath)
  }
 
  renv_bootstrap_run <- function(version, libpath) {
@@ -1012,19 +1055,14 @@ local({
 
  }
 
-
- renv_bootstrap_in_rstudio <- function() {
- commandArgs()[[1]] == "RStudio"
- }
-
  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))
+ json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
  if (!inherits(json, "error"))
  return(json)
 
@@ -1033,7 +1071,7 @@ local({
  }
 
  # otherwise, fall back to the default JSON reader
- json <- catch(renv_json_read_default(file, text))
+ json <- tryCatch(renv_json_read_default(file, text), error = identity)
  if (!inherits(json, "error"))
  return(json)
 
@@ -1046,14 +1084,14 @@ local({
  }
 
  renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
- text <- paste(text %||% read(file), collapse = "\n")
+ text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
  jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
  }
 
  renv_json_read_default <- function(file = NULL, text = NULL) {
 
  # find strings in the JSON
- text <- paste(text %||% read(file), collapse = "\n")
+ text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
  pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
  locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
 
@@ -1101,14 +1139,14 @@ local({
  map <- as.list(map)
 
  # remap strings in object
- remapped <- renv_json_remap(json, map)
+ remapped <- renv_json_read_remap(json, map)
 
  # evaluate
  eval(remapped, envir = baseenv())
 
  }
 
- renv_json_remap <- function(json, map) {
+ renv_json_read_remap <- function(json, map) {
 
  # fix names
  if (!is.null(names(json))) {
@@ -1135,7 +1173,7 @@ local({
  # recurse
  if (is.recursive(json)) {
  for (i in seq_along(json)) {
- json[i] <- list(renv_json_remap(json[[i]], map))
+ json[i] <- list(renv_json_read_remap(json[[i]], map))
  }
  }
 
@@ -1155,26 +1193,8 @@ local({
  # construct full libpath
  libpath <- file.path(root, prefix)
 
- # attempt to load
- if (renv_bootstrap_load(project, libpath, version))
- return(TRUE)
-
- if (renv_bootstrap_in_rstudio()) {
- setHook("rstudio.sessionInit", function(...) {
- renv_bootstrap_run(version, libpath)
-
- # Work around buglet in RStudio if hook uses readline
- tryCatch(
- {
- tools <- as.environment("tools:rstudio")
- tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE)
- },
- error = function(cnd) {}
- )
- })
- } else {
- renv_bootstrap_run(version, libpath)
- }
+ # run bootstrap code
+ renv_bootstrap_exec(project, libpath, version)
 
  invisible()