Pass .libPaths() as R_LIBS to quarto subprocess

.github/workflows/R-CMD-check.yaml

@@ -72,6 +72,8 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        env:
+          QUARTO_R_QUIET: FALSE
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

NEWS.md

@@ -29,6 +29,8 @@
 
 - `QUARTO_R_QUIET` environment variable can be used to set `quarto.quiet` option, which overrides any `quiet = TRUE` argument passed to `quarto_*` functions. This can be useful to debug Quarto rendering inside other packages, like **pkgdown**. Overrides will also now happens for [GHA debug logging](https://docs.github.com/en/actions/monitoring-and-troubleshooting-workflows/troubleshooting-workflows/enabling-debug-logging).
 
+- `.libPaths()` from the calling R session will now be passed by default to all call to quarto as a subprocess. This should solve issue with **pkgdown** or when building vignettes
+
 - Correctly report Quarto CLI error when background process call to `quarto` fails (thanks, @salim-b, [#235](https://github.com/quarto-dev/quarto-r/issues/235))
 
 # quarto 1.4.4

R/quarto.R

@@ -124,16 +124,37 @@ quarto_run <- function(
   args = character(),
   quarto_bin = find_quarto(),
   echo = FALSE,
+  libpaths = .libPaths(),
   echo_cmd = getOption("quarto.echo_cmd", FALSE),
   ...,
   .call = rlang::caller_env()
 ) {
+  # To store any environment variables to pass to the process
+  custom_env <- NULL
+
+  # handle session .libpaths() for background session
+  # It needs to be passed if .libPaths() was modified in the current R session
+  # (e.g. to install dev package in a temporary library)
+  opt_in_libpath <- getOption("quarto.use_libpaths", TRUE)
+  if (isTRUE(opt_in_libpath) && !is.null(libpaths)) {
+    custom_env <- c(
+      custom_env,
+      R_LIBS = paste(libpaths, collapse = .Platform$path.sep)
+    )
+  }
+
   # This is required due to a bug in QUARTO CLI, fixed only in 1.8+
   # https://github.com/quarto-dev/quarto-cli/pull/12887
-  custom_env <- NULL
   if (!quarto_available(min = "1.8.13")) {
-    custom_env <- c("current", QUARTO_R = R.home("bin"))
+    custom_env <- c(custom_env, QUARTO_R = R.home("bin"))
+  }
+
+  # This is required because `"current"` only is not supported by processx
+  # FIXME: https://github.com/r-lib/processx/issues/399
+  if (!is.null(custom_env)) {
+    custom_env <- c("current", custom_env)
   }
+
   res <- tryCatch(
     {
       processx::run(

R/render.R

@@ -52,6 +52,10 @@
 #'   advanced usage and useful for CLI arguments which are not yet mirrored in a
 #'   dedicated parameter of this \R function. See `quarto render --help` for options.
 #' @param pandoc_args Additional command line arguments to pass on to Pandoc.
+#' @param libpaths A character vector of library paths to use for the R session run by Quarto.
+#'   If `NULL`, no library paths will be pass to quarto subprocess and defaults R one will be used.
+#'   Setting `options(quarto.use_libpaths = FALSE)` will disable this behavior and
+#'   never pass library paths to quarto subprocess.
 #' @param as_job Render as an RStudio background job. Default is `"auto"`,
 #'   which will render individual documents normally and projects as
 #'   background jobs. Use the `quarto.render_as_job` \R option to control
@@ -93,6 +97,7 @@ quarto_render <- function(
   profile = NULL,
   quarto_args = NULL,
   pandoc_args = NULL,
+  libpaths = .libPaths(),
   as_job = getOption("quarto.render_as_job", "auto")
 ) {
   # get quarto binary
@@ -203,7 +208,7 @@ quarto_render <- function(
   }
 
   # run quarto
-  quarto_run(args, echo = TRUE, quarto_bin = quarto_bin)
+  quarto_run(args, echo = TRUE, quarto_bin = quarto_bin, libpaths = libpaths)
 
   # no return value
   invisible(NULL)

tests/testthat/test-quarto-args.R

@@ -24,6 +24,7 @@ test_that("create quiete arg", {
 })
 
 test_that("quarto.quiet options takes over", {
+  withr::local_envvar(list(QUARTO_R_QUIET = NA))
   expect_identical(is_quiet(TRUE), TRUE)
   expect_identical(is_quiet(FALSE), FALSE)
   expect_identical(is_quiet(NA), FALSE)
@@ -63,6 +64,7 @@ test_that("QUARTO_R_QUIET options takes over", {
 })
 
 test_that("quarto.quiet options takes over QUARTO_R_QUIET", {
+  withr::local_envvar(list(QUARTO_R_QUIET = NA))
   withr::with_options(list(quarto.quiet = TRUE), {
     withr::with_envvar(list(QUARTO_R_QUIET = FALSE), {
       expect_identical(is_quiet(TRUE), TRUE)

tests/testthat/test-quarto.R

@@ -123,6 +123,28 @@ test_that("quarto.quiet options controls echo and overwrite function argument",
   })
 })
 
+test_that("quarto sees same libpaths as main process", {
+  skip_if_no_quarto()
+  skip_on_cran()
+  qmd <- local_qmd_file(c("```{r}", "#| echo: false", ".libPaths()", "```"))
+  tmp_lib <- withr::local_tempdir("tmp_libpath")
+  withr::local_libpaths(tmp_lib, action = "prefix")
+  withr::local_dir(dirname(qmd))
+  out <- "out.md"
+  # .libPaths() is known in Quarto render
+  out <- .render_and_read(qmd, output_format = "gfm")
+  expect_match(out, basename(tmp_lib), all = FALSE, fixed = TRUE)
+  # Opting-out globally
+  withr::with_options(
+    list(quarto.use_libpaths = FALSE),
+    out <- .render_and_read(qmd, output_format = "gfm")
+  )
+  expect_no_match(out, basename(tmp_lib), fixed = TRUE)
+  # Opting-out at command
+  out <- .render_and_read(qmd, output_format = "gfm", libpaths = NULL)
+  expect_no_match(out, basename(tmp_lib), fixed = TRUE)
+})
+
 test_that("quarto_available()", {
   expect_error(
     quarto_available("1.5", "1.4"),

tests/testthat/test-render.R

@@ -54,6 +54,7 @@ test_that("metadata-file and metadata are merged in quarto_render", {
 
 test_that("quarto_args in quarto_render", {
   skip_if_no_quarto()
+  withr::local_envvar(list(QUARTO_R_QUIET = NA))
   qmd <- local_qmd_file(c("content"))
   local_quarto_run_echo_cmd()
   withr::local_dir(dirname(qmd))