Merge pull request #42 from e-kotov/2024-08-19-cran-resubmission

CRAN resubmission fixes

.Rbuildignore

@@ -2,6 +2,7 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^README\.Rmd$
+^README\.qmd$
 ^cran-comments\.md$
 ^_pkgdown\.yml$
 ^docs$
@@ -15,4 +16,7 @@
 ^doc$
 ^Meta$
 ^CODE_OF_CONDUCT\.md$
-^vignettes/why-rJavaEnv\.Rmd$
+^vignettes/why-rJavaEnv\.qmd$
+^vignettes/data-for-vignettes$
+^vignettes/bibliography.bib$
+^vignettes/media$

.gitignore

@@ -13,3 +13,5 @@ renv
 rjavaenv
 /doc/
 /Meta/
+
+/.quarto/

CITATION.cff

@@ -7,18 +7,24 @@ cff-version: 1.2.0
 message: 'To cite package "rJavaEnv" in publications use:'
 type: software
 license: MIT
-title: 'rJavaEnv: Java Environments for R Projects'
-version: 0.1.0
+title: 'rJavaEnv: ''Java'' Environments for R Projects'
+version: 0.1.1
 doi: 10.5281/zenodo.11403010
-abstract: Install specific version of Java runtime environment at the R project level.
-  The goal of rJavaEnv is to manage multiple Java JDKs in R projects by automating
-  the process of downloading, installing, and configuring Java environments on a per-project
-  basis. This package is inspired by the renv <https://rstudio.github.io/renv/> package
-  for managing R environments in R projects. You can request a specific Java Development
-  Kit (JDK) in your project, and rJavaEnv will download and install the requested
-  Java environment in a project-specific directory and set the PATH and JAVA_HOME
-  for when you are using this project. Therefore, you can have different Java versions
-  for different projects without contaminating your system with different Java versions.
+abstract: 'The ''rJavaEnv'' package addresses common issues with ''Java'' environment
+  management in ''R'' for users of ''Java''/''rJava''-dependent ''R'' packages such
+  as ''r5r'', ''opentripplanner'', ''xlsx'', ''openNLP'', ''rWeka'', ''RJDBC'', ''tabulapdf'',
+  and many more. It resolves common problems like ''Java'' not found, ''Java'' version
+  conflicts, missing ''Java'' installations, and the inability to install ''Java''
+  due to lack of administrative privileges. ''rJavaEnv'' automates the download, installation,
+  and setup of the ''Java Development Kit'' (''JDK'') on a per-project basis by setting
+  the relevant ''JAVA_HOME'' in the current ''R'' session or the current working directory
+  (via ''.Rprofile'', with the user''s consent). Similar to what ''renv'' does for
+  ''R'' packages, ''rJavaEnv'' allows different ''Java'' versions to be used across
+  different projects, but can also be configured to allow multiple versions within
+  the same project (e.g. with the help of ''targets'' package). Note: there are a
+  few extra steps for ''Linux'' users, who don''t have any ''Java'' previously installed
+  in their systemm, and who prefer package installation from source, rather then installing
+  binaries from ''Posit Package Manager''. See documentation for details.'
 authors:
 - family-names: Kotov
   given-names: Egor
@@ -107,16 +113,20 @@ references:
     address: Vienna, Austria
   year: '2024'
 - type: software
-  title: knitr
-  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
+  title: quarto
+  abstract: 'quarto: R Interface to ''Quarto'' Markdown Publishing System'
   notes: Suggests
-  url: https://yihui.org/knitr/
-  repository: https://CRAN.R-project.org/package=knitr
+  url: https://quarto-dev.github.io/quarto-r/
+  repository: https://CRAN.R-project.org/package=quarto
   authors:
-  - family-names: Xie
-    given-names: Yihui
-    email: xie@yihui.name
-    orcid: https://orcid.org/0000-0003-0645-5666
+  - family-names: Allaire
+    given-names: JJ
+    email: jj@posit.co
+    orcid: https://orcid.org/0000-0003-0174-9868
+  - family-names: Dervieux
+    given-names: Christophe
+    email: cderv@posit.co
+    orcid: https://orcid.org/0000-0003-4474-2498
   year: '2024'
 - type: software
   title: rJava
@@ -129,49 +139,6 @@ references:
     given-names: Simon
     email: simon.urbanek@r-project.org
   year: '2024'
-- type: software
-  title: rmarkdown
-  abstract: 'rmarkdown: Dynamic Documents for R'
-  notes: Suggests
-  url: https://pkgs.rstudio.com/rmarkdown/
-  repository: https://CRAN.R-project.org/package=rmarkdown
-  authors:
-  - family-names: Allaire
-    given-names: JJ
-    email: jj@posit.co
-  - family-names: Xie
-    given-names: Yihui
-    email: xie@yihui.name
-    orcid: https://orcid.org/0000-0003-0645-5666
-  - family-names: Dervieux
-    given-names: Christophe
-    email: cderv@posit.co
-    orcid: https://orcid.org/0000-0003-4474-2498
-  - family-names: McPherson
-    given-names: Jonathan
-    email: jonathan@posit.co
-  - family-names: Luraschi
-    given-names: Javier
-  - family-names: Ushey
-    given-names: Kevin
-    email: kevin@posit.co
-  - family-names: Atkins
-    given-names: Aron
-    email: aron@posit.co
-  - family-names: Wickham
-    given-names: Hadley
-    email: hadley@posit.co
-  - family-names: Cheng
-    given-names: Joe
-    email: joe@posit.co
-  - family-names: Chang
-    given-names: Winston
-    email: winston@posit.co
-  - family-names: Iannone
-    given-names: Richard
-    email: rich@posit.co
-    orcid: https://orcid.org/0000-0003-3925-190X
-  year: '2024'
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'

DESCRIPTION

@@ -1,23 +1,30 @@
 Package: rJavaEnv
-Title: Java Environments for R Projects
-Version: 0.1.0
+Title: 'Java' Environments for R Projects
+Version: 0.1.1
 Authors@R: c(
     person("Egor", "Kotov", , "kotov.egor@gmail.com", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-6690-5345")),
     person("Mauricio", "Vargas", , "mavargas11@uc.cl", role = "ctb",
            comment = c(ORCID = "0000-0003-1017-7574"))
   )
-Description: Install specific version of Java runtime environment at the R
-    project level. The goal of rJavaEnv is to manage multiple Java JDKs in
-    R projects by automating the process of downloading, installing, and
-    configuring Java environments on a per-project basis.  This package is
-    inspired by the renv <https://rstudio.github.io/renv/> package for
-    managing R environments in R projects. You can request a specific Java
-    Development Kit (JDK) in your project, and rJavaEnv will download and
-    install the requested Java environment in a project-specific directory
-    and set the PATH and JAVA_HOME for when you are using this project.
-    Therefore, you can have different Java versions for different projects
-    without contaminating your system with different Java versions.
+Description: The 'rJavaEnv' package addresses common issues with 'Java'
+    environment management in 'R' for users of 'Java'/'rJava'-dependent
+    'R' packages such as 'r5r', 'opentripplanner', 'xlsx', 'openNLP',
+    'rWeka', 'RJDBC', 'tabulapdf', and many more. It resolves common
+    problems like 'Java' not found, 'Java' version conflicts, missing
+    'Java' installations, and the inability to install 'Java' due to lack
+    of administrative privileges. 'rJavaEnv' automates the download,
+    installation, and setup of the 'Java Development Kit' ('JDK') on a
+    per-project basis by setting the relevant 'JAVA_HOME' in the current
+    'R' session or the current working directory (via '.Rprofile', with
+    the user's consent). Similar to what 'renv' does for 'R' packages,
+    'rJavaEnv' allows different 'Java' versions to be used across
+    different projects, but can also be configured to allow multiple
+    versions within the same project (e.g.  with the help of 'targets'
+    package). Note: there are a few extra steps for 'Linux' users, who
+    don't have any 'Java' previously installed in their systemm, and who
+    prefer package installation from source, rather then installing
+    binaries from 'Posit Package Manager'. See documentation for details.
 License: MIT + file LICENSE
 URL: https://github.com/e-kotov/rJavaEnv, https://www.ekotov.pro/rJavaEnv/
 BugReports: https://github.com/e-kotov/rJavaEnv/issues
@@ -28,12 +35,11 @@ Imports:
     jsonlite,
     utils
 Suggests: 
-    knitr,
+    quarto,
     rJava,
-    rmarkdown,
     testthat (>= 3.0.0)
 VignetteBuilder: 
-    knitr
+    quarto
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -3,17 +3,11 @@
 export(java_check_version_cmd)
 export(java_check_version_rjava)
 export(java_clear)
-export(java_clear_distrib_cache)
-export(java_clear_in_project)
-export(java_clear_installed_cache)
 export(java_download)
 export(java_env_set)
 export(java_env_unset)
 export(java_install)
 export(java_list)
-export(java_list_distrib_cache)
-export(java_list_in_project)
-export(java_list_installed_cache)
 export(java_quick_install)
 export(rje_consent)
 importFrom(utils,getFromNamespace)

NEWS.md

@@ -1,3 +1,11 @@
+# rJavaEnv 0.1.1
+
+* Improved documentation
+
+* Better handling of cache directory
+
+* Bug fixes and changes to address CRAN reviewer's comments to the first submission
+
 # rJavaEnv 0.1.0
 
 * Initial release

R/consent.R

@@ -24,6 +24,13 @@
 #' @return `TRUE` if consent is given, otherwise an error is raised.
 #' 
 #' @export
+#' @examples
+#' \dontrun{
+#' 
+#' # to provide consent and prevent other functions from interrupting to get the consent
+#' rje_consent(provided = TRUE)
+#' }
+#' 
 rje_consent <- function(provided = FALSE) {
 
   # Check if consent is already given via environment variable
@@ -33,16 +40,17 @@ rje_consent <- function(provided = FALSE) {
   }
 
   # Check if consent is already given via cache directory
-  user_pacakge_cache_dir <- tools::R_user_dir("rJavaEnv", which = "cache")
-  if (dir.exists(user_pacakge_cache_dir)) {
+  user_package_cache_path <- getOption("rJavaEnv.cache_path")
+  user_package_cache_path <- normalizePath(user_package_cache_path, winslash = "/", mustWork = FALSE)
+  if (dir.exists(user_package_cache_path)) {
     cli::cli_inform("Consent for using rJavaEnv has already been provided.")
     return(invisible(TRUE))
   }
 
   # write welcome message
   template <- system.file("resources/consent-info", package = "rJavaEnv")
   contents <- readLines(template)
-  contents <- gsub("\\$\\{rJavaEnv_CACHE\\}", user_pacakge_cache_dir, contents)
+  contents <- gsub("\\$\\{rJavaEnv_CACHE\\}", user_package_cache_path, contents)
   cli::cli_inform(contents)
 
   # Request user consent if not already provided
@@ -57,7 +65,7 @@ rje_consent <- function(provided = FALSE) {
 
   # Save user consent
   options(rJavaEnv.consent = TRUE)
-  dir.create(user_pacakge_cache_dir, recursive = TRUE, showWarnings = FALSE)
+  dir.create(user_package_cache_path, recursive = TRUE, showWarnings = FALSE)
   cli::cli_inform("Consent has been granted and recorded.")
 
   invisible(TRUE)
@@ -79,7 +87,7 @@ rje_consent_check <- function() {
   if (getOption("rJavaEnv.consent", FALSE)) {
     return(TRUE)
   }
-  if (dir.exists(tools::R_user_dir("rJavaEnv", which = "cache"))){
+  if (dir.exists(getOption("rJavaEnv.cache_path"))) {
     return(TRUE)
   }
 

R/global_params.R

@@ -0,0 +1,10 @@
+#' @title Global Quiet Parameter
+#'
+#' @description
+#' Documentation for the `quiet` parameter, used globally.
+#'
+#' @param quiet A `logical` value indicating whether to suppress messages. Can be `TRUE` or `FALSE`.
+#' @keywords internal
+global_quiet_param <- function(quiet){
+  # this is just a placeholder for global quiet parameter
+}

R/internal_utilities.R

@@ -1,10 +1,10 @@
 #' Detect platform and architecture
 #'
+#' @inheritParams global_quiet_param
 #' @keywords internal
-#' @param verbose Whether to print detailed messages. Defaults to FALSE.
 #' @return A list of length 2 with the detected platform and architecture.
 #'
-platform_detect <- function(verbose = FALSE) {
+platform_detect <- function(quiet = TRUE) {
   sys_info <- tolower(Sys.info())
 
   os <- switch(sys_info["sysname"],
@@ -24,7 +24,7 @@ platform_detect <- function(verbose = FALSE) {
     stop(cli::cli_abort("Unsupported architecture"))
   )
 
-  if (verbose) {
+  if (isFALSE(quiet)) {
     cli::cli_inform("Detected platform: {os}")
     cli::cli_inform("Detected architecture: {arch}")
   }