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Java El Capitan

  1. Java El Capitan Software
  2. Java El Capitan 7
  3. Java For El Capitan 10.11.6

Since I upgraded my Mac to OS X El Capitan (version 10.11.2) I am having problems with the R-package rJava. From what I understood, eventually, it is not a problem of rJava or R or RStudio in the first place, but newer versions of Mac OS X do not play well with the latest versions of Oracle’s Java (jdk). Furthermore, some new security features in Mac OS X prevent that environment path settings are passed along to applications like RStudio.

Even after upgrading to the latest version of Java, while running some applications on macOS Sierra (10.12), El Capitan (OS X 10.11), or Yosemite (OS X 10.10), users see a dialog box prompting to download Java. MacOS Sierra 10.12 or Yosemite (OS X 10.10) message: To open 'application' you need to install the legacy Java SE 6 runtime. I upgraded to El Capitan, with Homebrew & Ruby, and this is how I did it flawlessly. And Xcode and Java, etc. If you don't already have homebrew installed, do that first, so you don't have to deal with SIP issues. Install all Software Updates available in the Apple Menu, up to and including El Capitan.

In what follows, I listed the steps that solved for me the problem that the package rJava could not be loaded from within RStudio under Mac OS X El Capitan (version 10.11.2).

Problem statement

Unfortunately, the package rJava does not just fail to load, but the R GUI for Mac terminates instantly and in RStudio the R-session gets closed. Both effects are pretty annoying! See the screen shot below on how that might look like.

Some research

After searching the web, the details of the problem are still not clear to me. But it appears that OS X has problems recognizing newer versions Oracle’s Java. OS X seams to be looking for a legacy version 6 of Apple’s own build of Java. As shown in the next section one solution seams to be the installation of Apple’s legacy version 6 of Java and a newer version (e.g. 1.8.0_66) of Oracle’s Java at the same time.

The solution

The post available at https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X solved my problem with rJava on Mac OS X 10.11.2.

Java 6

I already had XCode command line tools installed, so I started at section Java 6. I downloaded the legacy Java 6 runtime from https://support.apple.com/kb/DL1572?locale=de_DE and installed the downloaded .dmg file.

Capitan

Java 8

Since I had already installed the latest version of Oracle’s jdk from http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html, I skipped the step.

The output of java_home on my machine looks as follows

Please note the 1.7 version are really not needed here.

R for OS X

The latest version of R was already running, so I skipped this step. The check with javareconf gave the following result.

rJava

As the version of rJava from CRAN did not work, I took the latest version from rforge and installed that one.

A quick check whether rJava can be loaded, is done as follows

RStudio

Running the above check on the RStudio console still gives the following error

For some reason which might be connected to a new security feature of Mac OS X, the file libjvm.dylib cannot be found. Loading this library explicitly, as was described in http://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite, finally solves the problem.


This document instructs you on how to set up a Java programming environment for your Mac OS X computer. It also provides a step-by-step guide for creatingand compiling a Java program in IntelliJ and executing itfrom the command line.

You will need a Mac runningMac OS X 10.13 (High Sierra) to Mac OS X 10.15 (Catalina).


0. Install the Java Programming Environment


The installer installs and configures a Java programming environment, includingOpenJDK 11 andIntelliJ IDEA, Community Edition 2021.1.

  • Log in to the user account in which you will be programming.Your account must have Administrator privileges.
  • Download the Mac OS X installerlift-java.pkg.
  • Double-click lift-java.pkg to install the software.Enter your Mac OS X password when prompted and use all of the default options.

    Warning

    If you have previously used IntelliJ,run this installer only if you want a clean re-install.The installer overwrites IntelliJ IDEA CE.app andthe accompanying user settings.

    Also, by default, the installer overwrite any pre-existing Bash configuration files,such as .bashrc.If you wish to keep yours, see the FAQ.

  • Delete lift-java.pkg (if it is not automatically deleted).

1. Open a Project in IntelliJ


You will develop your Java programs in an application called IntelliJ IDEA, Community Edition.

IntelliJ organizes Java programs into projects.In our context, each project corresponds to one programming assignment.A typical project contains Java programs, associated data files, andcourse-specific settings (such as compiler options, style rules, and textbook libraries).

  • Download the project for your programming assignment to a convenient location(such as the Desktop).

    [ sample project for COS 126 (Princeton) ]

    [ sample project for COS 226 (Princeton) ]

    [ sample project for Computer Science: Programming with a Purpose (Coursera) ]

    [ sample project for Algorithms, Part I or II (Coursera) ]

    Double click the zip file to unzip.This creates a project folder with thename of the corresponding programming assignment (such as hello).Delete the zip file.


    Warning

    The project folders contain course-specific information. Be sure to downloadthe one corresponding to your institution and course.


  • Launch IntelliJ via Finder → Applications → IntelliJ IDEA CE.app.
  • When you launch IntelliJ for the first time,
    • IntelliJ may displaytheJetBrains privacy policy.Scroll down and Accept.
    • IntelliJ may ask if you want to send anonymous usage statistics to JetBrains. Choose your preferred option.
    • IntelliJ will display the Welcome to IntelliJ IDEAscreen.
  • To open a project from the Welcome to IntelliJ IDEA screen,click Open and select the project folder.You should see an assignment logo (in the main editor window) and a list of project files (in the Project View sidebar at left).
    When you launch IntelliJ for the first time,it may take a minute or two to index your files;some features (such as auto importing) will be unavailable until this process completes.


    Warning

    Do not click New Project;this option is intended for advanced programmers.Also, always use Open with a project folder, not an individual file.

  • When you are finished working, select the menu optionIntelliJ IDEA → Quit IntelliJ IDEA (⌘Q) to exit IntelliJ.The next time you launch IntelliJ, your recent projectswill appear in the Welcome to IntelliJ IDEA screen for easy access.

Mac
2. Create a Program in IntelliJ


Now you are ready to write your first Java program.IntelliJ features many specialized programming toolsincluding line numbering, syntax highlighting, bracket matching, auto indenting,auto formatting, auto importing, variable renaming, and continuous code inspection.

  • To create a new Java program:
    • Re-open IntelliJ and the project (if you closed it in the previous step).
    • Click the project name in the Project View sidebar (at left), so that itbecomes highlighted.


    • Select the menu option LIFT → New Java Class.When prompted, type HelloWorld for the Name and click OK.


  • In the main editor window, complete the Java programHelloWorld.java exactly as it appears below.(IntelliJ generates the gray boilerplate code automatically,possibly with the addition of a course header block comment.)If you omit even a semicolon, the program won’t work.
  • As you type, IntelliJ highlights different syntactic elementsin different colors.When you type a left bracket, IntelliJ adds the matching right bracket.When you begin a new line, IntelliJ indents it.


  • To save the file, select the menu option File → Save All (⌘S).When you save the file, IntelliJ re-formats it (as necessary).


    Tip

    IntelliJ is configured to automatically save changes that you make to your files upon various events (such as compiling, executing, closing a file or project,or quitting the IDE).We still recommend using File → Save All (⌘S)to re-format your code.


3. Compile and Execute the Program (from IntelliJ)


Now, it is time to execute (or run) your program.This is the exciting part, where your computer follows the instructionsspecified by your program.Before doing so, you must compile your program intoa form more amenable for execution on a computer.

  • Select the program that you wish to compile and execute in the the Project View sidebar. The program should now appear in the main editor window.
  • To compile your program,select the menu optionLIFT → Recompile 'HelloWorld.java' (⌘B).If the compilation succeeds, you will receive confirmationin the status bar (at bottom).

    If the compilation fails, a Recompile panel will open up (at bottom),highlighting the compile-time errors or warnings.Check your program carefully for typos, using the error messages as a guide.

  • To execute your program,select the menu option LIFT → Run 'HelloWorld' with Arguments (⌘E).Since this program takes no command-line arguments, click OK.

    You should see the output of the program (in white), along with a messagethat the program finished normally (with exit code 0).


Tip

Use the LIFT menu to compile and execute your program from IntelliJ.The Build and Run menus support additional options for advanced programmers.

Also be sure that the main editor window is active before using the LIFTmenu (e.g., by clicking the code you want to compile or execute).


4. Compile and Execute the Program (from the command line)


The command line is a simple and powerful mechanism forcontrolling your programs (e.g., command-line arguments,file redirection, and piping).IntelliJ supplies an embedded terminalfor easy access to the command line.

  • Select the menu option View → Tool Windows → Terminal (⌘2).
  • This will launch a Bash terminal where you type commands.You will see a command prompt that looks something like this:

    The ~/Desktop/hello is the current working directory, where~ is shorthand for your home directory.

  • To compile your program,type the following javac command.More specifically, type the text in yellow that appears on the same line as thecommand prompt.Assuming that the file HelloWorld.java is in the current working directory,you should not see any compile-time errors or warnings.
  • To execute your program,type the following java command:You should see the output of your program beneath the line on which you typed the command.


    Tip

    Typically, you should compile from IntelliJ(because IntelliJ highlights the lines on which anycompile-time errors or warnings occur) and execute from the command line(because the command line makes it is easy to specify command-line argumentsand use file redirection).

Java El Capitan Software


Capitan

Java El Capitan 7

5. Textbook Libraries (from the command line)


To make our textbook libraries accessible to Java from the command line,you will use our wrapper scripts.

Java For El Capitan 10.11.6

  • Computer Science: An Interdisciplinary Approach (including COS 126 students).The programBarnsley.javauses our standard drawing and standard random libraries in stdlib.jar to draw aBarnsley fern.First download Barnsley.java.Then, use the Finder to move itto a project folder (such as hello).Finally, to compile and execute it,type the following commands in the terminal:When you execute the program, a standard drawing window will appearand an image like this one will be generated, one point at a time:

    To get your command prompt back, close the standard drawing window.

  • Algorithms, 4th Edition (including COS 226 and Coursera students).The programCollidingDisks.javauses various libraries in algs4.jarto simulate the motion of n disks subject to the lawsof elastic collision.First download CollidingDisks.javaThen, use the Finder to move it to a project folder (such as percolation).Finally, to compile and execute it,type the following commands in the terminal:When you execute the program, a standard drawing window will appearwith an animation of 20 colliding disks.To get your command prompt back, close the standard drawing window.


    Frequently Asked Questions



    I installed IntelliJ and Java using thelift-java.pkg installerlast semester or year. Should I rerun this semester?
    Yes. This installer includes IntelliJ 2021.1and Java 11.The old installer may have used an earlier version of IntelliJ or Java.
    What happens if I rerun the lift-java.pkg installer?
    It will re-install and re-configure OpenJDK 11, IntelliJ,SpotBugs, PMD, Checkstyle, our textbook libraries,and wrapper scripts.
    I want to install only a subset of the components. How can I accomplish this?
    Run the installer. On the Installation Type screen, click Customizeand mark the desired components:
    • OpenJDK 11: installs Java.
    • Command-Line Tools: installs wrapper scripts likejavac-introcs and javac-algs4.
    • Bash Configuration Files: installs our .bashrc,.bash_profile, and.inputrc files.
    • IntelliJ IDEA, Community Edition 2021.1: installs IntelliJ with our novice-friendly user preferences.

    Typically, we recommend a full install. A custom install can be useful if you already have a specialized.bashrc file.It might also speed things upif you need to re-install, say IntelliJ IDEA, Community Edition 2021.1, but not Java.

    The installer overwrote my specialized .bashrc file. How can I revert to the original version?
    If you didn't want this to happen, it's best to unmark the Bash Configuration Files component during installation, as described in the previous question.If it's too late for that, the autoinstallercreates a backup copy of your .bashrc file by appendinga timestamp to the filename, e.g., .bashrc.20210706-191748.
    The installer failed. How can I investigate why?
    Check the installer log at /var/log/lift.log.
    I have Mac OS X 10.12 (Sierra). Is that too old?
    Yes, sorry. IntelliJ 2021.1 requires Mac OS X 10.13 (High Sierra) or newer.
    How long will the installer take to complete installation?
    Once downloaded, it should take about a minute.If you have anti-malware protection software running (such as McAfee Endpoint), it couldtake 5–10 minutes.
    What does the lift-java.pkg installer do?
    In short, it installs and configures Java, IntelliJ,SpotBugs,PMD,Checkstyle,and our textbook libraries,along with accompanying command-line tools.Here is a more detailed list:
    • Installs OpenJDK 11.0.11.
    • InstallsIntelliJ 2021.1.3with novice-friendly user preferences.
    • Installs the following command-line tools for Java:
      • The textbook librariesstdlib.jar andalgs4.jar.
      • Java wrapper scripts, includingjavac-algs4 andjava-algs4.
      • Custom.bashrc,.bash_profile, and.inputrc files.
      • SpotBugs 4.2.3;our SpotBugs configuration filespotbugs.xml;and wrapper script spotbugs.
      • PMD 6.34.0;our PMD configuration file pmd.xml;and wrapper script pmd.
      • Checkstyle 8.31;various configuration files(checkstyle-cos126.xml,checkstyle-cos226.xml,checkstyle-coursera.xml, andcheckstyle-suppressions.xml);custom checks checkstyle-lift.jar;and wrapper script checkstyle.
    How is the software licensed?
    All of the included software is licensed under various open-source licenses.
    • IntelliJ IDEA, Community Edition is licensed under theApache License, Version 2.0.
    • OpenJDK 11 is licensed under theGNU General Public License,version 2, with the Classpath Exception.
    • SpotBugs is licensed under theGNU Lesser Public License, Version 2.1.
    • Checkstyle is licensed under theGNU Lesser Public License, Version 2.1.
    • PMD is licensed under a BSD-style license.
    • stdlib.jar and algs4.jar are licensed under theGNU General Public License, Version 3.
    What’s the sha256sum of lift-java.pkg?
    2d554fe9c63aa89e3d56b83424e1a2c55dd5d3218c1761e25967a12fc313f5b5
    Can I run the installer from the command line?
    Yes. Use the command sudo installer -verbose -pkg lift-java.pkg -target /
    How can I uninstall the software?
    • To uninstall OpenJDK 11,delete the following directory:
      • /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/
    • To uninstall IntelliJ, delete the following:
      • /Applications/IntelliJ IDEA CE.app
      • ~/Library/Application Support/JetBrains/IdeaIC2021.1/
      • ~/Library/Caches/JetBrains/IdeaIC2021.1/
      • ~/Library/Logs/JetBrains/IdeaIC2021.1/
    • To uninstall SpotBugs, PMD, Checkstyle,and our textbook libraries, delete the following directory:
      • /usr/local/lift/
    • To uninstall our wrapper scripts, delete the following files:
      • /usr/local/bin/javac-{algs4,introcs}
      • /usr/local/bin/java-{algs4,introcs}
      • /usr/local/bin/jshell-{algs4,introcs}
      • /usr/local/bin/spotbugs
      • /usr/local/bin/pmd
      • /usr/local/bin/checkstyle
    Java FAQ
    Can I use a vendor and version of Java other than OpenJDK 11?
    Yes.You may use any version of Java 8 or newer from either Oracle or OpenJDK.However, if you do so, you will need to manually configure the Platform SDK and Project SDK viaIntelliJ via File → Project Structure.We recommend sticking to the long-term support (LTS) versions: Java 8, Java 11, and Java 17.
    How can I check which version of Java is installed (and where it is installed)?
    Type the following commands in the terminal:It’s important that the Java version numbers match and that you see the number11,but the rest is not critical.
    How does this custom version of IntelliJ different from the standard one?
    IntelliJis an industrial-strength integrated development environment (IDE),suitable for use by professional programmers.The installer configures your user preferences to make itmore suitable for use by novice programmers:
    • Disables all built-in plugins except Terminal and JUnit. Installs the SpotBugs, Checkstyle-IDEA, Run-with-Arguments, Save-Actions, and Archive browser plugins.
    • Eliminates or reduces various popup elements (lightbulbs, code folding, breadcrumbs, gutter markers, notifications, parameter hints).
    • Simplifies menus and toolbars, hiding advanced options.
    • Disables live templates and postfix completion.
    • Adopts the Obsidian Black color scheme.
    • Auto-configures Java upon installation.
    • Adds a few keyboard shortcuts.

    The course-specific project folders perform additional customizations:

    • Streamlines autocomplete to display only relevant libraries(such as java.lang,java.util, and algs4.jar).
    • Configures SpotBugs and Checkstyle with course-specific rules.
    • Provides course-specific libraries (such as algs4.jar).
    • Enables auto-formatting of code on save.
    • Enables auto-importing of Java libraries.
    How can I manually configure the Platform SDK and Project SDK in IntelliJ?
    The installer should configure the Platform SDK automatically.To configure it manually,
    • Navigate to File → Project Structure → Platform Settings → SDKs.
    • Click the + symbol (top left) to add an SDK.
    • Locate an SDK. A typical location for a Java SDK onMac OS X is /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home/.
    • Use the shorthand name suggested by IntelliJ(e.g., 11 for version 11.0.11).

    To manually configure the Project SDK,

    • Navigate to File → Project Structure → Project Settings → Project.
    • Choose the desired Project SDK from the drop-down list.
    • Be sure to use 8 as the Project language level, as our autogradercurrently supports only Java 8 features.
    Which are the most important IntelliJ menu options to remember?
    Here are the most important ones (and their shortcuts).
    • LIFT → New Java Class (⌘N). Create a new Java class.
    • LIFT → Recompile (⌘B). Compile the current program.
    • LIFT → Run with Arguments (⌘E). Run the current program with command-line arguments.
    • LIFT → Open in Terminal (⌘T). Open a new Terminal tab.
    • File → Save All (⌘S). Save (and reformat) all open files.
    • View → Tool Windows → Project (⌘1). Show/hide the Project View sidebar.
    • View → Tool Windows → Terminal (⌘2). Show/hide the Terminal window.
    Any special characters to avoid when naming IntelliJ projects or files?
    Do not use an exclamation mark ! as the last characterin the project folder (or any directory name along the path to your project folder);that will confuse both IntelliJ and Checkstyle.
    How can I create a new project in IntelliJ?
    If you want to inherit all of the properties of an existing project,
    • Use the Finder to copy the project folder,giving it your preferred name.
    • Delete any unwanted files.
    • Be sure to keepthe .iml file (which defines the project),the .idea subdirectory (which containsthe IntelliJ course preferences), andthe .lift subdirectory (which contains the courselibraries).

    To create a new project from scratch, you can use the Create New Project option from theWelcome screen. But, we do not recommend this approach for novice programmers.

    Can I use a version of IntelliJ that is more recent than 2021.1.3?
    Yes, though if it is 2021.2 (or above),you will need to migrate your user preferences.
    How I can I restore the original IntelliJ settings(instead of the abbreviated novice-friendly ones)?
    • To restore the menus and toolbars: Preferences → Appearances & Behavior → Menus and Toolbars → Restore All Defaults.
    • To restore all settings: Help → Find Action → Restore Default Settings.
    Command-Line / Embedded Terminal FAQ
    When I compile or execute a program from the command line that uses one of thetextbook libraries, I get an error that it cannot find the library. How can I fix this?
    Make sure that you are using the appropriate wrapper script,such as javac-algs4or java-algs4.
    How should I configure Bash?
    If you followed our instructions, our wrapper scripts (such asjavac-algs4 andjava-algs4)should already be available.

    Our autoinstaller customizes the command line in a few ways by copying these three configuration files:.bashrc,.bash_profile, and.inputrc.

    How do I break out of a program in an infinite loop?
    Type Ctrl-C.
    How do I specify EOF to signal that standard input is empty?
    On Mac OS X and Linux, type EnterCtrl-D.On Windows, type EnterCtrl-ZEnter,even in Git Bash.
    How can I run SpotBugs, PMD, and Checkstyle from the command line?
    The installer includes wrapper scripts to simplify this process.
    • To run SpotBugs 4.2.3, type the following command in the terminal:The argument must be a list of .class files.Here is a list ofbug descriptions.
    • To run PMD 6.34.0, type the following command in the terminal:The argument must be either a single .java file ora directory containing one or more .java files.Here is a list of bug patterns.
    • To run Checkstyle 8.31, type one ofthe following commands in the terminal, depending on whether you are COS 126, COS 226, or Coursera student:The argument must be a list of .java files.Here is a list ofavailable checks.
    How can I change the default shell in the Terminal application from zshto bash?
    Beginning with OS X 10.15 (Catalina), the default shell is zsh.To change it to bash, type the following commandinto the Terminal application and enter your OS X password:Finally, close the Terminal application and reopen it.Note that the embedded terminal within IntelliJ isconfigured to use bash regardless ofthe default shell for the Terminal application.