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")'

DESCRIPTION

@@ -26,13 +26,13 @@ Imports:
     rstudioapi,
     tools,
     utils,
+    withr,
     yaml
 Suggests: 
     curl,
     knitr,
     rsconnect (>= 0.8.26),
     testthat (>= 3.1.7),
-    withr,
     xfun
 VignetteBuilder: 
     quarto

NEWS.md

@@ -12,6 +12,8 @@
 
 - `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 (thanks, )
+
 # quarto 1.4.4
 
 - `quarto_preview()` now looks at `quarto preview` log to browse to the correct url when inside RStudio viewer (thanks, @aronatkins, #167).

R/quarto.R

@@ -48,7 +48,13 @@ quarto_version <- function() {
 }
 
 #' @importFrom processx run
-quarto_run <- function(args = character(), quarto_bin = find_quarto(), echo = FALSE, echo_cmd = getOption("quarto.echo_cmd", FALSE), ..., .call = rlang::caller_env()) {
+quarto_run <- function(args = character(), quarto_bin = find_quarto(), echo = FALSE, libpaths = .libPaths(), echo_cmd = getOption("quarto.echo_cmd", FALSE), ..., .call = rlang::caller_env()) {
+  opt_in_libpath <- getOption("quarto.use_libpaths", TRUE)
+  if (isTRUE(opt_in_libpath) && !is.null(libpaths)) {
+    withr::local_envvar(list(
+      R_LIBS = paste(libpaths, collapse = .Platform$path.sep)
+    ))
+  }
   res <- tryCatch(
     {
       processx::run(quarto_bin, args = args, echo = echo, error_on_status = TRUE, echo_cmd = echo_cmd, ...)

R/render.R

@@ -46,6 +46,10 @@
 #'   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
@@ -88,6 +92,7 @@ quarto_render <- function(input = NULL,
                           profile = NULL,
                           quarto_args = NULL,
                           pandoc_args = NULL,
+                          libpaths = .libPaths(),
                           as_job = getOption("quarto.render_as_job", "auto")) {
   # get quarto binary
   quarto_bin <- find_quarto()
@@ -188,7 +193,7 @@ quarto_render <- function(input = NULL,
   }
 
   # 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

@@ -18,6 +18,7 @@ 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)
@@ -57,6 +58,7 @@ 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

@@ -88,3 +88,26 @@ test_that("quarto.quiet options controls echo and overwrite function argument",
     expect_output(quarto_render(qmd, quiet = TRUE))
   })
 })
+
+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)
+
+})

tests/testthat/test-render.R

@@ -48,6 +48,7 @@ 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))