From 4d1f41b7689c04ef57918778ac94d33d55e0f4cb Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 11:22:01 -0700
Subject: [PATCH 01/21] refactor cargo-processx functions

---
 R/clean.R               |  55 ++++++-------
 R/license_note.R        | 167 ++++++++++++++++++++++++++--------------
 R/read_cargo_metadata.R |  31 +++++---
 R/use_crate.R           |  45 ++++++-----
 4 files changed, 176 insertions(+), 122 deletions(-)

diff --git a/R/clean.R b/R/clean.R
index d59c475a..a3e21864 100644
--- a/R/clean.R
+++ b/R/clean.R
@@ -5,8 +5,19 @@
 #' (found by default at `pkg_root/src/rust/target/`).
 #' Useful when Rust code should be recompiled from scratch.
 #' @param path \[ string \] Path to the package root.
+#' @param echo logical scalar, should cargo command and outputs be printed to
+#' console (default is TRUE)
+#'
 #' @export
-clean <- function(path = ".") {
+#'
+#' @examples
+#' \dontrun{
+#' clean()
+#' }
+clean <- function(path = ".", echo = TRUE) {
+  check_string(path, class = "rextendr_error")
+  check_bool(echo, class = "rextendr_error")
+
   root <- rprojroot::find_package_root_file(path = path)
 
   rust_folder <- normalizePath(
@@ -15,7 +26,7 @@ clean <- function(path = ".") {
     mustWork = FALSE
   )
 
-  toml_path <- normalizePath(
+  manifest_path <- normalizePath(
     file.path(rust_folder, "Cargo.toml"),
     winslash = "/",
     mustWork = FALSE
@@ -28,7 +39,7 @@ clean <- function(path = ".") {
     mustWork = FALSE
   )
 
-  if (!file.exists(toml_path)) {
+  if (!file.exists(manifest_path)) {
     cli::cli_abort(c(
       "Unable to clean binaries.",
       "!" = "{.file Cargo.toml} not found in {.path {rust_folder}}.",
@@ -36,44 +47,26 @@ clean <- function(path = ".") {
     ))
   }
 
-  cargo_envvars <- get_cargo_envvars()
-
   args <- c(
     "clean",
-    glue("--manifest-path={toml_path}"),
-    glue("--target-dir={target_dir}"),
+    glue::glue("--manifest-path={manifest_path}"),
+    glue::glue("--target-dir={target_dir}"),
     if (tty_has_colors()) {
       "--color=always"
     } else {
       "--color=never"
-    },
-    "--quiet"
+    }
   )
-  exec_result <- processx::run(
+
+  out <- processx::run(
     command = "cargo",
     args = args,
-    echo_cmd = FALSE,
-    windows_verbatim_args = FALSE,
-    stderr = "|",
-    stdout = "|",
-    error_on_status = FALSE,
-    env = cargo_envvars
+    error_on_status = TRUE,
+    wd = rust_folder,
+    echo_cmd = echo,
+    echo = echo,
+    env = get_cargo_envvars()
   )
 
-  if (!isTRUE(exec_result$status == 0)) {
-    if (!tty_has_colors()) {
-      err_msg <- cli::ansi_strip(exec_result$stderr)
-    } else {
-      err_msg <- exec_result$stderr
-    }
-    cli::cli_abort(
-      c(
-        "Unable to execute {.code cargo clean}.",
-        "x" = paste(err_msg, collapse = "\n")
-      ),
-      call = caller_env(),
-      class = "rextendr_error"
-    )
-  }
   pkgbuild::clean_dll(path = root)
 }
diff --git a/R/license_note.R b/R/license_note.R
index d3c19b00..e52da7f5 100644
--- a/R/license_note.R
+++ b/R/license_note.R
@@ -1,92 +1,141 @@
 #' Generate LICENSE.note file.
 #'
-#' LICENSE.note generated by this function contains information about Rust crate dependencies.
-#' To use this function, the [cargo-license](https://crates.io/crates/cargo-license) command must be installed.
-#' @param force Logical indicating whether to regenerate LICENSE.note if LICENSE.note already exists.
-#' @inheritParams register_extendr
+#' LICENSE.note generated by this function contains information about Rust crate
+#' dependencies. To use this function, the
+#' [cargo-license](https://crates.io/crates/cargo-license) command must be
+#' installed.
+#'
+#' @param path character scalar, the R package directory
+#' @param echo logical scalar, whether to print cargo command and outputs to the
+#' console (default is `TRUE`)
+#' @param quiet logical scalar, whether to signal successful writing of
+#' LICENSE.note (default is `FALSE`)
+#' @param force logical scalar, whether to regenerate LICENSE.note if
+#' LICENSE.note already exists (default is `TRUE`)
+#'
 #' @return No return value, called for side effects.
+#'
 #' @export
-write_license_note <- function(path = ".", quiet = FALSE, force = TRUE) {
+#'
+#' @examples
+#' \dontrun{
+#' write_license_note()
+#' }
+write_license_note <- function(
+    path = ".",
+    echo = TRUE,
+    quiet = FALSE,
+    force = TRUE) {
+  check_string(path, class = "rextendr_error")
+  check_bool(echo, class = "rextendr_error")
+  check_bool(force, class = "rextendr_error")
+
   if (!cargo_command_available(c("license", "--help"))) {
     cli::cli_abort(
       c(
-        "The {.code cargo license} command is required to run the {.fun write_license_note} function.",
-        "*" = "Please install cargo-license ({.url https://crates.io/crates/cargo-license}) first.",
+        "The {.code cargo license} command is required \\
+        to run the {.fun write_license_note} function.",
+        "*" = "Please install cargo-license \\
+        ({.url https://crates.io/crates/cargo-license}) first.",
         i = "Run {.code cargo install cargo-license} from your terminal."
       ),
       class = "rextendr_error"
     )
   }
 
-  manifest_file <- rprojroot::find_package_root_file("src", "rust", "Cargo.toml", path = path)
-  outfile <- rprojroot::find_package_root_file("LICENSE.note", path = path)
+  rust_folder <- rprojroot::find_package_root_file(
+    "src", "rust",
+    path = path
+  )
+
+  manifest_path <- normalizePath(
+    file.path(rust_folder, "Cargo.toml"),
+    winslash = "/",
+    mustWork = FALSE
+  )
 
-  if (!isTRUE(force) && file.exists(outfile)) {
+  outfile <- rprojroot::find_package_root_file(
+    "LICENSE.note",
+    path = path
+  )
+
+  if (isFALSE(force) && file.exists(outfile)) {
     cli::cli_abort(
       c(
         "LICENSE.note already exists.",
-        "If you want to regenerate LICENSE.note, set `force = TRUE` to {.fun write_license_note}."
+        "If you want to regenerate LICENSE.note, \\
+        set `force = TRUE` to {.fun write_license_note}."
       ),
       class = "rextendr_error"
     )
   }
 
-  list_license <- processx::run(
-    "cargo",
-    c(
-      "license",
-      "--authors",
-      "--json",
-      "--avoid-build-deps",
-      "--avoid-dev-deps",
-      "--manifest-path", manifest_file
-    )
-  )$stdout %>%
-    jsonlite::parse_json()
-
-  package_names <- processx::run(
-    "cargo",
-    c(
-      "metadata",
-      "--no-deps",
-      "--format-version", "1",
-      "--manifest-path", manifest_file
-    )
-  )$stdout %>%
-    jsonlite::parse_json() %>%
-    purrr::pluck("packages") %>%
-    purrr::map_chr("name")
+  args <- c(
+    "license",
+    "--authors",
+    "--json",
+    "--avoid-build-deps",
+    "--avoid-dev-deps",
+    "--manifest-path", manifest_path
+  )
+
+  out <- processx::run(
+    command = "cargo",
+    args = args,
+    error_on_status = TRUE,
+    wd = rust_folder,
+    echo_cmd = echo,
+    echo = echo,
+    env = get_cargo_envvars()
+  )
+
+  licenses <- jsonlite::parse_json(
+    out[["stdout"]],
+    simplifyDataFrame = TRUE
+  )
+
+  metadata <- read_cargo_metadata(path = path)
+
+  package_names <- metadata[["packages"]][["dependencies"]][[1]][["name"]]
+
+  licenses <- licenses[licenses[["name"]] %in% package_names, ]
 
   .prep_authors <- function(authors, package) {
-    ifelse(!is.null(authors), authors, paste0(package, " authors")) %>%
-      stringi::stri_replace_all_regex(r"(\ <.+?>)", "") %>%
-      stringi::stri_replace_all_regex(r"(\|)", ", ")
+    authors <- ifelse(
+      is.na(authors),
+      paste0(package, " authors"),
+      authors
+    )
+
+    authors <- stringi::stri_replace_all_regex(authors, r"(\ <.+?>)", "")
+
+    stringi::stri_replace_all_regex(authors, r"(\|)", ", ")
   }
 
   separator <- "-------------------------------------------------------------"
 
-  note_header <- paste0(
-    "The binary compiled from the source code of this package contains the following Rust crates:\n",
-    "\n",
-    "\n",
-    separator
+  note_header <- glue::glue(
+    "
+    The binary compiled from the source code of this package \\
+    contains the following Rust crates:
+
+
+    {separator}
+    "
   )
 
-  note_body <- list_license %>%
-    purrr::discard(function(x) x$name %in% package_names) %>%
-    purrr::map_chr(
-      function(x) {
-        paste0(
-          "\n",
-          "Name:        ", x$name, "\n",
-          "Repository:  ", x$repository, "\n",
-          "Authors:     ", .prep_authors(x$authors, x$name), "\n",
-          "License:     ", x$license, "\n",
-          "\n",
-          separator
-        )
-      }
-    )
+  note_body <- glue::glue_data(
+    licenses,
+    "
+
+    Name:        {name}
+    Repository:  {repository}
+    Authors:     {.prep_authors(authors, name)}
+    License:     {license}
+
+    {separator}
+    "
+  )
 
   write_file(
     text = c(note_header, note_body),
diff --git a/R/read_cargo_metadata.R b/R/read_cargo_metadata.R
index 4e314c3d..43817d02 100644
--- a/R/read_cargo_metadata.R
+++ b/R/read_cargo_metadata.R
@@ -1,6 +1,8 @@
 #' Retrieve metadata for packages and workspaces
 #'
 #' @param path character scalar, the R package directory
+#' @param echo logical scalar, should cargo command and outputs be printed to
+#' console (default is TRUE)
 #'
 #' @details
 #' For more details, see
@@ -25,22 +27,29 @@
 #' read_cargo_metadata()
 #' }
 #'
-read_cargo_metadata <- function(path = ".") {
+read_cargo_metadata <- function(path = ".", echo = TRUE) {
   check_string(path, class = "rextendr_error")
+  check_bool(echo, class = "rextendr_error")
 
-  root <- rprojroot::find_package_root_file(path = path)
-
-  rust_folder <- normalizePath(
-    file.path(root, "src", "rust"),
-    winslash = "/",
-    mustWork = FALSE
+  rust_folder <- rprojroot::find_package_root_file(
+    "src", "rust",
+    path = path
   )
 
+  args <- c("metadata", "--format-version=1", "--no-deps")
+
   out <- processx::run(
-    "cargo",
-    args = c("metadata", "--format-version=1", "--no-deps"),
-    wd = rust_folder
+    command = "cargo",
+    args = args,
+    error_on_status = TRUE,
+    wd = rust_folder,
+    echo_cmd = echo,
+    echo = echo,
+    env = get_cargo_envvars()
   )
 
-  jsonlite::fromJSON(out[["stdout"]])
+  jsonlite::parse_json(
+    out[["stdout"]],
+    simplifyDataFrame = TRUE
+  )
 }
diff --git a/R/use_crate.R b/R/use_crate.R
index 66496a7c..5cf287ea 100644
--- a/R/use_crate.R
+++ b/R/use_crate.R
@@ -10,6 +10,8 @@
 #' @param optional boolean scalar, whether to mark the dependency as optional
 #' (FALSE by default)
 #' @param path character scalar, the package directory
+#' @param echo logical scalar, should cargo command and outputs be printed to
+#' console (default is TRUE)
 #'
 #' @details
 #' For more details regarding these and other options, see the
@@ -43,14 +45,15 @@ use_crate <- function(
     git = NULL,
     version = NULL,
     optional = FALSE,
-    path = ".") {
-  # check args
-  check_string(crate)
-  check_character(features, allow_null = TRUE)
-  check_string(git, allow_null = TRUE)
-  check_string(version, allow_null = TRUE)
-  check_bool(optional)
-  check_string(path)
+    path = ".",
+    echo = TRUE) {
+  check_string(crate, class = "rextendr_error")
+  check_character(features, allow_null = TRUE, class = "rextendr_error")
+  check_string(git, allow_null = TRUE, class = "rextendr_error")
+  check_string(version, allow_null = TRUE, class = "rextendr_error")
+  check_bool(optional, class = "rextendr_error")
+  check_string(path, class = "rextendr_error")
+  check_bool(echo, class = "rextendr_error")
 
   if (!is.null(version) && !is.null(git)) {
     cli::cli_abort(
@@ -80,21 +83,21 @@ use_crate <- function(
     optional <- NULL
   }
 
-  # get rust directory in project folder
-  root <- rprojroot::find_package_root_file(path = path)
-
-  rust_folder <- normalizePath(
-    file.path(root, "src", "rust"),
-    winslash = "/",
-    mustWork = FALSE
+  rust_folder <- rprojroot::find_package_root_file(
+    "src", "rust",
+    path = path
   )
 
-  # run the commmand
-  processx::run(
-    "cargo",
-    c("add", crate, features, git, optional),
-    echo_cmd = TRUE,
-    wd = rust_folder
+  args <- c("add", crate, features, git, optional)
+
+  out <- processx::run(
+    command = "cargo",
+    args = args,
+    error_on_status = TRUE,
+    wd = rust_folder,
+    echo_cmd = echo,
+    echo = echo,
+    env = get_cargo_envvars()
   )
 
   invisible()

From d930a476c7aa862ebcd23386ab8ed8c2ac2a658d Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 15:17:50 -0700
Subject: [PATCH 02/21] set display color option

---
 R/read_cargo_metadata.R | 16 ++++++++++++++--
 R/use_crate.R           | 13 ++++++++++++-
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/R/read_cargo_metadata.R b/R/read_cargo_metadata.R
index 43817d02..d6b7744a 100644
--- a/R/read_cargo_metadata.R
+++ b/R/read_cargo_metadata.R
@@ -27,7 +27,10 @@
 #' read_cargo_metadata()
 #' }
 #'
-read_cargo_metadata <- function(path = ".", echo = TRUE) {
+read_cargo_metadata <- function(
+    path = ".",
+    dependencies = FALSE,
+    echo = TRUE) {
   check_string(path, class = "rextendr_error")
   check_bool(echo, class = "rextendr_error")
 
@@ -36,7 +39,16 @@ read_cargo_metadata <- function(path = ".", echo = TRUE) {
     path = path
   )
 
-  args <- c("metadata", "--format-version=1", "--no-deps")
+  args <- c(
+    "metadata",
+    "--format-version=1",
+    "--no-deps",
+    if (tty_has_colors()) {
+      "--color=always"
+    } else {
+      "--color=never"
+    }
+  )
 
   out <- processx::run(
     command = "cargo",
diff --git a/R/use_crate.R b/R/use_crate.R
index 5cf287ea..97f9657b 100644
--- a/R/use_crate.R
+++ b/R/use_crate.R
@@ -88,7 +88,18 @@ use_crate <- function(
     path = path
   )
 
-  args <- c("add", crate, features, git, optional)
+  args <- c(
+    "add",
+    crate,
+    features,
+    git,
+    optional,
+    if (tty_has_colors()) {
+      "--color=always"
+    } else {
+      "--color=never"
+    }
+  )
 
   out <- processx::run(
     command = "cargo",

From c985f030c9e61497072aaeffc6b9b932bdc544b2 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 15:21:12 -0700
Subject: [PATCH 03/21] make --no-deps optional in read_cargo_metadata

---
 R/read_cargo_metadata.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/read_cargo_metadata.R b/R/read_cargo_metadata.R
index d6b7744a..af0c9d3f 100644
--- a/R/read_cargo_metadata.R
+++ b/R/read_cargo_metadata.R
@@ -1,6 +1,8 @@
 #' Retrieve metadata for packages and workspaces
 #'
 #' @param path character scalar, the R package directory
+#' @param dependencies logical scalar, whether to include all recursive
+#' dependencies in stdout (default is FALSE)
 #' @param echo logical scalar, should cargo command and outputs be printed to
 #' console (default is TRUE)
 #'
@@ -32,6 +34,7 @@ read_cargo_metadata <- function(
     dependencies = FALSE,
     echo = TRUE) {
   check_string(path, class = "rextendr_error")
+  check_bool(dependencies, class = "rextendr_error")
   check_bool(echo, class = "rextendr_error")
 
   rust_folder <- rprojroot::find_package_root_file(
@@ -42,7 +45,9 @@ read_cargo_metadata <- function(
   args <- c(
     "metadata",
     "--format-version=1",
-    "--no-deps",
+    if (isFALSE(dependencies)) {
+      "--no-deps"
+    },
     if (tty_has_colors()) {
       "--color=always"
     } else {

From b38534a58e83a7859603e573d0e687efedae829d Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 15:48:56 -0700
Subject: [PATCH 04/21] fix lintr issues

---
 R/clean.R     | 2 +-
 R/use_crate.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/clean.R b/R/clean.R
index a3e21864..ba2762c9 100644
--- a/R/clean.R
+++ b/R/clean.R
@@ -58,7 +58,7 @@ clean <- function(path = ".", echo = TRUE) {
     }
   )
 
-  out <- processx::run(
+  processx::run(
     command = "cargo",
     args = args,
     error_on_status = TRUE,
diff --git a/R/use_crate.R b/R/use_crate.R
index 97f9657b..ed9495e4 100644
--- a/R/use_crate.R
+++ b/R/use_crate.R
@@ -101,7 +101,7 @@ use_crate <- function(
     }
   )
 
-  out <- processx::run(
+  processx::run(
     command = "cargo",
     args = args,
     error_on_status = TRUE,

From 2fac744a532ca93551eac9c2fe66beaa26e17fc4 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 15:50:36 -0700
Subject: [PATCH 05/21] use updated read_cargo_metadata

---
 R/license_note.R | 88 +++++++++++-------------------------------------
 1 file changed, 19 insertions(+), 69 deletions(-)

diff --git a/R/license_note.R b/R/license_note.R
index e52da7f5..45968ae3 100644
--- a/R/license_note.R
+++ b/R/license_note.R
@@ -1,16 +1,14 @@
 #' Generate LICENSE.note file.
 #'
-#' LICENSE.note generated by this function contains information about Rust crate
-#' dependencies. To use this function, the
-#' [cargo-license](https://crates.io/crates/cargo-license) command must be
-#' installed.
+#' LICENSE.note generated by this function contains information about all
+#' recursive dependencies in Rust crate.
 #'
 #' @param path character scalar, the R package directory
 #' @param echo logical scalar, whether to print cargo command and outputs to the
 #' console (default is `TRUE`)
 #' @param quiet logical scalar, whether to signal successful writing of
 #' LICENSE.note (default is `FALSE`)
-#' @param force logical scalar, whether to regenerate LICENSE.note if
+#' @param overwrite logical scalar, whether to regenerate LICENSE.note if
 #' LICENSE.note already exists (default is `TRUE`)
 #'
 #' @return No return value, called for side effects.
@@ -25,80 +23,26 @@ write_license_note <- function(
     path = ".",
     echo = TRUE,
     quiet = FALSE,
-    force = TRUE) {
+    overwrite = TRUE) {
   check_string(path, class = "rextendr_error")
   check_bool(echo, class = "rextendr_error")
-  check_bool(force, class = "rextendr_error")
-
-  if (!cargo_command_available(c("license", "--help"))) {
-    cli::cli_abort(
-      c(
-        "The {.code cargo license} command is required \\
-        to run the {.fun write_license_note} function.",
-        "*" = "Please install cargo-license \\
-        ({.url https://crates.io/crates/cargo-license}) first.",
-        i = "Run {.code cargo install cargo-license} from your terminal."
-      ),
-      class = "rextendr_error"
-    )
-  }
+  check_bool(quiet, class = "rextendr_error")
+  check_bool(overwrite, class = "rextendr_error")
 
   rust_folder <- rprojroot::find_package_root_file(
     "src", "rust",
     path = path
   )
 
-  manifest_path <- normalizePath(
-    file.path(rust_folder, "Cargo.toml"),
-    winslash = "/",
-    mustWork = FALSE
-  )
-
   outfile <- rprojroot::find_package_root_file(
     "LICENSE.note",
     path = path
   )
 
-  if (isFALSE(force) && file.exists(outfile)) {
-    cli::cli_abort(
-      c(
-        "LICENSE.note already exists.",
-        "If you want to regenerate LICENSE.note, \\
-        set `force = TRUE` to {.fun write_license_note}."
-      ),
-      class = "rextendr_error"
-    )
-  }
-
-  args <- c(
-    "license",
-    "--authors",
-    "--json",
-    "--avoid-build-deps",
-    "--avoid-dev-deps",
-    "--manifest-path", manifest_path
-  )
-
-  out <- processx::run(
-    command = "cargo",
-    args = args,
-    error_on_status = TRUE,
-    wd = rust_folder,
-    echo_cmd = echo,
-    echo = echo,
-    env = get_cargo_envvars()
-  )
-
-  licenses <- jsonlite::parse_json(
-    out[["stdout"]],
-    simplifyDataFrame = TRUE
-  )
-
-  metadata <- read_cargo_metadata(path = path)
-
-  package_names <- metadata[["packages"]][["dependencies"]][[1]][["name"]]
-
-  licenses <- licenses[licenses[["name"]] %in% package_names, ]
+  packages <- read_cargo_metadata(
+    path = path,
+    dependencies = TRUE
+  )[["packages"]]
 
   .prep_authors <- function(authors, package) {
     authors <- ifelse(
@@ -112,6 +56,11 @@ write_license_note <- function(
     stringi::stri_replace_all_regex(authors, r"(\|)", ", ")
   }
 
+  packages[["authors"]] <- lapply(
+    packages[["authors"]],
+    function(x) .prep_authors(x, packages[["name"]])
+  )
+
   separator <- "-------------------------------------------------------------"
 
   note_header <- glue::glue(
@@ -125,12 +74,12 @@ write_license_note <- function(
   )
 
   note_body <- glue::glue_data(
-    licenses,
+    packages,
     "
 
     Name:        {name}
     Repository:  {repository}
-    Authors:     {.prep_authors(authors, name)}
+    Authors:     {authors}
     License:     {license}
 
     {separator}
@@ -141,6 +90,7 @@ write_license_note <- function(
     text = c(note_header, note_body),
     path = outfile,
     search_root_from = path,
-    quiet = quiet
+    quiet = quiet,
+    overwrite = overwrite
   )
 }

From e9c97ea055ff28c95590dd271435c1b8f5217899 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 16:15:37 -0700
Subject: [PATCH 06/21] replace missing values in license note

---
 R/license_note.R | 32 +++++++++++++++++++++++++++-----
 1 file changed, 27 insertions(+), 5 deletions(-)

diff --git a/R/license_note.R b/R/license_note.R
index 45968ae3..c54a06f5 100644
--- a/R/license_note.R
+++ b/R/license_note.R
@@ -44,7 +44,28 @@ write_license_note <- function(
     dependencies = TRUE
   )[["packages"]]
 
-  .prep_authors <- function(authors, package) {
+  replace_na <- function(data, replace = NA, ...) {
+    if (vctrs::vec_any_missing(data)) {
+      missing <- vctrs::vec_detect_missing(data)
+      data <- vctrs::vec_assign(data, missing, replace,
+        x_arg = "data",
+        value_arg = "replace"
+      )
+    }
+    data
+  }
+
+  packages[["respository"]] <- replace_na(
+    packages[["repository"]],
+    "unknown"
+  )
+
+  packages[["licenses"]] <- replace_na(
+    packages[["repository"]],
+    "not provided"
+  )
+
+  prep_authors <- function(authors, package) {
     authors <- ifelse(
       is.na(authors),
       paste0(package, " authors"),
@@ -53,13 +74,14 @@ write_license_note <- function(
 
     authors <- stringi::stri_replace_all_regex(authors, r"(\ <.+?>)", "")
 
-    stringi::stri_replace_all_regex(authors, r"(\|)", ", ")
+    paste0(authors, collapse = ", ")
   }
 
-  packages[["authors"]] <- lapply(
+  packages[["authors"]] <- unlist(Map(
+    prep_authors,
     packages[["authors"]],
-    function(x) .prep_authors(x, packages[["name"]])
-  )
+    packages[["name"]]
+  ))
 
   separator <- "-------------------------------------------------------------"
 

From 2c4c1a4352569a2f2882d000669d8286c7148bdc Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 16:22:18 -0700
Subject: [PATCH 07/21] remove error tests for write_license_note

---
 tests/testthat/test-license_note.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/testthat/test-license_note.R b/tests/testthat/test-license_note.R
index 280cb870..2785f534 100644
--- a/tests/testthat/test-license_note.R
+++ b/tests/testthat/test-license_note.R
@@ -7,6 +7,4 @@ test_that("LICENSE.note is generated properly", {
   write_license_note()
 
   expect_snapshot(cat_file("LICENSE.note"))
-  expect_rextendr_error(write_license_note(), NA)
-  expect_rextendr_error(write_license_note(force = FALSE), "LICENSE.note already exists.")
 })

From 4e65a61d143ca42efd77d6d9d49febb3687eaf10 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 16:36:34 -0700
Subject: [PATCH 08/21] exclude current package from license note

---
 R/license_note.R | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/R/license_note.R b/R/license_note.R
index c54a06f5..5a86a359 100644
--- a/R/license_note.R
+++ b/R/license_note.R
@@ -39,10 +39,17 @@ write_license_note <- function(
     path = path
   )
 
-  packages <- read_cargo_metadata(
+  metadata <- read_cargo_metadata(
     path = path,
     dependencies = TRUE
-  )[["packages"]]
+  )
+
+  packages <- metadata[["packages"]]
+
+  # exclude current package from LICENSE.note
+  current_package <- metadata[["resolve"]][["root"]]
+
+  packages <- packages[packages[["id"]] != current_package, ]
 
   replace_na <- function(data, replace = NA, ...) {
     if (vctrs::vec_any_missing(data)) {

From 448e4573131aeb8404d3185a3f5f75a9ec92bac8 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 16:43:26 -0700
Subject: [PATCH 09/21] update license note snapshot

---
 tests/testthat/_snaps/license_note.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/_snaps/license_note.md b/tests/testthat/_snaps/license_note.md
index d2757ccb..d32c1ba9 100644
--- a/tests/testthat/_snaps/license_note.md
+++ b/tests/testthat/_snaps/license_note.md
@@ -32,35 +32,35 @@
       Name:        once_cell
       Repository:  https://github.com/matklad/once_cell
       Authors:     Aleksey Kladov
-      License:     Apache-2.0 OR MIT
+      License:     MIT OR Apache-2.0
       
       -------------------------------------------------------------
       
       Name:        paste
       Repository:  https://github.com/dtolnay/paste
       Authors:     David Tolnay
-      License:     Apache-2.0 OR MIT
+      License:     MIT OR Apache-2.0
       
       -------------------------------------------------------------
       
       Name:        proc-macro2
       Repository:  https://github.com/dtolnay/proc-macro2
       Authors:     David Tolnay, Alex Crichton
-      License:     Apache-2.0 OR MIT
+      License:     MIT OR Apache-2.0
       
       -------------------------------------------------------------
       
       Name:        quote
       Repository:  https://github.com/dtolnay/quote
       Authors:     David Tolnay
-      License:     Apache-2.0 OR MIT
+      License:     MIT OR Apache-2.0
       
       -------------------------------------------------------------
       
       Name:        syn
       Repository:  https://github.com/dtolnay/syn
       Authors:     David Tolnay
-      License:     Apache-2.0 OR MIT
+      License:     MIT OR Apache-2.0
       
       -------------------------------------------------------------
       

From 2e8b8198cf1c606eb733949e8f87ea093f5a4fd8 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 16:59:22 -0700
Subject: [PATCH 10/21] fix lintr issue

---
 R/license_note.R | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/R/license_note.R b/R/license_note.R
index 5a86a359..1ac29a00 100644
--- a/R/license_note.R
+++ b/R/license_note.R
@@ -29,11 +29,6 @@ write_license_note <- function(
   check_bool(quiet, class = "rextendr_error")
   check_bool(overwrite, class = "rextendr_error")
 
-  rust_folder <- rprojroot::find_package_root_file(
-    "src", "rust",
-    path = path
-  )
-
   outfile <- rprojroot::find_package_root_file(
     "LICENSE.note",
     path = path

From 8550996690e3ff4d4fe374be7a296d63c29652d0 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Mon, 18 Nov 2024 16:59:46 -0700
Subject: [PATCH 11/21] devtools::document

---
 man/clean.Rd               | 10 +++++++++-
 man/read_cargo_metadata.Rd |  8 +++++++-
 man/use_crate.Rd           |  6 +++++-
 man/write_license_note.Rd  | 23 ++++++++++++++++-------
 4 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/man/clean.Rd b/man/clean.Rd
index 9f0646e4..bf93399c 100644
--- a/man/clean.Rd
+++ b/man/clean.Rd
@@ -4,10 +4,13 @@
 \alias{clean}
 \title{Clean Rust binaries and package cache.}
 \usage{
-clean(path = ".")
+clean(path = ".", echo = TRUE)
 }
 \arguments{
 \item{path}{[ string ] Path to the package root.}
+
+\item{echo}{logical scalar, should cargo command and outputs be printed to
+console (default is TRUE)}
 }
 \description{
 Removes Rust binaries (such as \code{.dll}/\code{.so} libraries), C wrapper object files,
@@ -15,3 +18,8 @@ invokes \verb{cargo clean} to reset cargo target directory
 (found by default at \verb{pkg_root/src/rust/target/}).
 Useful when Rust code should be recompiled from scratch.
 }
+\examples{
+\dontrun{
+clean()
+}
+}
diff --git a/man/read_cargo_metadata.Rd b/man/read_cargo_metadata.Rd
index 70d20284..61509c8b 100644
--- a/man/read_cargo_metadata.Rd
+++ b/man/read_cargo_metadata.Rd
@@ -4,10 +4,16 @@
 \alias{read_cargo_metadata}
 \title{Retrieve metadata for packages and workspaces}
 \usage{
-read_cargo_metadata(path = ".")
+read_cargo_metadata(path = ".", dependencies = FALSE, echo = TRUE)
 }
 \arguments{
 \item{path}{character scalar, the R package directory}
+
+\item{dependencies}{logical scalar, whether to include all recursive
+dependencies in stdout (default is FALSE)}
+
+\item{echo}{logical scalar, should cargo command and outputs be printed to
+console (default is TRUE)}
 }
 \value{
 \code{list}, including the following elements:
diff --git a/man/use_crate.Rd b/man/use_crate.Rd
index 1500d6bd..a9489281 100644
--- a/man/use_crate.Rd
+++ b/man/use_crate.Rd
@@ -10,7 +10,8 @@ use_crate(
   git = NULL,
   version = NULL,
   optional = FALSE,
-  path = "."
+  path = ".",
+  echo = TRUE
 )
 }
 \arguments{
@@ -27,6 +28,9 @@ crate}
 (FALSE by default)}
 
 \item{path}{character scalar, the package directory}
+
+\item{echo}{logical scalar, should cargo command and outputs be printed to
+console (default is TRUE)}
 }
 \value{
 \code{NULL}, invisibly
diff --git a/man/write_license_note.Rd b/man/write_license_note.Rd
index cfdfb835..ff20923f 100644
--- a/man/write_license_note.Rd
+++ b/man/write_license_note.Rd
@@ -4,20 +4,29 @@
 \alias{write_license_note}
 \title{Generate LICENSE.note file.}
 \usage{
-write_license_note(path = ".", quiet = FALSE, force = TRUE)
+write_license_note(path = ".", echo = TRUE, quiet = FALSE, overwrite = TRUE)
 }
 \arguments{
-\item{path}{Path from which package root is looked up.}
+\item{path}{character scalar, the R package directory}
 
-\item{quiet}{Logical indicating whether any progress messages should be
-generated or not.}
+\item{echo}{logical scalar, whether to print cargo command and outputs to the
+console (default is \code{TRUE})}
 
-\item{force}{Logical indicating whether to regenerate LICENSE.note if LICENSE.note already exists.}
+\item{quiet}{logical scalar, whether to signal successful writing of
+LICENSE.note (default is \code{FALSE})}
+
+\item{overwrite}{logical scalar, whether to regenerate LICENSE.note if
+LICENSE.note already exists (default is \code{TRUE})}
 }
 \value{
 No return value, called for side effects.
 }
 \description{
-LICENSE.note generated by this function contains information about Rust crate dependencies.
-To use this function, the \href{https://crates.io/crates/cargo-license}{cargo-license} command must be installed.
+LICENSE.note generated by this function contains information about all
+recursive dependencies in Rust crate.
+}
+\examples{
+\dontrun{
+write_license_note()
+}
 }

From 823f786a6af41c9bd893c36e7414a68d726b8779 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Tue, 19 Nov 2024 18:50:50 -0700
Subject: [PATCH 12/21] fix roxygen typo

---
 R/find_extendr.R | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/R/find_extendr.R b/R/find_extendr.R
index f423b5bc..033a567c 100644
--- a/R/find_extendr.R
+++ b/R/find_extendr.R
@@ -6,12 +6,8 @@
 #'
 #' @return character scalar, path to Rust crate
 #'
-#' @examples
-#' \dontrun{
-#' find_extendr_crate()
 #' @keywords internal
 #' @noRd
-#' }
 find_extendr_crate <- function(
     path = ".",
     error_call = rlang::caller_call()) {
@@ -41,12 +37,8 @@ find_extendr_crate <- function(
 #'
 #' @return character scalar, path to Cargo manifest
 #'
-#' @examples
-#' \dontrun{
-#' find_extendr_manifest()
 #' @keywords internal
 #' @noRd
-#' }
 find_extendr_manifest <- function(
     path = ".",
     error_call = rlang::caller_call()) {

From d3fa7c5629968986cfe5c6d8e3dc45d4172e64d6 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Wed, 20 Nov 2024 16:12:23 -0700
Subject: [PATCH 13/21] add replace_na utility

---
 R/utils.R | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/R/utils.R b/R/utils.R
index 7b18d76f..d408c454 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -57,3 +57,23 @@ try_exec_cmd <- function(cmd, args = character()) {
     stringi::stri_split_lines1(result$stdout)
   }
 }
+
+#' Replace missing values in vector
+#'
+#' @param data vector, data with missing values to replace
+#' @param replace scalar, value to substitute for missing values in data
+#' @param ... currently ignored
+#'
+#' @keywords internal
+#' @noRd
+#'
+replace_na <- function(data, replace = NA, ...) {
+  if (vctrs::vec_any_missing(data)) {
+    missing <- vctrs::vec_detect_missing(data)
+    data <- vctrs::vec_assign(data, missing, replace,
+      x_arg = "data",
+      value_arg = "replace"
+    )
+  }
+  data
+}

From 96e97e0ad4972779f1b69b54254ed3705e8182a8 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Wed, 20 Nov 2024 16:13:11 -0700
Subject: [PATCH 14/21] add run_cargo utility

---
 R/run_cargo.R | 69 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 R/run_cargo.R

diff --git a/R/run_cargo.R b/R/run_cargo.R
new file mode 100644
index 00000000..4cbd11b0
--- /dev/null
+++ b/R/run_cargo.R
@@ -0,0 +1,69 @@
+#' Run Cargo subcommands
+#'
+#' This internal function allows us to maintain consistent specifications for
+#' `processx::run()` everywhere it uses.
+#'
+#' @param args character vector, the Cargo subcommand and flags to be executed.
+#' @param wd character scalar, location of the Rust crate, (default is
+#' `find_extendr_crate()`).
+#' @param error_on_status, logical scalar, whether to error if `status != 0`,
+#' (default is `TRUE`).
+#' @param echo_cmd logical scalar, whether to print Cargo subcommand and flags
+#' to the console (default is `TRUE`).
+#' @param echo logical scalar, whether to print standard output and error to the
+#' console (default is `TRUE`).
+#' @param env character vector, environment variables of the child process.
+#' @param parse_json logical scalar, whether to parse JSON-structured standard
+#' output (default is `FALSE`).
+#' @param error_call call scalar, from rlang docs: "the defused call with which
+#' the function running in the frame was invoked." (default is
+#' `rlang::caller_call()`)
+#'
+#' @return if `parse_json = TRUE`, result of parsing JSON-structured standard
+#' output; otherwise, standard output is returned as a character scalar.
+#'
+#' @keywords internal
+#' @noRd
+run_cargo <- function(
+    args,
+    wd = find_extendr_crate(),
+    error_on_status = TRUE,
+    echo_cmd = TRUE,
+    echo = TRUE,
+    env = get_cargo_envvars(),
+    parse_json = FALSE,
+    error_call = rlang::caller_call()) {
+  check_character(args, call = error_call, class = "rextendr_error")
+  check_string(wd, call = error_call, class = "rextendr_error")
+  check_bool(error_on_status, call = error_call, class = "rextendr_error")
+  check_bool(echo_cmd, call = error_call, class = "rextendr_error")
+  check_bool(echo, call = error_call, class = "rextendr_error")
+  check_character(env, call = error_call, class = "rextendr_error")
+  check_bool(parse_json, call = error_call, class = "rextendr_error")
+
+  out <- processx::run(
+    command = "cargo",
+    args = args,
+    error_on_status = error_on_status,
+    wd = wd,
+    echo_cmd = echo_cmd,
+    echo = echo,
+    env = env
+  )
+
+  stdout <- out[["stdout"]]
+
+  if (length(stdout) != 1L || !is.character(stdout) || is.null(stdout)) {
+    cli::cli_abort(
+      "{.code cargo paste(args, collapse = ' ')} failed to return stdout.",
+      call = error_call,
+      class = "rextendr_error"
+    )
+  }
+
+  if (parse_json) {
+    stdout <- jsonlite::parse_json(stdout, simplifyDataFrame = TRUE)
+  }
+
+  stdout
+}

From 9aa742af992ff552668c527a5aa02a31e41d0974 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Wed, 20 Nov 2024 16:27:33 -0700
Subject: [PATCH 15/21] use run_cargo

---
 R/clean.R               |  49 ++++++----------
 R/license_note.R        | 123 ++++++++++++++++++++++++----------------
 R/read_cargo_metadata.R |  22 ++-----
 R/use_crate.R           |   2 +-
 4 files changed, 98 insertions(+), 98 deletions(-)

diff --git a/R/clean.R b/R/clean.R
index ba2762c9..d889e5b8 100644
--- a/R/clean.R
+++ b/R/clean.R
@@ -4,9 +4,12 @@
 #' invokes `cargo clean` to reset cargo target directory
 #' (found by default at `pkg_root/src/rust/target/`).
 #' Useful when Rust code should be recompiled from scratch.
-#' @param path \[ string \] Path to the package root.
+#'
+#' @param path character scalar, path to R package root.
 #' @param echo logical scalar, should cargo command and outputs be printed to
-#' console (default is TRUE)
+#' console (default is `TRUE`)
+#'
+#' @return character vector with names of all deleted files (invisibly).
 #'
 #' @export
 #'
@@ -18,33 +21,20 @@ clean <- function(path = ".", echo = TRUE) {
   check_string(path, class = "rextendr_error")
   check_bool(echo, class = "rextendr_error")
 
-  root <- rprojroot::find_package_root_file(path = path)
-
-  rust_folder <- normalizePath(
-    file.path(root, "src", "rust"),
-    winslash = "/",
-    mustWork = FALSE
-  )
-
-  manifest_path <- normalizePath(
-    file.path(rust_folder, "Cargo.toml"),
-    winslash = "/",
-    mustWork = FALSE
-  )
+  manifest_path <- find_extendr_manifest(path = path)
 
   # Note: This should be adjusted if `TARGET_DIR` changes in `Makevars`
-  target_dir <- normalizePath( # nolint: object_usage_linter
-    file.path(rust_folder, "target"),
-    winslash = "/",
-    mustWork = FALSE
+  target_dir <- rprojroot::find_package_root_file(
+    "src", "rust", "target",
+    path = path
   )
 
-  if (!file.exists(manifest_path)) {
-    cli::cli_abort(c(
-      "Unable to clean binaries.",
-      "!" = "{.file Cargo.toml} not found in {.path {rust_folder}}.",
+  if (!dir.exists(target_dir)) {
+    cli::cli_abort(
+      "Could not clean binaries.",
+      "Target directory not found at {.path target_dir}.",
       class = "rextendr_error"
-    ))
+    )
   }
 
   args <- c(
@@ -58,14 +48,11 @@ clean <- function(path = ".", echo = TRUE) {
     }
   )
 
-  processx::run(
-    command = "cargo",
-    args = args,
-    error_on_status = TRUE,
-    wd = rust_folder,
+  run_cargo(
+    args,
+    wd = find_extendr_crate(path = path),
     echo_cmd = echo,
-    echo = echo,
-    env = get_cargo_envvars()
+    echo = echo
   )
 
   pkgbuild::clean_dll(path = root)
diff --git a/R/license_note.R b/R/license_note.R
index 1ac29a00..2f5cfa03 100644
--- a/R/license_note.R
+++ b/R/license_note.R
@@ -8,10 +8,10 @@
 #' console (default is `TRUE`)
 #' @param quiet logical scalar, whether to signal successful writing of
 #' LICENSE.note (default is `FALSE`)
-#' @param overwrite logical scalar, whether to regenerate LICENSE.note if
+#' @param force logical scalar, whether to regenerate LICENSE.note if
 #' LICENSE.note already exists (default is `TRUE`)
 #'
-#' @return No return value, called for side effects.
+#' @return text printed to LICENSE.note (invisibly).
 #'
 #' @export
 #'
@@ -23,40 +23,68 @@ write_license_note <- function(
     path = ".",
     echo = TRUE,
     quiet = FALSE,
-    overwrite = TRUE) {
+    force = TRUE) {
   check_string(path, class = "rextendr_error")
   check_bool(echo, class = "rextendr_error")
   check_bool(quiet, class = "rextendr_error")
-  check_bool(overwrite, class = "rextendr_error")
+  check_bool(force, class = "rextendr_error")
 
   outfile <- rprojroot::find_package_root_file(
     "LICENSE.note",
     path = path
   )
 
-  metadata <- read_cargo_metadata(
-    path = path,
-    dependencies = TRUE
+  args <- c(
+    "metadata",
+    "--format-version=1"
+  )
+
+  metadata <- run_cargo(
+    args,
+    wd = find_extendr_crate(path = path),
+    echo_cmd = echo,
+    echo = echo,
+    parse_json = TRUE
   )
 
   packages <- metadata[["packages"]]
 
+  # did we actually get the recursive dependency metadata we need?
+  required_variables <- c("name", "repository", "authors", "license", "id")
+
+  packages_exist <- is.data.frame(packages) &&
+    !is.null(packages) &&
+    nrow(packages) > 0 &&
+    all(required_variables %in% names(packages))
+
+  if (!packages_exist) {
+    cli::cli_abort(
+      "Unable to write LICENSE.note.",
+      "Metadata for recursive dependencies not found.",
+      call = rlang::caller_call(),
+      class = "rextendr_error"
+    )
+  }
+
   # exclude current package from LICENSE.note
   current_package <- metadata[["resolve"]][["root"]]
 
-  packages <- packages[packages[["id"]] != current_package, ]
+  current_package_exists <- length(current_package) == 1 &&
+    is.character(current_package) &&
+    !is.null(current_package)
 
-  replace_na <- function(data, replace = NA, ...) {
-    if (vctrs::vec_any_missing(data)) {
-      missing <- vctrs::vec_detect_missing(data)
-      data <- vctrs::vec_assign(data, missing, replace,
-        x_arg = "data",
-        value_arg = "replace"
-      )
-    }
-    data
+  if (!current_package_exists) {
+    cli::cli_abort(
+      "Unable to write LICENSE.note.",
+      "Failed to identify current Rust crate.",
+      call = rlang::caller_call(),
+      class = "rextendr_error"
+    )
   }
 
+  packages <- packages[packages[["id"]] != current_package, ]
+
+  # replace missing values
   packages[["respository"]] <- replace_na(
     packages[["repository"]],
     "unknown"
@@ -67,18 +95,8 @@ write_license_note <- function(
     "not provided"
   )
 
-  prep_authors <- function(authors, package) {
-    authors <- ifelse(
-      is.na(authors),
-      paste0(package, " authors"),
-      authors
-    )
-
-    authors <- stringi::stri_replace_all_regex(authors, r"(\ <.+?>)", "")
-
-    paste0(authors, collapse = ", ")
-  }
-
+  # remove email addresses and special characters and combine all authors
+  # of a crate into a single character scalar
   packages[["authors"]] <- unlist(Map(
     prep_authors,
     packages[["authors"]],
@@ -87,27 +105,22 @@ write_license_note <- function(
 
   separator <- "-------------------------------------------------------------"
 
-  note_header <- glue::glue(
-    "
-    The binary compiled from the source code of this package \\
-    contains the following Rust crates:
-
-
-    {separator}
-    "
+  note_header <- paste0(
+    "The binary compiled from the source code of this package ",
+    "contains the following Rust crates:\n",
+    "\n",
+    "\n",
+    separator, "\n"
   )
 
-  note_body <- glue::glue_data(
-    packages,
-    "
-
-    Name:        {name}
-    Repository:  {repository}
-    Authors:     {authors}
-    License:     {license}
-
-    {separator}
-    "
+  note_body <- paste0(
+    "\n",
+    "Name:        ", packages[["name"]], "\n",
+    "Repository:  ", packages[["repository"]], "\n",
+    "Authors:     ", packages[["authors"]], "\n",
+    "License      ", packages[["license"]], "\n",
+    "\n",
+    separator, "\n"
   )
 
   write_file(
@@ -115,6 +128,18 @@ write_license_note <- function(
     path = outfile,
     search_root_from = path,
     quiet = quiet,
-    overwrite = overwrite
+    overwrite = force
+  )
+}
+
+prep_authors <- function(authors, package) {
+  authors <- ifelse(
+    is.na(authors),
+    paste0(package, " authors"),
+    authors
   )
+
+  authors <- stringi::stri_replace_all_regex(authors, r"(\ <.+?>)", "")
+
+  paste0(authors, collapse = ", ")
 }
diff --git a/R/read_cargo_metadata.R b/R/read_cargo_metadata.R
index af0c9d3f..30c13360 100644
--- a/R/read_cargo_metadata.R
+++ b/R/read_cargo_metadata.R
@@ -37,15 +37,10 @@ read_cargo_metadata <- function(
   check_bool(dependencies, class = "rextendr_error")
   check_bool(echo, class = "rextendr_error")
 
-  rust_folder <- rprojroot::find_package_root_file(
-    "src", "rust",
-    path = path
-  )
-
   args <- c(
     "metadata",
     "--format-version=1",
-    if (isFALSE(dependencies)) {
+    if (!dependencies) {
       "--no-deps"
     },
     if (tty_has_colors()) {
@@ -55,18 +50,11 @@ read_cargo_metadata <- function(
     }
   )
 
-  out <- processx::run(
-    command = "cargo",
-    args = args,
-    error_on_status = TRUE,
-    wd = rust_folder,
+  run_cargo(
+    args,
+    wd = find_extendr_crate(path = path),
     echo_cmd = echo,
     echo = echo,
-    env = get_cargo_envvars()
-  )
-
-  jsonlite::parse_json(
-    out[["stdout"]],
-    simplifyDataFrame = TRUE
+    parse_json = TRUE
   )
 }
diff --git a/R/use_crate.R b/R/use_crate.R
index ed9495e4..561ab6ee 100644
--- a/R/use_crate.R
+++ b/R/use_crate.R
@@ -18,7 +18,7 @@
 #' \href{https://doc.rust-lang.org/cargo/commands/cargo-add.html}{Cargo docs}
 #' for `cargo-add`.
 #'
-#' @return `NULL`, invisibly
+#' @return `NULL` (invisibly)
 #'
 #' @export
 #'

From ccf2264d56e299bdef42fdb640072010e151f340 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Wed, 20 Nov 2024 16:31:41 -0700
Subject: [PATCH 16/21] use run_cargo

---
 R/use_crate.R | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/R/use_crate.R b/R/use_crate.R
index 561ab6ee..e8c492af 100644
--- a/R/use_crate.R
+++ b/R/use_crate.R
@@ -83,11 +83,6 @@ use_crate <- function(
     optional <- NULL
   }
 
-  rust_folder <- rprojroot::find_package_root_file(
-    "src", "rust",
-    path = path
-  )
-
   args <- c(
     "add",
     crate,
@@ -101,14 +96,11 @@ use_crate <- function(
     }
   )
 
-  processx::run(
-    command = "cargo",
-    args = args,
-    error_on_status = TRUE,
-    wd = rust_folder,
+  run_cargo(
+    args,
+    wd = find_extendr_crate(path = path),
     echo_cmd = echo,
-    echo = echo,
-    env = get_cargo_envvars()
+    echo = echo
   )
 
   invisible()

From 993f6d763cde3115cd05aae7076d7278f9a4658a Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Wed, 20 Nov 2024 16:47:20 -0700
Subject: [PATCH 17/21] pass root to clean_dll

---
 R/clean.R | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/R/clean.R b/R/clean.R
index d889e5b8..38452988 100644
--- a/R/clean.R
+++ b/R/clean.R
@@ -33,6 +33,7 @@ clean <- function(path = ".", echo = TRUE) {
     cli::cli_abort(
       "Could not clean binaries.",
       "Target directory not found at {.path target_dir}.",
+      call = rlang::caller_call(),
       class = "rextendr_error"
     )
   }
@@ -55,5 +56,16 @@ clean <- function(path = ".", echo = TRUE) {
     echo = echo
   )
 
+  root <- rprojroot::find_package_root_file(path = path)
+
+  if (!dir.exists(root)) {
+    cli::cli_abort(
+      "Could not clean binaries.",
+      "R package directory not found at {.path root}.",
+      call = rlang::caller_call(),
+      class = "rextendr_error"
+    )
+  }
+
   pkgbuild::clean_dll(path = root)
 }

From 381de67e316b278ac88dc07e91e44fa53e033403 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Wed, 20 Nov 2024 17:14:02 -0700
Subject: [PATCH 18/21] replace glue with paste, update snapshot to reflect new
 unicode license

---
 R/license_note.R                      | 6 +++---
 tests/testthat/_snaps/license_note.md | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/license_note.R b/R/license_note.R
index 2f5cfa03..b1508c10 100644
--- a/R/license_note.R
+++ b/R/license_note.R
@@ -110,7 +110,7 @@ write_license_note <- function(
     "contains the following Rust crates:\n",
     "\n",
     "\n",
-    separator, "\n"
+    separator
   )
 
   note_body <- paste0(
@@ -118,9 +118,9 @@ write_license_note <- function(
     "Name:        ", packages[["name"]], "\n",
     "Repository:  ", packages[["repository"]], "\n",
     "Authors:     ", packages[["authors"]], "\n",
-    "License      ", packages[["license"]], "\n",
+    "License:     ", packages[["license"]], "\n",
     "\n",
-    separator, "\n"
+    separator
   )
 
   write_file(
diff --git a/tests/testthat/_snaps/license_note.md b/tests/testthat/_snaps/license_note.md
index d32c1ba9..44be7cc5 100644
--- a/tests/testthat/_snaps/license_note.md
+++ b/tests/testthat/_snaps/license_note.md
@@ -67,7 +67,7 @@
       Name:        unicode-ident
       Repository:  https://github.com/dtolnay/unicode-ident
       Authors:     David Tolnay
-      License:     (MIT OR Apache-2.0) AND Unicode-DFS-2016
+      License:     (MIT OR Apache-2.0) AND Unicode-3.0
       
       -------------------------------------------------------------
 

From 97463492b1e7a97323de7fa000a81881aaf48691 Mon Sep 17 00:00:00 2001
From: kbvernon <kenneth.b.vernon@gmail.com>
Date: Wed, 20 Nov 2024 18:30:36 -0700
Subject: [PATCH 19/21] devtools::document()

---
 man/clean.Rd              | 7 +++++--
 man/use_crate.Rd          | 2 +-
 man/write_license_note.Rd | 6 +++---
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/man/clean.Rd b/man/clean.Rd
index bf93399c..6a756a9b 100644
--- a/man/clean.Rd
+++ b/man/clean.Rd
@@ -7,10 +7,13 @@
 clean(path = ".", echo = TRUE)
 }
 \arguments{
-\item{path}{[ string ] Path to the package root.}
+\item{path}{character scalar, path to R package root.}
 
 \item{echo}{logical scalar, should cargo command and outputs be printed to
-console (default is TRUE)}
+console (default is \code{TRUE})}
+}
+\value{
+character vector with names of all deleted files (invisibly).
 }
 \description{
 Removes Rust binaries (such as \code{.dll}/\code{.so} libraries), C wrapper object files,
diff --git a/man/use_crate.Rd b/man/use_crate.Rd
index a9489281..2341681f 100644
--- a/man/use_crate.Rd
+++ b/man/use_crate.Rd
@@ -33,7 +33,7 @@ crate}
 console (default is TRUE)}
 }
 \value{
-\code{NULL}, invisibly
+\code{NULL} (invisibly)
 }
 \description{
 Analogous to \code{usethis::use_package()} but for crate dependencies.
diff --git a/man/write_license_note.Rd b/man/write_license_note.Rd
index ff20923f..56872675 100644
--- a/man/write_license_note.Rd
+++ b/man/write_license_note.Rd
@@ -4,7 +4,7 @@
 \alias{write_license_note}
 \title{Generate LICENSE.note file.}
 \usage{
-write_license_note(path = ".", echo = TRUE, quiet = FALSE, overwrite = TRUE)
+write_license_note(path = ".", echo = TRUE, quiet = FALSE, force = TRUE)
 }
 \arguments{
 \item{path}{character scalar, the R package directory}
@@ -15,11 +15,11 @@ console (default is \code{TRUE})}
 \item{quiet}{logical scalar, whether to signal successful writing of
 LICENSE.note (default is \code{FALSE})}
 
-\item{overwrite}{logical scalar, whether to regenerate LICENSE.note if
+\item{force}{logical scalar, whether to regenerate LICENSE.note if
 LICENSE.note already exists (default is \code{TRUE})}
 }
 \value{
-No return value, called for side effects.
+text printed to LICENSE.note (invisibly).
 }
 \description{
 LICENSE.note generated by this function contains information about all

From f90145f4780ca4ee45d44a87eb247b327e3abd32 Mon Sep 17 00:00:00 2001
From: Josiah Parry <josiah.parry@gmail.com>
Date: Thu, 21 Nov 2024 13:25:57 -0800
Subject: [PATCH 20/21] appease codecov. modify docs. and refactor run_cargo

---
 DESCRIPTION                        |  1 +
 R/clean.R                          |  7 ++--
 R/license_note.R                   |  7 +---
 R/read_cargo_metadata.R            | 30 ++++++++---------
 R/run_cargo.R                      | 54 ++++++++++++++++++------------
 R/use_crate.R                      |  1 -
 man/read_cargo_metadata.Rd         | 28 ++++++++--------
 man/vendor_pkgs.Rd                 |  3 +-
 man/write_license_note.Rd          |  5 +--
 tests/testthat/test-clean.R        |  7 ++++
 tests/testthat/test-license_note.R |  9 ++++-
 tests/testthat/test-use_crate.R    |  5 ++-
 tests/testthat/test-utils.R        | 13 +++++++
 13 files changed, 99 insertions(+), 71 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f3a90aef..ffefa8c5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -73,3 +73,4 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 SystemRequirements: Rust 'cargo'; the crate 'libR-sys' must compile
     without error
+Config/rextendr/version: 0.3.1.9001
diff --git a/R/clean.R b/R/clean.R
index 38452988..0a57070f 100644
--- a/R/clean.R
+++ b/R/clean.R
@@ -31,8 +31,10 @@ clean <- function(path = ".", echo = TRUE) {
 
   if (!dir.exists(target_dir)) {
     cli::cli_abort(
-      "Could not clean binaries.",
-      "Target directory not found at {.path target_dir}.",
+      c(
+        "Could not clean binaries.",
+        "Target directory not found at {.path target_dir}."
+      ),
       call = rlang::caller_call(),
       class = "rextendr_error"
     )
@@ -52,7 +54,6 @@ clean <- function(path = ".", echo = TRUE) {
   run_cargo(
     args,
     wd = find_extendr_crate(path = path),
-    echo_cmd = echo,
     echo = echo
   )
 
diff --git a/R/license_note.R b/R/license_note.R
index b1508c10..214ef961 100644
--- a/R/license_note.R
+++ b/R/license_note.R
@@ -4,8 +4,6 @@
 #' recursive dependencies in Rust crate.
 #'
 #' @param path character scalar, the R package directory
-#' @param echo logical scalar, whether to print cargo command and outputs to the
-#' console (default is `TRUE`)
 #' @param quiet logical scalar, whether to signal successful writing of
 #' LICENSE.note (default is `FALSE`)
 #' @param force logical scalar, whether to regenerate LICENSE.note if
@@ -21,11 +19,9 @@
 #' }
 write_license_note <- function(
     path = ".",
-    echo = TRUE,
     quiet = FALSE,
     force = TRUE) {
   check_string(path, class = "rextendr_error")
-  check_bool(echo, class = "rextendr_error")
   check_bool(quiet, class = "rextendr_error")
   check_bool(force, class = "rextendr_error")
 
@@ -42,8 +38,7 @@ write_license_note <- function(
   metadata <- run_cargo(
     args,
     wd = find_extendr_crate(path = path),
-    echo_cmd = echo,
-    echo = echo,
+    echo = FALSE,
     parse_json = TRUE
   )
 
diff --git a/R/read_cargo_metadata.R b/R/read_cargo_metadata.R
index 30c13360..e3c9ffb7 100644
--- a/R/read_cargo_metadata.R
+++ b/R/read_cargo_metadata.R
@@ -1,10 +1,10 @@
 #' Retrieve metadata for packages and workspaces
 #'
 #' @param path character scalar, the R package directory
-#' @param dependencies logical scalar, whether to include all recursive
-#' dependencies in stdout (default is FALSE)
-#' @param echo logical scalar, should cargo command and outputs be printed to
-#' console (default is TRUE)
+#' @param dependencies Default `FALSE`. A logical scalar, whether to include
+#' all recursive dependencies in stdout.
+#' @param echo Default `FALSE`. A logical scalar, should cargo command and
+#'  outputs be printed to the console.
 #'
 #' @details
 #' For more details, see
@@ -12,15 +12,16 @@
 #' for `cargo-metadata`. See especially "JSON Format" to get a sense of what you
 #' can expect to find in the returned list.
 #'
-#' @return `list`, including the following elements:
-#' - "packages"
-#' - "workspace_members"
-#' - "workspace_default_members"
-#' - "resolve"
-#' - "target_directory"
-#' - "version"
-#' - "workspace_root"
-#' - "metadata"
+#' @returns
+#' A `list` including the following elements:
+#' - `packages`
+#' - `workspace_members`
+#' - `workspace_default_members`
+#' - `resolve`
+#' - `target_directory`
+#' - `version`
+#' - `workspace_root`
+#' - `metadata`
 #'
 #' @export
 #'
@@ -32,7 +33,7 @@
 read_cargo_metadata <- function(
     path = ".",
     dependencies = FALSE,
-    echo = TRUE) {
+    echo = FALSE) {
   check_string(path, class = "rextendr_error")
   check_bool(dependencies, class = "rextendr_error")
   check_bool(echo, class = "rextendr_error")
@@ -53,7 +54,6 @@ read_cargo_metadata <- function(
   run_cargo(
     args,
     wd = find_extendr_crate(path = path),
-    echo_cmd = echo,
     echo = echo,
     parse_json = TRUE
   )
diff --git a/R/run_cargo.R b/R/run_cargo.R
index 4cbd11b0..2d521f17 100644
--- a/R/run_cargo.R
+++ b/R/run_cargo.R
@@ -6,21 +6,20 @@
 #' @param args character vector, the Cargo subcommand and flags to be executed.
 #' @param wd character scalar, location of the Rust crate, (default is
 #' `find_extendr_crate()`).
-#' @param error_on_status, logical scalar, whether to error if `status != 0`,
-#' (default is `TRUE`).
-#' @param echo_cmd logical scalar, whether to print Cargo subcommand and flags
-#' to the console (default is `TRUE`).
-#' @param echo logical scalar, whether to print standard output and error to the
-#' console (default is `TRUE`).
+#' @param error_on_status Default `TRUE`. A logical scalar, whether to error on a non-zero exist status.
+#' @param echo_cmd Default `TRUE`. A logical scalar, whether to print Cargo subcommand and flags
+#' to the console.
+#' @param echo Default `TRUE`. Alogical scalar, whether to print standard output and error to the
+#' console.
 #' @param env character vector, environment variables of the child process.
-#' @param parse_json logical scalar, whether to parse JSON-structured standard
-#' output (default is `FALSE`).
-#' @param error_call call scalar, from rlang docs: "the defused call with which
-#' the function running in the frame was invoked." (default is
-#' `rlang::caller_call()`)
-#'
-#' @return if `parse_json = TRUE`, result of parsing JSON-structured standard
-#' output; otherwise, standard output is returned as a character scalar.
+#' @param parse_json Default `FALSE`. A logical scalar, whether to parse JSON-structured standard
+#' output using [`jsonlite::parse_json()`] with `simplifyDataFrame = TRUE`.
+#' @param error_call Default [`rlang::caller_call()`]. The defused call with which
+#' the function running in the frame was invoked.
+#' @param ... additional arguments passed to [`processx::run()`].
+#' @returns
+#' A list with elements `status`, `stdout`, `stderr`, and `timeout`. See [`processx::run()`]. If `parse_json = TRUE`, result of parsing JSON-structured standard
+#' output.
 #'
 #' @keywords internal
 #' @noRd
@@ -28,15 +27,15 @@ run_cargo <- function(
     args,
     wd = find_extendr_crate(),
     error_on_status = TRUE,
-    echo_cmd = TRUE,
     echo = TRUE,
     env = get_cargo_envvars(),
     parse_json = FALSE,
-    error_call = rlang::caller_call()) {
+    error_call = rlang::caller_call(), 
+    ...
+) {
   check_character(args, call = error_call, class = "rextendr_error")
   check_string(wd, call = error_call, class = "rextendr_error")
   check_bool(error_on_status, call = error_call, class = "rextendr_error")
-  check_bool(echo_cmd, call = error_call, class = "rextendr_error")
   check_bool(echo, call = error_call, class = "rextendr_error")
   check_character(env, call = error_call, class = "rextendr_error")
   check_bool(parse_json, call = error_call, class = "rextendr_error")
@@ -46,9 +45,10 @@ run_cargo <- function(
     args = args,
     error_on_status = error_on_status,
     wd = wd,
-    echo_cmd = echo_cmd,
+    echo_cmd = echo,
     echo = echo,
-    env = env
+    env = env,
+    ...
   )
 
   stdout <- out[["stdout"]]
@@ -62,8 +62,18 @@ run_cargo <- function(
   }
 
   if (parse_json) {
-    stdout <- jsonlite::parse_json(stdout, simplifyDataFrame = TRUE)
+    res <- rlang::try_fetch(
+      jsonlite::parse_json(stdout, simplifyDataFrame = TRUE),
+      error = function(cnd) {
+        cli::cli_abort(
+          c("Failed to {.code stdout} as json:", " " = "{stdout}"),
+          parent = cnd,
+          class = "rextendr_error"
+        )
+      }
+    )
+    return(res)
   }
 
-  stdout
-}
+  out
+}
\ No newline at end of file
diff --git a/R/use_crate.R b/R/use_crate.R
index e8c492af..f249c4e3 100644
--- a/R/use_crate.R
+++ b/R/use_crate.R
@@ -99,7 +99,6 @@ use_crate <- function(
   run_cargo(
     args,
     wd = find_extendr_crate(path = path),
-    echo_cmd = echo,
     echo = echo
   )
 
diff --git a/man/read_cargo_metadata.Rd b/man/read_cargo_metadata.Rd
index 61509c8b..16aea079 100644
--- a/man/read_cargo_metadata.Rd
+++ b/man/read_cargo_metadata.Rd
@@ -4,28 +4,28 @@
 \alias{read_cargo_metadata}
 \title{Retrieve metadata for packages and workspaces}
 \usage{
-read_cargo_metadata(path = ".", dependencies = FALSE, echo = TRUE)
+read_cargo_metadata(path = ".", dependencies = FALSE, echo = FALSE)
 }
 \arguments{
 \item{path}{character scalar, the R package directory}
 
-\item{dependencies}{logical scalar, whether to include all recursive
-dependencies in stdout (default is FALSE)}
+\item{dependencies}{Default \code{FALSE}. A logical scalar, whether to include
+all recursive dependencies in stdout.}
 
-\item{echo}{logical scalar, should cargo command and outputs be printed to
-console (default is TRUE)}
+\item{echo}{Default \code{FALSE}. A logical scalar, should cargo command and
+outputs be printed to the console.}
 }
 \value{
-\code{list}, including the following elements:
+A \code{list} including the following elements:
 \itemize{
-\item "packages"
-\item "workspace_members"
-\item "workspace_default_members"
-\item "resolve"
-\item "target_directory"
-\item "version"
-\item "workspace_root"
-\item "metadata"
+\item \code{packages}
+\item \code{workspace_members}
+\item \code{workspace_default_members}
+\item \code{resolve}
+\item \code{target_directory}
+\item \code{version}
+\item \code{workspace_root}
+\item \code{metadata}
 }
 }
 \description{
diff --git a/man/vendor_pkgs.Rd b/man/vendor_pkgs.Rd
index 98e75d57..8e133c19 100644
--- a/man/vendor_pkgs.Rd
+++ b/man/vendor_pkgs.Rd
@@ -30,8 +30,7 @@ compressed \code{vendor.tar.xz} which will be shipped with package itself.
 If you have modified your dependencies, you will need need to repackage
 }
 \examples{
-
 \dontrun{
-  vendor_pkgs()
+vendor_pkgs()
 }
 }
diff --git a/man/write_license_note.Rd b/man/write_license_note.Rd
index 56872675..6bf93d53 100644
--- a/man/write_license_note.Rd
+++ b/man/write_license_note.Rd
@@ -4,14 +4,11 @@
 \alias{write_license_note}
 \title{Generate LICENSE.note file.}
 \usage{
-write_license_note(path = ".", echo = TRUE, quiet = FALSE, force = TRUE)
+write_license_note(path = ".", quiet = FALSE, force = TRUE)
 }
 \arguments{
 \item{path}{character scalar, the R package directory}
 
-\item{echo}{logical scalar, whether to print cargo command and outputs to the
-console (default is \code{TRUE})}
-
 \item{quiet}{logical scalar, whether to signal successful writing of
 LICENSE.note (default is \code{FALSE})}
 
diff --git a/tests/testthat/test-clean.R b/tests/testthat/test-clean.R
index 3ee022ee..b20c8354 100644
--- a/tests/testthat/test-clean.R
+++ b/tests/testthat/test-clean.R
@@ -11,8 +11,15 @@ test_that("rextendr::clean() removes cargo target directory & binaries", {
 
   expect_equal(length(dir("src", pattern = "testpkg\\..*")), 1)
   expect_true(dir.exists(file.path("src", "rust", "target")))
+
+  # clean once
   clean()
 
+  # we expect an error the second time
+  expect_error(clean())
+
+  expect_error(clean(1L))
+  expect_error(clean(echo = NULL))
   expect_equal(length(dir("src", pattern = "testpkg\\..*")), 0)
   expect_false(dir.exists(file.path("src", "rust", "target")))
 })
diff --git a/tests/testthat/test-license_note.R b/tests/testthat/test-license_note.R
index 2785f534..1092e6ae 100644
--- a/tests/testthat/test-license_note.R
+++ b/tests/testthat/test-license_note.R
@@ -3,8 +3,15 @@ test_that("LICENSE.note is generated properly", {
   skip_if_cargo_unavailable(c("license", "--help"))
 
   local_package("testPackage")
+
+  # try running write_license_note() when there is nothing present
+  dir.create(file.path("src", "rust"), recursive = TRUE)
+  expect_error(write_license_note())
+
+  # create license note for extendr package 
   use_extendr()
   write_license_note()
-
   expect_snapshot(cat_file("LICENSE.note"))
+  expect_error(write_license_note(path = NULL))
+  expect_error(write_license_note(force = "yup"))
 })
diff --git a/tests/testthat/test-use_crate.R b/tests/testthat/test-use_crate.R
index b3419279..8f7328ed 100644
--- a/tests/testthat/test-use_crate.R
+++ b/tests/testthat/test-use_crate.R
@@ -15,16 +15,15 @@ test_that("use_crate() adds dependency to package or workspace", {
     path = path
   )
 
-  metadata <- read_cargo_metadata(path)
+  metadata <- read_cargo_metadata(path, echo = FALSE)
 
   dependency <- metadata[["packages"]][["dependencies"]][[1]]
   dependency <- dependency[dependency[["name"]] == "serde", ]
 
   expect_equal(dependency[["name"]], "serde")
-
   expect_equal(dependency[["features"]][[1]], "derive")
-
   expect_equal(dependency[["req"]], "^1.0.1")
+
 })
 
 test_that("use_crate() errors when user passes git and version arguments", {
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index bc45a226..8f975eeb 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -20,3 +20,16 @@ test_that("`try_exec_cmd()` returns stdout when command is available", {
   echo <- "This is an echo"
   expect_equal(try_exec_cmd("echo", echo), echo)
 })
+
+
+test_that("`replace_na()` respects type", {
+  x <- 1:5
+  x[2] <- NA
+  expect_error(replace_na(x, "L"))
+})
+
+test_that("`replace_na()` replaces with the correct value", {
+  x <- 1:5
+  x[2] <- NA_integer_
+  expect_identical(replace_na(x, -99L), c(1L, -99L, 3L, 4L, 5L))
+})

From d46ee515c90ff7a86150c04d09b1a51a369d704c Mon Sep 17 00:00:00 2001
From: Josiah Parry <josiah.parry@gmail.com>
Date: Thu, 21 Nov 2024 13:45:12 -0800
Subject: [PATCH 21/21] lintr

---
 R/run_cargo.R                      | 23 ++++++++++++-----------
 tests/testthat/test-license_note.R |  2 +-
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/R/run_cargo.R b/R/run_cargo.R
index 2d521f17..1db8ed13 100644
--- a/R/run_cargo.R
+++ b/R/run_cargo.R
@@ -18,20 +18,21 @@
 #' the function running in the frame was invoked.
 #' @param ... additional arguments passed to [`processx::run()`].
 #' @returns
-#' A list with elements `status`, `stdout`, `stderr`, and `timeout`. See [`processx::run()`]. If `parse_json = TRUE`, result of parsing JSON-structured standard
-#' output.
+#' A list with elements `status`, `stdout`, `stderr`, and `timeout`.
+#' See [`processx::run()`]. If `parse_json = TRUE`, result of parsing
+#' JSON-structured standard output.
 #'
 #' @keywords internal
 #' @noRd
 run_cargo <- function(
-    args,
-    wd = find_extendr_crate(),
-    error_on_status = TRUE,
-    echo = TRUE,
-    env = get_cargo_envvars(),
-    parse_json = FALSE,
-    error_call = rlang::caller_call(), 
-    ...
+  args,
+  wd = find_extendr_crate(),
+  error_on_status = TRUE,
+  echo = TRUE,
+  env = get_cargo_envvars(),
+  parse_json = FALSE,
+  error_call = rlang::caller_call(),
+  ...
 ) {
   check_character(args, call = error_call, class = "rextendr_error")
   check_string(wd, call = error_call, class = "rextendr_error")
@@ -76,4 +77,4 @@ run_cargo <- function(
   }
 
   out
-}
\ No newline at end of file
+}
diff --git a/tests/testthat/test-license_note.R b/tests/testthat/test-license_note.R
index 1092e6ae..92bf73cb 100644
--- a/tests/testthat/test-license_note.R
+++ b/tests/testthat/test-license_note.R
@@ -8,7 +8,7 @@ test_that("LICENSE.note is generated properly", {
   dir.create(file.path("src", "rust"), recursive = TRUE)
   expect_error(write_license_note())
 
-  # create license note for extendr package 
+  # create license note for extendr package
   use_extendr()
   write_license_note()
   expect_snapshot(cat_file("LICENSE.note"))