cleanup examples, update metadata

Author: e-kotov

.Rbuildignore

@@ -8,6 +8,7 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^\.sync$
 ^\.Rprofile$
 ^rjavaenv$
 ^private$
@@ -33,3 +34,5 @@
 ^\.jupyter$
 ^[.]?air[.]toml$
 ^\.vscode$
+^\.devcontainer$
+^\.claude$

CITATION.cff

@@ -81,7 +81,7 @@ references:
   institution:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
-  year: '2025'
+  year: '2026'
   version: '>= 4.0'
 - type: software
   title: checkmate
@@ -94,7 +94,7 @@ references:
     given-names: Michel
     email: michellang@gmail.com
     orcid: https://orcid.org/0000-0001-9754-0393
-  year: '2025'
+  year: '2026'
   doi: 10.32614/CRAN.package.checkmate
 - type: software
   title: cli
@@ -106,7 +106,7 @@ references:
   - family-names: Csárdi
     given-names: Gábor
     email: gabor@posit.co
-  year: '2025'
+  year: '2026'
   doi: 10.32614/CRAN.package.cli
 - type: software
   title: curl
@@ -119,21 +119,64 @@ references:
     given-names: Jeroen
     email: jeroenooms@gmail.com
     orcid: https://orcid.org/0000-0002-4035-0289
-  year: '2025'
+  year: '2026'
   doi: 10.32614/CRAN.package.curl
 - type: software
-  title: jsonlite
-  abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
+  title: digest
+  abstract: 'digest: Create Compact Hash Digests of R Objects'
   notes: Imports
-  url: https://jeroen.r-universe.dev/jsonlite
-  repository: https://CRAN.R-project.org/package=jsonlite
+  url: https://eddelbuettel.github.io/digest/
+  repository: https://CRAN.R-project.org/package=digest
   authors:
-  - family-names: Ooms
-    given-names: Jeroen
-    email: jeroenooms@gmail.com
-    orcid: https://orcid.org/0000-0002-4035-0289
-  year: '2025'
-  doi: 10.32614/CRAN.package.jsonlite
+  - family-names: Eddelbuettel
+    given-names: Dirk
+    email: edd@debian.org
+    orcid: https://orcid.org/0000-0001-6419-907X
+  year: '2026'
+  doi: 10.32614/CRAN.package.digest
+- type: software
+  title: memoise
+  abstract: 'memoise: ''Memoisation'' of Functions'
+  notes: Imports
+  url: https://memoise.r-lib.org
+  repository: https://CRAN.R-project.org/package=memoise
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@rstudio.com
+  - family-names: Hester
+    given-names: Jim
+  - family-names: Chang
+    given-names: Winston
+    email: winston@rstudio.com
+  - family-names: Müller
+    given-names: Kirill
+    email: krlmlr+r@mailbox.org
+  - family-names: Cook
+    given-names: Daniel
+    email: danielecook@gmail.com
+  year: '2026'
+  doi: 10.32614/CRAN.package.memoise
+- type: software
+  title: RcppSimdJson
+  abstract: 'RcppSimdJson: ''Rcpp'' Bindings for the ''simdjson'' Header-Only Library
+    for ''JSON'' Parsing'
+  notes: Imports
+  url: https://github.com/eddelbuettel/rcppsimdjson/
+  repository: https://CRAN.R-project.org/package=RcppSimdJson
+  authors:
+  - family-names: Eddelbuettel
+    given-names: Dirk
+    email: edd@debian.org
+    orcid: https://orcid.org/0000-0001-6419-907X
+  - family-names: Knapp
+    given-names: Brendan
+    orcid: https://orcid.org/0000-0003-3284-4972
+  - family-names: Lemire
+    given-names: Daniel
+    orcid: https://orcid.org/0000-0003-3306-6922
+  year: '2026'
+  doi: 10.32614/CRAN.package.RcppSimdJson
 - type: software
   title: rlang
   abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
@@ -147,7 +190,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: hadley@posit.co
-  year: '2025'
+  year: '2026'
   doi: 10.32614/CRAN.package.rlang
 - type: software
   title: utils
@@ -158,7 +201,60 @@ references:
   institution:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
-  year: '2025'
+  year: '2026'
+- type: software
+  title: withr
+  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
+  notes: Imports
+  url: https://withr.r-lib.org
+  repository: https://CRAN.R-project.org/package=withr
+  authors:
+  - family-names: Hester
+    given-names: Jim
+  - family-names: Henry
+    given-names: Lionel
+    email: lionel@posit.co
+  - family-names: Müller
+    given-names: Kirill
+    email: krlmlr+r@mailbox.org
+  - family-names: Ushey
+    given-names: Kevin
+    email: kevinushey@gmail.com
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+  - family-names: Chang
+    given-names: Winston
+  year: '2026'
+  doi: 10.32614/CRAN.package.withr
+- type: software
+  title: yaml
+  abstract: 'yaml: Methods to Convert R Data to YAML and Back'
+  notes: Imports
+  url: https://yaml.r-lib.org
+  repository: https://CRAN.R-project.org/package=yaml
+  authors:
+  - family-names: Stephens
+    given-names: Jeremy
+  - family-names: Simonov
+    given-names: Kirill
+  year: '2026'
+  doi: 10.32614/CRAN.package.yaml
+- type: software
+  title: callr
+  abstract: 'callr: Call R from R'
+  notes: Suggests
+  url: https://callr.r-lib.org
+  repository: https://CRAN.R-project.org/package=callr
+  authors:
+  - family-names: Csárdi
+    given-names: Gábor
+    email: csardi.gabor@gmail.com
+    orcid: https://orcid.org/0000-0001-7098-9676
+  - family-names: Chang
+    given-names: Winston
+  year: '2026'
+  doi: 10.32614/CRAN.package.callr
 - type: software
   title: quarto
   abstract: 'quarto: R Interface to ''Quarto'' Markdown Publishing System'
@@ -174,7 +270,7 @@ references:
     given-names: Christophe
     email: cderv@posit.co
     orcid: https://orcid.org/0000-0003-4474-2498
-  year: '2025'
+  year: '2026'
   doi: 10.32614/CRAN.package.quarto
 - type: software
   title: rJava
@@ -186,7 +282,7 @@ references:
   - family-names: Urbanek
     given-names: Simon
     email: simon.urbanek@r-project.org
-  year: '2025'
+  year: '2026'
   doi: 10.32614/CRAN.package.rJava
 - type: software
   title: testthat
@@ -198,32 +294,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: hadley@posit.co
-  year: '2025'
+  year: '2026'
   doi: 10.32614/CRAN.package.testthat
   version: '>= 3.0.0'
-- type: software
-  title: withr
-  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
-  notes: Suggests
-  url: https://withr.r-lib.org
-  repository: https://CRAN.R-project.org/package=withr
-  authors:
-  - family-names: Hester
-    given-names: Jim
-  - family-names: Henry
-    given-names: Lionel
-    email: lionel@posit.co
-  - family-names: Müller
-    given-names: Kirill
-    email: krlmlr+r@mailbox.org
-  - family-names: Ushey
-    given-names: Kevin
-    email: kevinushey@gmail.com
-  - family-names: Wickham
-    given-names: Hadley
-    email: hadley@posit.co
-  - family-names: Chang
-    given-names: Winston
-  year: '2025'
-  doi: 10.32614/CRAN.package.withr
 

R/global_params.R

@@ -15,23 +15,23 @@ global_quiet_param <- function(quiet) {
 #' Documentation template for rJava path-locking behavior.
 #'
 #' @section rJava Path-Locking:
-#' **Important for \strong{rJava} Users**: This function sets environment variables
-#' (JAVA_HOME, PATH) that affect both command-line Java tools and \strong{rJava} initialization.
-#' However, due to \strong{rJava}'s path-locking behavior when \code{\link[rJava]{.jinit}} is called
+#' **Important for rJava Users**: This function sets environment variables
+#' (JAVA_HOME, PATH) that affect both command-line Java tools and rJava initialization.
+#' However, due to rJava's path-locking behavior when \code{\link[rJava]{.jinit}} is called
 #' (see \url{https://github.com/s-u/rJava/issues/25}, \url{https://github.com/s-u/rJava/issues/249}, and \url{https://github.com/s-u/rJava/issues/334}),
 #' this function must be called **BEFORE** \code{\link[rJava]{.jinit}} is invoked. Once \code{\link[rJava]{.jinit}}
 #' initializes, the Java version is locked for that R session and cannot be changed without restarting R.
 #'
 #' \code{\link[rJava]{.jinit}} is invoked (and Java locked) when you:
 #' \itemize{
 #'   \item Explicitly call \code{library(rJava)}
-#'   \item Load any package that imports \strong{rJava} (which auto-loads it as a dependency)
+#'   \item Load any package that imports rJava (which auto-loads it as a dependency)
 #'   \item Even just use IDE autocomplete with \code{rJava::} (this triggers initialization!)
-#'   \item Call any \strong{rJava}-dependent function
+#'   \item Call any rJava-dependent function
 #' }
 #'
-#' Once any of these happen, the Java version used by \strong{rJava} for that session is locked in.
-#' For command-line Java tools that don't use \strong{rJava}, this function can be called at any
+#' Once any of these happen, the Java version used by rJava for that session is locked in.
+#' For command-line Java tools that don't use rJava, this function can be called at any
 #' time to switch Java versions for subsequent system calls.
 #'
 #' @keywords internal

R/java_download.R

@@ -37,14 +37,13 @@ java_download <- function(
   force = FALSE,
   temp_dir = FALSE
 ) {
+  # Override cache_path if temp_dir is set to TRUE
   # Override cache_path if temp_dir is set to TRUE
   if (temp_dir) {
-    temp_dir <- tempdir()
-    setwd(temp_dir)
-    if (!dir.exists("rJavaEnv_cache")) {
-      dir.create("rJavaEnv_cache", recursive = TRUE)
+    cache_path <- file.path(tempdir(), "rJavaEnv_cache")
+    if (!dir.exists(cache_path)) {
+      dir.create(cache_path, recursive = TRUE)
     }
-    cache_path <- file.path(temp_dir, "rJavaEnv_cache")
   }
 
   # Validate version

R/java_list_available.R

@@ -25,7 +25,7 @@
 #'
 #' @export
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' # List all available versions for current platform
 #' java_list_available()
 #'

R/java_manage_project.R

@@ -7,8 +7,9 @@
 #' @export
 #'
 #' @examples
-#' java_list_project(project_path)
-
+#' \donttest{
+#' java_list_project()
+#' }
 java_list_project <- function(
   project_path = NULL,
   output = c("data.frame", "vector"),

R/java_quick_install.R

@@ -26,16 +26,18 @@ java_quick_install <- function(
   rje_consent_check()
 
   if (temp_dir) {
-    temp_dir <- tempdir()
-    setwd(temp_dir)
-    if (!dir.exists("rJavaEnv_cache")) {
-      dir.create("rJavaEnv_cache", recursive = TRUE)
+    # Use session temp directory
+    temp_path <- tempdir()
+
+    cache_path <- file.path(temp_path, "rJavaEnv_cache")
+    if (!dir.exists(cache_path)) {
+      dir.create(cache_path, recursive = TRUE)
     }
-    cache_path <- file.path(temp_dir, "rJavaEnv_cache")
-    if (!dir.exists("rJavaEnv_project")) {
-      dir.create("rJavaEnv_project", recursive = TRUE)
+
+    project_path <- file.path(temp_path, "rJavaEnv_project")
+    if (!dir.exists(project_path)) {
+      dir.create(project_path, recursive = TRUE)
     }
-    project_path <- file.path(temp_dir, "rJavaEnv_project")
   } else {
     cache_path <- getOption("rJavaEnv.cache_path")
   }

R/java_scoped.R

@@ -22,26 +22,26 @@
 #' @return Invisibly returns the path to the selected JAVA_HOME.
 #' @export
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' # Using system2
 #' my_tool_wrapper <- function() {
 #'   rJavaEnv::local_java_env(version = 21)
 #'   system2("java", "-version")
 #' } # Environment restored automatically here
 #'
 #' # Using processx
-#' run_java_jar <- function(jar_path, args) {
-#'   rJavaEnv::local_java_env(version = 21)
-#'   processx::run("java", c("-jar", jar_path, args))
-#' }
+#' # run_java_jar <- function(jar_path, args) {
+#' #  rJavaEnv::local_java_env(version = 21)
+#' #  processx::run("java", c("-jar", jar_path, args))
+#' # }
 #'
 #' # With caching for repeated calls
-#' process_files <- function(files) {
-#'   for (f in files) {
-#'     rJavaEnv::local_java_env(version = 21, .use_cache = TRUE)
-#'     processx::run("java", c("-jar", "processor.jar", f))
-#'   }
-#' }
+#' # process_files <- function(files) {
+#' #  for (f in files) {
+#' #    rJavaEnv::local_java_env(version = 21, .use_cache = TRUE)
+#' #   processx::run("java", c("-jar", "processor.jar", f))
+#' #  }
+#' # }
 #' }
 local_java_env <- function(
   version,
@@ -114,9 +114,9 @@ local_java_env <- function(
 #' })
 #'
 #' # Using processx
-#' rJavaEnv::with_java_env(version = 21, {
-#'   processx::run("java", c("-jar", "tool.jar", "--help"))
-#' })
+#' # rJavaEnv::with_java_env(version = 21, {
+#' #  processx::run("java", c("-jar", "tool.jar", "--help"))
+#' # })
 #' }
 with_java_env <- function(version, code, ...) {
   local_java_env(version = version, ...)

R/java_unpack.R

@@ -12,7 +12,7 @@
 #' @return A `character` vector containing of length 1 containing the path to the unpacked Java directory.
 #' @export
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'
 #' # set cache dir to temporary directory
 #' options(rJavaEnv.cache_path = tempdir())