Pass .libPaths() as R_LIBS to quarto subprocess

Author: cderv

DESCRIPTION

@@ -30,6 +30,7 @@ Imports:
     rstudioapi,
     tools,
     utils,
+    withr,
     xfun,
     yaml (>= 2.3.10)
 Suggests: 
@@ -53,8 +54,7 @@ Suggests:
     thematic,
     tidyverse,
     tinytable,
-    whoami,
-    withr
+    whoami
 VignetteBuilder: 
     quarto
 Config/testthat/edition: 3

NEWS.md

@@ -1,5 +1,7 @@
 # quarto (development version)
 
+- `.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 1.5.1
 
 - Make sure tests pass on CRAN checks even when Quarto is not installed by adding a gihub action to test when no quarto is available. Also fix tests that were

R/quarto.R

@@ -128,6 +128,7 @@ quarto_run <- function(
   args = character(),
   quarto_bin = find_quarto(),
   echo = FALSE,
+  libpaths = .libPaths(),
   echo_cmd = getOption("quarto.echo_cmd", FALSE),
   ...,
   .call = rlang::caller_env()
@@ -138,6 +139,12 @@ quarto_run <- function(
   if (!quarto_available(min = "1.8.13")) {
     custom_env <- c("current", QUARTO_R = R.home("bin"))
   }
+  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 <- withCallingHandlers(
     processx::run(
       quarto_bin,

R/render.R

@@ -51,6 +51,10 @@
 #'   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
@@ -95,6 +99,7 @@ quarto_render <- function(
   profile = NULL,
   quarto_args = NULL,
   pandoc_args = NULL,
+  libpaths = .libPaths(),
   as_job = getOption("quarto.render_as_job", "auto")
 ) {
   # get quarto binary
@@ -222,7 +227,7 @@ 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)

man/quarto_render.Rd

@@ -157,3 +157,26 @@ test_that("quarto_available()", {
     regexp = "Minimum version expected is 1.9.5"
   )
 })
+
+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
+  quarto_render(qmd, output_format = "gfm", output_file = out, quiet = TRUE)
+  expect_match(readLines(out), basename(tmp_lib), all = FALSE, fixed = TRUE)
+  # Opting-out globally
+  withr::with_options(
+    list(quarto.use_libpaths = FALSE), 
+    quarto_render(qmd, output_format = "gfm", output_file = out, quiet = TRUE)
+  )
+  expect_no_match(readLines(out), basename(tmp_lib), fixed = TRUE)
+  # Opting-out at command
+  quarto_render(qmd, output_format = "gfm", output_file = out, quiet = TRUE, libpaths = NULL)
+  expect_no_match(readLines(out), basename(tmp_lib), fixed = TRUE)
+
+})