Merge pull request #46 from e-kotov/44-interface-that-doesnt-affect-rprofile

44 interface that doesnt affect rprofile

Author: e-kotov

.Rbuildignore

@@ -21,3 +21,4 @@
 ^vignettes/bibliography.bib$
 ^vignettes/media$
 ^CRAN-SUBMISSION$
+^vignettes/.quarto$

DESCRIPTION

@@ -45,3 +45,5 @@ Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Depends: 
+    R (>= 4.0)

NAMESPACE

@@ -9,5 +9,7 @@ export(java_env_unset)
 export(java_install)
 export(java_list)
 export(java_quick_install)
+export(java_unpack)
 export(rje_consent)
+export(use_java)
 importFrom(utils,getFromNamespace)

R/java_download.R

@@ -1,7 +1,7 @@
 #' Download a Java distribution
 #'
-#' @param version The Java version to download. If not specified, defaults to the latest LTS version.
-#' @param distribution The Java distribution to download. If not specified, defaults to "Corretto".
+#' @param version `Integer` or `character` vector of length 1 for major version of Java to download or install. If not specified, defaults to the latest LTS version. Can be "8", "11", "17", "21", "22", or 8, 11, 17, 21, or 22.
+#' @param distribution The Java distribution to download. If not specified, defaults to "Amazon Corretto". Currently only \href{https://aws.amazon.com/corretto/}{"Amazon Corretto"} is supported.
 #' @param cache_path The destination directory to download the Java distribution to. Defaults to a user-specific data directory.
 #' @param platform The platform for which to download the Java distribution. Defaults to the current platform.
 #' @param arch The architecture for which to download the Java distribution. Defaults to the current architecture.
@@ -40,18 +40,18 @@ java_download <- function(
     cache_path <- file.path(temp_dir, "rJavaEnv_cache")
   }
 
-  rje_consent_check()
+  # rje_consent_check() # disabling consent check for now
   java_urls <- java_urls_load()
 
   valid_distributions <- names(java_urls)
   valid_platforms <- names(java_urls[[distribution]])
   valid_architectures <- names(java_urls[[distribution]][[platform]])
 
   # Checks for the parameters
-  checkmate::assert(
-    checkmate::check_integerish(version, lower = 1),
-    checkmate::check_character(version, pattern = "^[0-9]+$")
-  )
+  checkmate::check_vector(version, len = 1)
+  version <- as.character(version)
+  checkmate::assert_choice(version, getOption("rJavaEnv.valid_major_java_versions"))
+
   checkmate::assert_choice(distribution, valid_distributions)
 
   # Create the distrib subfolder within the destination directory

R/java_env.R

@@ -38,14 +38,13 @@ java_env_set <- function(
   project_path = NULL,
   quiet = FALSE
 ) {
-  rje_consent_check()
-
+  
   where <- match.arg(where)
   checkmate::assertString(java_home)
   checkmate::assertFlag(quiet)
-
-
-
+  
+  
+  
   if (where %in% c("session", "both")) {
     java_env_set_session(java_home)
     if (!quiet) {
@@ -55,7 +54,8 @@ java_env_set <- function(
       ))
     }
   }
-
+  
+  rje_consent_check()
   if (where %in% c("project", "both")) {
     # consistent with renv behavior for using
     # the current working directory by default
@@ -82,6 +82,14 @@ java_env_set <- function(
 #' @keywords internal
 #'
 java_env_set_session <- function(java_home) {
+  
+  # check if rJava is installed and alread initialized
+  if (requireNamespace("rJava", quietly = TRUE)) {
+    if( getFromNamespace(".jniInitialized", "rJava") == TRUE ) {
+      cli::cli_inform(c("!" = "You have already initialised `rJava` directly or via your Java-dependent R package in the current session. `Java` version can only be set once per session for packages that rely on `rJava`. Unless you restart the R session or run your code in a new R subprocess using `targets` or `callr`, the new `JAVA_HOME` and `PATH` will not take effect."))
+    }
+  }
+  
   Sys.setenv(JAVA_HOME = java_home)
   old_path <- Sys.getenv("PATH")
   new_path <- file.path(java_home, "bin")
@@ -137,17 +145,15 @@ java_env_set_rprofile <- function(
 
 #' Check Java Version with a Specified JAVA_HOME Using a Separate R Session
 #'
-#' This function sets the JAVA_HOME environment variable, initializes the JVM using rJava,
-#' and prints the Java version that would be used if the user sets the given JAVA_HOME
-#' in the current R session. This check is performed in a separate R session to avoid
-#' having to reload the current R session. The reason for this is that once Java is initialized in an R session,
-#' it cannot be uninitialized unless the current R session is restarted.
+#' This function sets the JAVA_HOME environment variable, initializes the JVM using rJava, and prints the Java version that would be used if the user sets the given JAVA_HOME in the current R session. This check is performed in a separate R session to avoid having to reload the current R session. The reason for this is that once Java is initialized in an R session, it cannot be uninitialized unless the current R session is restarted.
 #'
-#' @param java_home The path to the desired JAVA_HOME. If NULL, uses the current JAVA_HOME environment variable.
 #' @inheritParams global_quiet_param
-#' @return TRUE if successful, otherwise FALSE.
+#' @inheritParams java_check_version_cmd
+#' @return A `character` vector of length 1 containing the major Java version.
 #' @examples
+#' \dontrun{
 #' java_check_version_rjava()
+#' }
 #'
 #' @export
 java_check_version_rjava <- function(
@@ -214,28 +220,37 @@ java_check_version_rjava <- function(
         } else {
           cli::cli_inform("With the user-specified JAVA_HOME {output}")
         }
-      } else {
-        cli::cli_inform(c("OK", paste("Java version:", java_version)))
       }
-      return(TRUE)
     }
   } else {
     if (!quiet) cli::cli_alert_danger("Failed to retrieve Java version.")
   }
+
+  matches <- gregexpr('(?<=Java version: \\\")[0-9]{1,2}(?=\\.)', output, perl = TRUE)
+  major_java_ver <- regmatches(output, matches)[[1]]
+  major_java_ver
+
+  # fix 1 to 8, as Java 8 prints "1.8"
+  if (major_java_ver == "1") {
+    major_java_ver <- "8"
+  }
+
+  return(major_java_ver)
 }
 
 #' Check installed Java version using terminal commands
 #'
 #' @param java_home Path to Java home directory. If NULL, the function uses the JAVA_HOME environment variable.
-#'
-#' @return TRUE if successful, otherwise FALSE.
+#' @inheritParams global_quiet_param
+#' @return A `character` vector of length 1 containing the major Java version.
 #' @export
 #'
 #' @examples
 #' java_check_version_cmd()
 #'
 java_check_version_cmd <- function(
-  java_home = NULL
+  java_home = NULL,
+  quiet = FALSE
 ) {
   # Backup the current JAVA_HOME
   old_java_home <- Sys.getenv("JAVA_HOME")
@@ -248,13 +263,13 @@ java_check_version_cmd <- function(
   # Get JAVA_HOME again and check if it's set
   current_java_home <- Sys.getenv("JAVA_HOME")
   if (current_java_home == "") {
-    cli::cli_alert_warning("JAVA_HOME is not set.")
+    if (!quiet) cli::cli_inform(c("!" = "JAVA_HOME is not set."))
     if (!is.null(java_home)) {
       Sys.setenv(JAVA_HOME = old_java_home)
     }
     return(FALSE)
   } else {
-    cli::cli_inform("JAVA_HOME: {.path {current_java_home}}")
+    if (!quiet) cli::cli_inform("JAVA_HOME: {.path {current_java_home}}")
   }
 
   # Check if java executable exists in the PATH
@@ -267,27 +282,29 @@ java_check_version_cmd <- function(
   }
 
   # Check Java path and version using system commands
-  success <- java_check_version_system()
+  major_java_version <- java_check_version_system(quiet = quiet)
 
   # restore original JAVA_HOME that was in the environment before the function was called
   if (!is.null(java_home)) {
     Sys.setenv(JAVA_HOME = old_java_home)
   }
 
-  return(success)
+  return(major_java_version)
 }
 
-#' Check and print Java path and version
+#' Check and print Java path and version using system commands
 #'
 #' This function checks the Java executable path and retrieves the Java version,
 #' then prints these details to the console.
-#'
+#' @inheritParams java_check_version_cmd
+#' @return A `character` vector of length 1 containing the major Java version.
 #' @keywords internal
-#'
-#' @return TRUE if successful, otherwise FALSE.
-java_check_version_system <- function() {
+#' 
+java_check_version_system <- function(
+  quiet
+) {
   which_java <- tryCatch(
-    system2("which", args = "java", stdout = TRUE, stderr = TRUE),
+    Sys.which("java"),
     error = function(e) NULL
   )
   if (is.null(which_java)) {
@@ -303,12 +320,24 @@ java_check_version_system <- function() {
     return(FALSE)
   }
 
-  cli::cli_inform(c(
-    "Java path: {.path {which_java}}",
-    "Java version:\n{.val {paste(java_ver, collapse = '\n')}}"
-  ))
+  if (!quiet) {
+    cli::cli_inform(c(
+      "Java path: {.path {which_java}}",
+      "Java version:\n{.val {paste(java_ver, collapse = '\n')}}"
+    ))
+  }
+
+  # extract Java version
+  java_ver_string <- java_ver[[1]]
+  matches <- gregexpr('(?<=openjdk version \\\")[0-9]{1,2}(?=\\.)', java_ver_string, perl = TRUE)
+  major_java_ver <- regmatches(java_ver_string, matches)[[1]]
+  
+  # fix 1 to 8, as Java 8 prints "1.8"
+  if (major_java_ver == "1") {
+    major_java_ver <- "8"
+  }
 
-  invisible(TRUE)
+  return(major_java_ver)
 }
 
 
@@ -346,7 +375,7 @@ java_env_unset <- function(
     }
   } else {
     if (!quiet) {
-      cli::cli_alert_warning("No .Rprofile found in the project directory: {.path project_path}")
+      cli::cli_inform(c("!" = "No .Rprofile found in the project directory: {.path project_path}"))
     }
   }
 }

R/java_install.R

@@ -1,8 +1,11 @@
 #' Install Java from a distribution file
 #'
-#' @param java_distrib_path The path to the Java distribution file.
-#' @param project_path The project directory where Java should be installed. If not specified or `NULL`, defaults to the current working directory.
-#' @param autoset_java_env Whether to set the `JAVA_HOME` and `PATH` environment variables to the installed Java directory. Defaults to `TRUE`.
+#' @description
+#' Unpack Java distribution file into cache directory and link the installation into a project directory, optionally setting the `JAVA_HOME` and `PATH` environment variables to the Java version that was just installed.
+#' 
+#' @param java_distrib_path A `character` vector of length 1 containing the path to the Java distribution file.
+#' @param project_path A `character` vector of length 1 containing the project directory where Java should be installed. If not specified or `NULL`, defaults to the current working directory.
+#' @param autoset_java_env A `logical` indicating whether to set the `JAVA_HOME` and `PATH` environment variables to the installed Java directory. Defaults to `TRUE`.
 #' @inheritParams java_download
 #' @inheritParams global_quiet_param
 #' @return The path to the installed Java directory.
@@ -24,16 +27,21 @@ java_install <- function(
   quiet = FALSE
 ) {
   rje_consent_check()
-  
-  platforms <- c("windows", "linux", "macos")
-  architectures <- c("x64", "aarch64", "arm64")
-  java_versions <- c("8", "11", "17", "21", "22")
 
   # Resolve the project path
   # consistent with renv behavior
   # https://github.com/rstudio/renv/blob/d6bced36afa0ad56719ca78be6773e9b4bbb078f/R/init.R#L69-L86
   project_path <- ifelse(is.null(project_path), getwd(), project_path)
 
+  installed_path <- java_unpack(
+    java_distrib_path = java_distrib_path,
+    quiet = quiet
+  )
+
+  platforms <- c("windows", "linux", "macos")
+  architectures <- c("x64", "aarch64", "arm64")
+  java_versions <- getOption("rJavaEnv.valid_major_java_versions")
+
   # Extract information from the file name
   filename <- basename(java_distrib_path)
   parts <- strsplit(gsub("\\.tar\\.gz|\\.zip", "", filename), "-")[[1]]
@@ -43,61 +51,6 @@ java_install <- function(
   arch <- parts[vapply(parts, function(x) x %in% architectures, logical(1))][1]
   platform <- parts[vapply(parts, function(x) x %in% platforms, logical(1))][1]
 
-  if (is.na(version)) stop(cli::cli_abort("Unable to detect Java version from filename.", .envir = environment()))
-  if (is.na(arch)) stop(cli::cli_abort("Unable to detect architecture from filename.", .envir = environment()))
-  if (is.na(platform)) stop(cli::cli_abort("Unable to detect platform from filename.", .envir = environment()))
-
-  # Create the installation path in the package cache
-  cache_path <- getOption("rJavaEnv.cache_path")
-  installed_path <- file.path(cache_path, "installed", platform, arch, version)
-
-  # Check if the distribution has already been unpacked
-  if (!dir.exists(installed_path) || length(list.files(installed_path)) == 0) {
-    # Create the directories if they don't exist
-    if (!dir.exists(installed_path)) {
-      dir.create(installed_path, recursive = TRUE)
-    }
-
-    # Determine extraction path based on platform
-    if (platform == "macos") {
-      extract_subdir <- "Contents/Home"
-    } else {
-      extract_subdir <- "."
-    }
-
-    # Extract the files
-    temp_dir <- file.path(tempdir(), "java_temp")
-    if (dir.exists(temp_dir)) {
-      unlink(temp_dir, recursive = TRUE)
-    }
-
-    dir.create(temp_dir, recursive = TRUE)
-
-    if (grepl("\\.tar\\.gz$", java_distrib_path)) {
-      utils::untar(java_distrib_path, exdir = temp_dir)
-    } else if (grepl("\\.zip$", java_distrib_path)) {
-      utils::unzip(java_distrib_path, exdir = temp_dir)
-    } else {
-      stop(cli::cli_abort("Unsupported file format", .envir = environment()))
-    }
-
-    # Safely find the extracted directory
-    extracted_root_dir <- list.files(temp_dir, full.names = TRUE)[1]
-    if (platform == "macos") {
-      extracted_dir <- file.path(extracted_root_dir, "Contents", "Home")
-    } else {
-      extracted_dir <- extracted_root_dir
-    }
-
-    # Move the extracted files to the installation path
-    file.copy(list.files(extracted_dir, full.names = TRUE), installed_path, recursive = TRUE)
-
-    # Clean up temporary directory
-    unlink(temp_dir, recursive = TRUE)
-  } else {
-    if (!quiet) cli::cli_inform("Java distribution {filename} already unpacked at {.path {installed_path}}")
-  }
-
   # Create a symlink in the project directory
   project_version_path <- file.path(project_path, "rjavaenv", platform, arch, version)
   if (!dir.exists(dirname(project_version_path))) {