Merge pull request #21 from e-kotov/main

resync to main

.github/workflows/pkgdown.yaml

@@ -34,7 +34,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, any::bookdown, local::.
           needs: website
 
       - name: Build site

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

CITATION.cff

@@ -43,6 +43,63 @@ contact:
   email: kotov.egor@gmail.com
   orcid: https://orcid.org/0000-0001-6690-5345
 references:
+- type: software
+  title: checkmate
+  abstract: 'checkmate: Fast and Versatile Argument Checks'
+  notes: Imports
+  url: https://mllg.github.io/checkmate/
+  repository: https://CRAN.R-project.org/package=checkmate
+  authors:
+  - family-names: Lang
+    given-names: Michel
+    email: michellang@gmail.com
+    orcid: https://orcid.org/0000-0001-9754-0393
+  year: '2024'
+- type: software
+  title: cli
+  abstract: 'cli: Helpers for Developing Command Line Interfaces'
+  notes: Imports
+  url: https://cli.r-lib.org
+  repository: https://CRAN.R-project.org/package=cli
+  authors:
+  - family-names: Csárdi
+    given-names: Gábor
+    email: csardi.gabor@gmail.com
+  year: '2024'
+- type: software
+  title: curl
+  abstract: 'curl: A Modern and Flexible Web Client for R'
+  notes: Imports
+  url: https://jeroen.r-universe.dev/curl
+  repository: https://CRAN.R-project.org/package=curl
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: jeroen@berkeley.edu
+    orcid: https://orcid.org/0000-0002-4035-0289
+  year: '2024'
+- type: software
+  title: jsonlite
+  abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
+  notes: Imports
+  url: https://jeroen.r-universe.dev/jsonlite
+  repository: https://CRAN.R-project.org/package=jsonlite
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: jeroen@berkeley.edu
+    orcid: https://orcid.org/0000-0002-4035-0289
+  year: '2024'
+- type: software
+  title: utils
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  institution:
+    name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -55,6 +112,17 @@ references:
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
   year: '2024'
+- type: software
+  title: rJava
+  abstract: 'rJava: Low-Level R to Java Interface'
+  notes: Suggests
+  url: http://www.rforge.net/rJava/
+  repository: https://CRAN.R-project.org/package=rJava
+  authors:
+  - family-names: Urbanek
+    given-names: Simon
+    email: simon.urbanek@r-project.org
+  year: '2024'
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -98,17 +166,6 @@ references:
     email: rich@posit.co
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2024'
-- type: software
-  title: rJava
-  abstract: 'rJava: Low-Level R to Java Interface'
-  notes: Suggests
-  url: http://www.rforge.net/rJava/
-  repository: https://CRAN.R-project.org/package=rJava
-  authors:
-  - family-names: Urbanek
-    given-names: Simon
-    email: simon.urbanek@r-project.org
-  year: '2024'
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -121,61 +178,4 @@ references:
     email: hadley@posit.co
   year: '2024'
   version: '>= 3.0.0'
-- type: software
-  title: checkmate
-  abstract: 'checkmate: Fast and Versatile Argument Checks'
-  notes: Imports
-  url: https://mllg.github.io/checkmate/
-  repository: https://CRAN.R-project.org/package=checkmate
-  authors:
-  - family-names: Lang
-    given-names: Michel
-    email: michellang@gmail.com
-    orcid: https://orcid.org/0000-0001-9754-0393
-  year: '2024'
-- type: software
-  title: cli
-  abstract: 'cli: Helpers for Developing Command Line Interfaces'
-  notes: Imports
-  url: https://cli.r-lib.org
-  repository: https://CRAN.R-project.org/package=cli
-  authors:
-  - family-names: Csárdi
-    given-names: Gábor
-    email: csardi.gabor@gmail.com
-  year: '2024'
-- type: software
-  title: curl
-  abstract: 'curl: A Modern and Flexible Web Client for R'
-  notes: Imports
-  url: https://jeroen.r-universe.dev/curl
-  repository: https://CRAN.R-project.org/package=curl
-  authors:
-  - family-names: Ooms
-    given-names: Jeroen
-    email: jeroen@berkeley.edu
-    orcid: https://orcid.org/0000-0002-4035-0289
-  year: '2024'
-- type: software
-  title: jsonlite
-  abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
-  notes: Imports
-  url: https://jeroen.r-universe.dev/jsonlite
-  repository: https://CRAN.R-project.org/package=jsonlite
-  authors:
-  - family-names: Ooms
-    given-names: Jeroen
-    email: jeroen@berkeley.edu
-    orcid: https://orcid.org/0000-0002-4035-0289
-  year: '2024'
-- type: software
-  title: utils
-  abstract: 'R: A Language and Environment for Statistical Computing'
-  notes: Imports
-  authors:
-  - name: R Core Team
-  institution:
-    name: R Foundation for Statistical Computing
-    address: Vienna, Austria
-  year: '2024'
 

DESCRIPTION

@@ -1,9 +1,12 @@
 Package: rJavaEnv
 Title: Java Environments for R Projects
 Version: 0.0.1
-Authors@R: 
+Authors@R: c(
     person("Egor", "Kotov", , "kotov.egor@gmail.com", role = c("aut", "cre", "cph"),
-           comment = c(ORCID = "0000-0001-6690-5345"))
+           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 automatingthe process of downloading, installing, and
@@ -34,4 +37,4 @@ VignetteBuilder:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2.9000

R/internal_utilities.R

@@ -47,7 +47,6 @@ java_urls_load <- function() {
   jsonlite::fromJSON(json_file, simplifyVector = FALSE)
 }
 
-
 #' Test all Java URLs
 #'
 #' @keywords internal

R/java_download.R

@@ -69,8 +69,11 @@ java_download <- function(version = 21,
 
   url_template <- java_urls[[distribution]][[platform]][[arch]]
   url <- gsub("\\{version\\}", version, url_template)
+  url_md5 <- gsub("latest/", "latest_checksum/", url)
 
   dest_file <- file.path(dest_dir, basename(url))
+  dest_file_md5 <- paste0(file.path(dest_dir, basename(url_md5)), ".md5")
+
 
   if (verbose) {
     cli::cli_inform("Downloading Java {version} ({distribution}) for {platform} {arch} to {dest_file}", .envir = environment())
@@ -82,8 +85,20 @@ java_download <- function(version = 21,
     }
   } else {
     curl::curl_download(url, dest_file, quiet = FALSE)
+    curl::curl_download(url_md5, dest_file_md5, quiet = TRUE)
     if (verbose) {
       cli::cli_inform("Download completed.", .envir = environment())
+
+      md5sum <- tools::md5sum(dest_file)
+      md5sum_expected <- readLines(dest_file_md5, warn = FALSE)
+
+      if (md5sum != md5sum_expected) {
+        cli::cli_alert_danger("MD5 checksum mismatch. Please try downloading the file again.", .envir = environment())
+        unlink(dest_file)
+        return(NULL)
+      } else {
+        cli::cli_inform("MD5 checksum verified.", .envir = environment())
+      }
     }
   }
 

R/java_env.R

@@ -13,7 +13,7 @@
 #' }
 java_env_set <- function(java_home,
                          where = c("both", "session", "project"),
-                         verbose = T) {
+                         verbose = TRUE) {
   where <- match.arg(where)
   checkmate::assertString(java_home)
   checkmate::assertFlag(verbose)
@@ -159,7 +159,7 @@ java_check_version_rjava <- function(java_home = NULL, verbose = TRUE) {
 
   # Process and print the output
   if (length(output) > 0) {
-    if (any(grepl("error", tolower(output)))){
+    if (any(grepl("error", tolower(output)))) {
       cli::cli_alert_danger("Failed to retrieve Java version.")
       return(FALSE)
     } else {
@@ -179,7 +179,6 @@ java_check_version_rjava <- function(java_home = NULL, verbose = TRUE) {
   } else {
     if (verbose) cli::cli_alert_danger("Failed to retrieve Java version.")
   }
-
 }
 
 #' Check installed Java version using terminal commands