pages tagged macOS

Installing and configuring mutt

Tue, 04 Feb 2020 19:44:45 +0000

Intro to Mutt

mutt is a text-based mail client for Unix operating systems.

Installing `mutt`

brew install mutt

Installing `getmail`

brew install getmail

Installing and configuring Homebrew

Sun, 02 Jul 2017 02:09:51 +0000

Topics

How to upgrade if Homebrew stuck at an old version?

$ "$(brew --repo)" && git fetch && git reset --hard origin/master && brew update

Installing and configuring Apache HTTP Server on macOS

Tue, 16 May 2017 23:59:39 +0000

previous version of Apache configuration files

Apache configuration file

$ cd /etc/apache2/users
$ touch "${USERNAME}.conf"
$ sudo chmod 644 "${USERNAME}.conf"

The configuration file "${USERNAME}.conf":

<Directory "/Users/XXX/Sites/">
  AllowOverride All
  Options Indexes MultiViews FollowSymLinks
  Require all granted
</Directory>

`/etc/apache2/httpd.conf`

LoadModule authz_host_module libexec/apache2/mod_authz_host.so
LoadModule authz_core_module libexec/apache2/mod_authz_core.so
LoadModule userdir_module libexec/apache2/mod_userdir.so
LoadModule vhost_alias_module libexec/apache2/mod_vhost_alias.so
Include /private/etc/apache2/extra/httpd-userdir.conf
Include /private/etc/apache2/extra/httpd-vhosts.conf

`/etc/apache2/extra/httpd-userdir.conf`

Include /private/etc/apache2/users/*.conf

Restarting Apache server

$ sudo apachectl restart

References

John Foderaro, How to Set up Apache in macOS Sierra 10.12, 2016.
How does ServerName and ServerAlias work?
Common Apache Misconfigurations

Installing and configuring Java on macOS

Tue, 16 May 2017 23:59:39 +0000

This is a note on my experience of installing Java on macOS 10.9.2.

macOS has its own system Java which as of macOS 10.9.2 is at version 1.6.0_65. It's more or less consistent with Java 6 (Java Language and Virtual Machine Specifications version SE 6). I'd like to keep macOS's system Java for various tasks and applications such as Mathematica which requires on Java 6. It's said that Apple no longer supports Java as a system component, so it's possile there will not be future major version update to Java 7 and higher.

The new "Java" I'd like to install is Oracle's Java. Oracle calls it "Java Platform (JDK) Platform". JDK is Java Development Kit which is the software package one needs to do Java software development. It's currently at version "Java SE 7" and is updated to "JDK SE 8" in March 2014. I'd like to install it for learning new Java features and used it in some projects.

macOS's system Java

The 'java' executable and Java Virtual Machines

The default command-line java on macOS 10.9.2 is version 1.6.0_65:

$ which java
/usr/bin/java
$ java -version
java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)

This java along with other Java related binaries in the same path /usr/bin/ are actually symbolic links pointing to OS X's default installation directory for Java which in turn is part of system libraries /System/Library/:

$ ls -l /usr/bin/*java*
lrwxr-xr-x  1 root  wheel  74 Nov  3 10:29 /usr/bin/java -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java
lrwxr-xr-x  1 root  wheel  75 Nov  3 10:29 /usr/bin/javac -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javac
lrwxr-xr-x  1 root  wheel  77 Nov  3 10:29 /usr/bin/javadoc -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javadoc
lrwxr-xr-x  1 root  wheel  75 Nov  3 10:29 /usr/bin/javah -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javah
lrwxr-xr-x  1 root  wheel  75 Nov  3 10:29 /usr/bin/javap -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javap
lrwxr-xr-x  1 root  wheel  76 Nov  3 10:29 /usr/bin/javaws -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javaws

So the java at command line is actually using /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java. The Current directory is actually also a symbolic link:

$ ls -la /System/Library/Frameworks/JavaVM.framework/Versions/
total 64
drwxr-xr-x  11 root  wheel  374 Nov  3 10:30 .
drwxr-xr-x  12 root  wheel  408 Nov  3 10:30 ..
lrwxr-xr-x   1 root  wheel   10 Nov  3 10:29 1.4 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Nov  3 10:29 1.4.2 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Nov  3 10:29 1.5 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Nov  3 10:29 1.5.0 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Nov  3 10:29 1.6 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Nov  3 10:29 1.6.0 -> CurrentJDK
drwxr-xr-x   8 root  wheel  272 Nov  3 10:30 A
lrwxr-xr-x   1 root  wheel    1 Nov  3 10:29 Current -> A
lrwxr-xr-x   1 root  wheel   59 Nov  3 10:29 CurrentJDK -> /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents

So this further mean the java at command line is actually using /System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/java:

$ ls -la /System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/java
-rwxr-xr-x  1 root  wheel  54624 Nov  3 10:29 /System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/java
$ /System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/java -version
java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)

Difference between /System/Library/Frameworks/ and /Library/:

The /System/Library/Frameworks/ path is where macOS installs its essential framework packages such as Java. The framework packages are shared by multiple applications. Different applications may need different versions of the same package so in general there can be multiple versions of the same package. Third-party libraries is installed in /Library/.

/System/Library/Java/:

All the previous versions of Java {1.4, 1.5, ..., 1.6.0} is redirected to CurrentJDK and then to /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents, perhaps for backwards compatibility. And the "current" Java is pointed to Current/ and then to A/. I guess 'A' stands for "Automatic". Also, I noted that there is one Apple's Java VM:

$ ls -la /System/Library/Java/JavaVirtualMachines/
total 0
drwxr-xr-x  3 root  wheel  102 Oct 10 11:13 .
drwxr-xr-x  5 root  wheel  170 Nov  3 10:30 ..
drwxr-xr-x  3 root  wheel  102 Oct 10 11:13 1.6.0.jdk

I'm not sure what's the relation between /System/Library/Frameworks/JavaVM.framework/ and /System/Library/Java. My guess is that JavaVM.framework is newly introduced and used 1) as an "interface" which maintain various links to /System/Library/Java/ for previous versions; 2) to store the "current" version of system "Java" in /System/Library/Frameworks/JavaVM.framework/Versions/A/.

Apple has a web site that provides downloading of macOS system Java.

`JAVA_HOME` environment variable

$ echo $JAVA_HOME
/System/Library/Frameworks/JavaVM.framework/Home
$ ls -la /System/Library/Frameworks/JavaVM.framework/Home
lrwxr-xr-x  1 root  wheel  24 Apr  1 19:36 /System/Library/Frameworks/JavaVM.framework/Home -> Versions/CurrentJDK/Home
$ ls -la /System/Library/Frameworks/JavaVM.framework/Versions/
total 64
drwxr-xr-x  11 root  wheel  374 Apr  1 19:37 .
drwxr-xr-x  12 root  wheel  408 Apr  1 19:37 ..
lrwxr-xr-x   1 root  wheel   10 Apr  1 19:36 1.4 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Apr  1 19:36 1.4.2 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Apr  1 19:36 1.5 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Apr  1 19:36 1.5.0 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Apr  1 19:36 1.6 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Apr  1 19:36 1.6.0 -> CurrentJDK
drwxr-xr-x   8 root  wheel  272 Apr  1 19:37 A
lrwxr-xr-x   1 root  wheel    1 Apr  1 19:36 Current -> A
lrwxr-xr-x   1 root  wheel   59 Apr  1 19:36 CurrentJDK -> /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents

Notice that it does not point to a Home inside /System/Library/Frameworks/JavaVM.framework/Versions/A/. Actually A/ does not contain a Home/. I'm not sure why there are both /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Commands (which points to /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/) and /System/Library/Frameworks/JavaVM.framework/Versions/A/Commands.

(Re-)install macOS's system Java

If for some reason you need to (re-)install Apple's system Java, you can download it from Apple's support site http://support.apple.com/downloads/#java. For example, as of April 2014, I will choose "Java for OS X 2013-005" for macOS 10.9.2.

There is also packages called "Java for macOS 10.6 Update 17 Developer Package" or "Java for OS X 2013-005 Developer Package" that "contains JavaDoc, tools documentation, and native framework headers". I've never tried these.

Preventing future macOS update to Java

If you decide to use Oracle JDK exclusively in future, it maybe desirable to more "thoroughly" delete Apple's Java. This is what I've not attempted to do.

The possible removals you'd need are

$ rm -rf /System/Library/Java/JavaVirtualMachines/
$ rm /private/var/db/receipts/com.apple.pkg.JavaForMacOSX*

and edit the installation receipts /Library/Receipts/InstallHistory.plist and remove the <dict> XML elements that has com.apple.Java* in it:

$ ack "com\.apple.*ava.*" /Library/Receipts/InstallHistory.plist
            <string>com.apple.pkg.JavaSDKLeo</string>
            <string>com.apple.pkg.JavaForMacOSX10.6Update3</string>
            <string>com.apple.pkg.JavaForMacOSX10.6Update4</string>
            <string>com.apple.pkg.JavaForMacOSX10.6Update5</string>
            <string>com.apple.pkg.JavaForMacOSX10.6</string>
            <string>com.apple.pkg.JavaForMacOSX10.6</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaForMacOSX10.6</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaForMacOSX10.6</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaForMacOSX10.6</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaForMacOSX10.6</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaForMacOSX10.6</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaForMacOSX10.6</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaTools</string>
            <string>com.apple.pkg.JavaEssentials</string>
            <string>com.apple.pkg.JavaEssentials</string>
            <string>com.apple.pkg.JavaForMacOSX107</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaMDNS</string>
            <string>com.apple.pkg.JavaEssentials</string>
            <string>com.apple.pkg.JavaForMacOSX107</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaMDNS</string>
            <string>com.apple.pkg.JavaTools</string>
            <string>com.apple.pkg.JavaEssentials</string>
            <string>com.apple.pkg.JavaEssentials</string>
            <string>com.apple.pkg.JavaForMacOSX107</string>
            <string>com.apple.pkg.JavaSecurity</string>
            <string>com.apple.pkg.JavaMDNS</string>

Installing Oracle's Java

The path `/Library/Java/`

Third-party Java will be installed to /Library/Java. Note there is not a /System/ in front of it.

$ ls -la  /Library/Java
total 8
drwxrwxr-x   5 root  admin   170 Nov  3 10:30 .
drwxr-xr-x+ 72 root  wheel  2448 Mar  8 08:08 ..
drwxrwxr-x   2 root  admin    68 Nov  3 10:30 Extensions
lrwxr-xr-x   1 root  wheel    48 Nov  3 10:29 Home -> /System/Library/Frameworks/JavaVM.framework/Home
drwxr-xr-x   2 root  wheel    68 Nov  3 10:30 JavaVirtualMachines
$ ls -la /Library/Java/JavaVirtualMachines/
total 0
drwxr-xr-x  2 root  wheel   68 Nov  3 10:30 .
drwxrwxr-x  5 root  admin  170 Nov  3 10:30 ..

The symbolic link Home -> /System/Library/Frameworks/JavaVM.framework/Home is how macOS by default manages the $JAVA_HOME environment variable for third-party Java. $JAVA_HOME by default is set to /Library/Java/Home which is updated to point to the current version of Java /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/.

Currently I have no third-party Java and hence an empty /Library/Java/JavaVirtualMachines/.

To install a new non-system non-Apple Java on Mac, one can install Oracle's JDK, and possibly OpenJDK). These have versions newer than Apple's Java.

My goal at the time of writing this note is to install the newer Java (Java Language and Virtual Specification, version SE 7 or even version "Java SE 8") while keep macOS's own system Java (version "Java SE 6"), since I need both for different work.

Installing Oracle's JDK

To install "Java 7", download "Java SE Development Kit 7" for "macOS x64" from Oracle. Install that. After that, you should find /Library/Java/JavaVirtualMachines/ has the newly installed Oracle JDK:

$ ls /Library/Java/JavaVirtualMachines
jdk1.7.0_51.jdk
$ /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/bin/java -version
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)

But this does not affect the default command-line java:

$ java -version
java 1.6.0_65

Now you have both Java 6 and 7 on the computer and can use them for different purposes.

Making Oracle Java binaries available at command line

Depending on if it's desirable to you, you may want to link Java related binaries in /usr/bin

$ ls -la /usr/bin/*java*
lrwxr-xr-x  1 root  wheel  74 Nov  3 10:29 /usr/bin/java -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java
lrwxr-xr-x  1 root  wheel  75 Nov  3 10:29 /usr/bin/javac -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javac
lrwxr-xr-x  1 root  wheel  77 Nov  3 10:29 /usr/bin/javadoc -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javadoc
lrwxr-xr-x  1 root  wheel  75 Nov  3 10:29 /usr/bin/javah -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javah
lrwxr-xr-x  1 root  wheel  75 Nov  3 10:29 /usr/bin/javap -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javap
lrwxr-xr-x  1 root  wheel  76 Nov  3 10:29 /usr/bin/javaws -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javaws

to Oracle's Java, either under a different name, say java7, or the default name java, and optionally rename the existing macOS's java to java6 first. I created java7:

$ sudo ln -s /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/bin/java /usr/bin/java7
$ sudo ln -s /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/bin/javac /usr/bin/javac7
...

And you probably want to keep $JAVA_HOME consistent with java. If java is pointing to Oracle Java, you'd want

$ ln -s /Library/Java/Home /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home

Managing `JAVA_HOME` for different environments

JAVA_HOME is a UNIX envrionment variable that are sometimes used to determine which and how Java Virtual Machine is run. It's a somewhat complex issue to set them appropriately for different purposes.

Here is what I've done:

Setting `JAVA_HOME` for Bash

Add the following code to shell configuration file. There are multiple configuration files for Bash shell including .profile, .bashrc, /etc/profile. For me, I used $HOME/.bashrc:

## Method 1: Set JAVA_HOME to macOS's system Java Home/ which is a symlink pointing to
## /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home as of macOS 10.9.2
## When there are multiple versions of Java installed, using the /usr/libexec/java_home method below is better.
# export JAVA_HOME="/System/Library/Frameworks/JavaVM.framework/Home"

## Method 2: Alternatively, set the path using the /usr/libexec/java_home command with a parameter -v to choose specific version of Java
## Use the following to see verbose info about available versions of Java when unsure.
## /usr/libexec/java_home -V
## /usr/libexec/java_home -Vv 1.6

## Use Java 6    
export JAVA_HOME=`/usr/libexec/java_home -v 1.6`
## Use Java 7  
# export JAVA_HOME=`/usr/libexec/java_home -v 1.7`
## Use Java 8  
# export JAVA_HOME=`/usr/libexec/java_home -v 1.8`

So, potentially, one can tweak the lines in method 2 and choose different version to use. Notice that the binary /usr/libexec/java_home is used to determine the Java home directory:

$ /usr/libexec/java_home -V
Matching Java Virtual Machines (4):
    1.8.0, x86_64:  "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home
    1.7.0_51, x86_64:   "Java SE 7" /Library/Java/JavaVirtualMachines/jdk1.7.0_51/Contents/Home
    1.6.0_65-b14-462, x86_64:   "Java SE 6" /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
    1.6.0_65-b14-462, i386: "Java SE 6" /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home

/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home

It seems it recognizes all available JVMs and picks the home directory from the latest version.

Setting `JAVA_HOME` for Mathematica

I'm a heavy user of Mathematica. As of Mathematica 9, it is developed based on Java 6 and its Java related functionalities such as J/Link package may not work properly if a different version of Java is used.

There are two configurations to set and/or check.

`JAVA_HOME`

As of Mathematica 9, verify that Mathematica's $JAVA_HOME is pointing to macOS's system Java's JVM 1.6.*:

In[1]:= Import["!echo $JAVA_HOME", "Text"]

Out[1]= "/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"

In[2]:= Environment["JAVA_HOME"]

Out[2]= "/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"

I'm not sure why the following does not work:

In[3]:= Import["!java -version", "Text"]

Out[3]= ""

`CommandLine -> "java"`

One can "install" Java inside Mathematica runtime by the function InstallJava and then use Java classes inside Mathematica programs.

The InstallJava function or its close relative ReinstallJava has an option called CommandLine:

CommandLine -> "cmd"    use the specified command line to launch the Java runtime, instead of "java"

Some examples of that is

InstallJava[]

InstallJava[CommandLine -> "java"]

InstallJava[CommandLine -> "java --Xmx1024m"]

The source code in $InstallationDirectory/SystemFiles/Links/JLink/Kernel/InstallJava.m indicates that if CommandLine is not used, it will uses Mathematica's own Java ToFileName[{getJLinkAppDir[], "JLink.app", "Contents", "MacOS"}, "JavaApplicationStub"]. If CommandLine -> "java" is used, make sure it's the right version:

In[8]:= Needs["JLink`"]
ReinstallJava[CommandLine->"java"]
LoadJavaClass["java.lang.System"]
java`lang`System`getProperty["java.version"]
Out[9]= LinkObject[java -classpath "/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.jar" -Xdock:name=J/Link -Xmx256m  -Djava.system.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "/tmp/m00000347291",166,4]
Out[10]= JavaClass[java.lang.System,<>]
Out[11]= 1.6.0_65

If the output of getProperty["java.version"] is not consistent with JAVA_HOME, or if LoadJavaClass["java.lang.System"] issues errors, there must be some problem.

See the attached notebook containing these testing code.

Methods for starting Mathematica

`open -a Mathematica`

If I start Mathematica with open -a Mathematica from command line, which would lead Mathematica to inherit JAVA_HOME set in .bashrc, I get the correct JAVA_HOME value

In[1]:= Import["!echo $JAVA_HOME", "Text"]

Out[1]= "/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/\
Home"

In[2]:= Environment["JAVA_HOME"]

Out[2]= "/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/\
Home"

as well as correct version of Java:

In[16]:= Needs["JLink`"]
ReinstallJava[CommandLine -> "java"]
LoadJavaClass["java.lang.System"]
java`lang`System`getProperty["java.version"]

Out[17]= LinkObject["'/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.app/Contents/MacOS/JavaApplicationStub' -init \"/tmp/m00000847291\"", 219, 4]

Out[18]= JLink`JavaClass["java.lang.System", 0, {JLink`JVM["vm1"],JLink`JVM["vm2"]}, 1, "java`lang`System`", False, True]

Out[19]= "1.6.0_65"

At the same time Oracle JDK 1.7 and 1.8 are installed on the system.

Double clicking "/Applications/Mathematica.app"

If I start Mathematica by double clicking "/Applications/Mathematica.app" in Finder or a link to it in Dock,

ReinstallJava[CommandLine -> "java"]
LoadJavaClass["java.lang.System"]

issues a LinkObject::linkn error, and Environment["JAVA_HOME"] returns $Failed:

In[1]:= Needs["JLink`"]
ReinstallJava[CommandLine->"java"]
LoadJavaClass["java.lang.System"]
java`lang`System`getProperty["java.version"]
Out[2]= LinkObject[java -classpath "/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.jar" -Xdock:name=J/Link -Xmx256m  -Djava.system.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "/tmp/m00000155721",125,4]
During evaluation of In[1]:= LinkObject::linkn: Argument LinkObject[java -classpath "/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.jar" -Xdock:name=J/Link -Xmx256m  -Djava.system.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "/tmp/m00000155721",125,4] in LinkReadyQ[LinkObject[java -classpath "/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.jar" -Xdock:name=J/Link -Xmx256m  -Djava.system.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "/tmp/m00000155721",125,4]] has an invalid LinkObject number; the link may be closed. >>
During evaluation of In[1]:= LinkObject::linkn: Argument LinkObject[java -classpath "/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.jar" -Xdock:name=J/Link -Xmx256m  -Djava.system.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "/tmp/m00000155721",125,4] in LinkConnectedQ[LinkObject[java -classpath "/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.jar" -Xdock:name=J/Link -Xmx256m  -Djava.system.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "/tmp/m00000155721",125,4]] has an invalid LinkObject number; the link may be closed. >>
During evaluation of In[1]:= LinkObject::linkn: Argument LinkObject[java -classpath "/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.jar" -Xdock:name=J/Link -Xmx256m  -Djava.system.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "/tmp/m00000155721",125,4] in LinkReadyQ[LinkObject[java -classpath "/Applications/Mathematica.app/SystemFiles/Links/JLink/JLink.jar" -Xdock:name=J/Link -Xmx256m  -Djava.system.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "/tmp/m00000155721",125,4]] has an invalid LinkObject number; the link may be closed. >>
During evaluation of In[1]:= General::stop: Further output of LinkObject::linkn will be suppressed during this calculation. >>
During evaluation of In[1]:= InstallJava::fail: A link to the Java runtime could not be established. >>
During evaluation of In[1]:= LoadJavaClass::fail: Java failed to load class java.lang.System. >>
Out[3]= $Failed
Out[4]= java`lang`System`getProperty[java.version]

I don't fully understand what causes the LinkObject::linkn error and its possible relation to JAVA_HOME. My guess is this is due to JAVA_HOME not being correctly set for Mathematica and and somewhere in the processing an implied and incorrect Java home is used, possibly computed by

$ /usr/libexec/java_home
/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home

For both ways of starting Mathematica,

ReinstallJava[]  (* notice there is NO CommandLine -> "java" used *)
LoadJavaClass["java.lang.System"]

works. This is probably expected as CommandLine -> Automatic seems to lead Mathematica to use its own Java $InstallationDirectory/SystemFiles/Links/JLink/JLink.app/Contents/MacOS/JavaApplicationStub. The logic controlling this can be found in source file $InstallationDirectory/SystemFiles/Links/JLink/Kernel/InstallJava.m.

So if you have multiple Java installed and if /usr/libexec/java_home finds the wrong version of Java home directory for Mathematica (i.e. not 1.6.*)

$ /usr/libexec/java_home
/Library/Java/JavaVirtualMachines/jdk1.8.0.jdk/Contents/Home

you'll need to start Mathematica with open -a Mathematica.

Wrapper application OpenMathematicaAppFromCLIWithJava1.6.app made with Automator

If you prefer double clicking an icon on Dock than opening terminal and typing open -a Mathematica, you can create an application equivalent to setting JAVA_HOME and open -a Mathematica and put a link to it in Dock.

1) Start /Applications/Automator.app by double clicking it;

2) Choose "Application" and press button "Choose";

3) In "Variables" input field, type "Run Shell Script", and double click it;

4) In the RHS window, replace the default content 'cat' with

export JAVA_HOME=$(/usr/libexec/java_home -v 1.6*)  
open -a "/Applications/Mathematica.app"

5) Save it somewhere as a standalone application. I chose name OpenMathematicaAppFromCLIWithJava1.6.app;

6) Optionally, you can make the icon of OpenMathematicaAppFromCLIWithJava1.6.app same as Mathematica.app's by clicking "Get Info" in the context menu of the two applictions, and copy the icon in the top left part of the pop-up window by selecting the icon by clicking on it and Cmd-C and Cmd-V;

7) Drag OpenMathematicaAppFromCLIWithJava1.6.app onto Dock to create a link to it;

8) Start Mathematica by clicking the icon on Dock, and verify that Environment["JAVA_HOME"] and getProperty[java.version] behave correctly.

Configuring IDEs (virtually Eclipse and IntelliJ IDEA)

In IDEs such as Eclipse and IntelliJ IDEA, it's actually easier to use multiple versions of JDK, and different versions for different projects/modules. It's fairly easy to find the related documentation. My understanding is IDEs' JDK version does not have to be same as command-line java. They are basically different and unrelated Java development environments.

A relatively more complex issue is, as Eclipse and IntelliJ IDEA themselves are Java applications, what JVM are they running off of? And do you possibly want to start them using Oracle Java?

Here are some information:

IntelliJ IDEA

Selecting the JDK version the IDE will run under.

Eclipse

(This part about Eclipse is a drat and needs verification.)

Method 1: `-vm <Oracle JDK 1.7 Home/ path>` in Eclipse.ini

Add something like

-vm /Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/

at the end of eclipse.ini.

Method 2: shell script + Automator application

Make a shell script that takes care of JAVA_HOME and JVM:

#!/bin/sh
export JAVA_HOME=$(/usr/libexec/java_home -v 1.7)
LAUNCHER_JAR=/Applications/eclipse/plugins/org.eclipse.equinox.launcher_1.2.0.v20110502.jar

java \
-showversion \
-XX:MaxPermSize=256m \
-Xms1024m \
-Xmx1024m \
-Xdock:icon=/Applications/eclipse/Eclipse.app/Contents/Resources/Eclipse.icns \
-XstartOnFirstThread \
-Dorg.eclipse.swt.internal.carbon.smallFonts \
-Dosgi.requiredJavaVersion=1.5 \
-jar $LAUNCHER_JAR

and then make a wrapper application using Automator.

Installing Oracle JDK from command-line

Download DMG

$ wget --no-cookies --no-check-certificate --header "Cookie: gpw_e24=http%3A%2F%2Fwww.oracle.com%2F; oraclelicense=accept-securebackup-cookie" "http://download.oracle.com/otn-pub/java/jdk/8u60-b27/jdk-8u60-macosx-x64.dmg"
Mount DMG:

$ hdiutil mount jdk-8u60-macosx-x64.dmg
Install

$ sudo installer -pkg /Volumes/JDK\ 8\ Update\ 60/JDK\ 8\ Update\ 60.pkg -dominfo LocalSystem $ sudo installer -pkg /Volumes/JDK\ 8\ Update\ 60/JDK\ 8\ Update\ 60.pkg -target LocalSystem

References

Key bindings of macOS

Tue, 16 May 2017 23:59:39 +0000

Installing and configuring pkgsrc

Sat, 08 Apr 2017 21:30:47 +0000

Intro to pkgsrc

pkgsrc is a package management system for Unix-like operating systems. It supports OS X. Therefore, it's an viable alternative to Homebrew and Macports, which are the most widely used package management systems on Mac computers. I originally became interested in trying pkgsrc because some softwares I would like to install are not available via Homebrew.

Install, configure, manage pkgsrc and software packages in it

Installing and configuring pkgsrc on macOS (64-bit, version 10.9 or later)

The following is based on https://pkgsrc.joyent.com/install-on-osx/.

Copy and paste the lines below to install the 64-bit 10.9+ set.

  BOOTSTRAP_TAR="bootstrap-trunk-x86_64-20170205.tar.gz"
  BOOTSTRAP_SHA="177e0be390b57ef9d7f61511a8169268000693df"

Download the bootstrap kit to the current directory.

  curl -O https://pkgsrc.joyent.com/packages/Darwin/bootstrap/${BOOTSTRAP_TAR}

Verify the SHA1 checksum.

  echo "${BOOTSTRAP_SHA}  ${BOOTSTRAP_TAR}" >check-shasum
  shasum -c check-shasum

Verify PGP signature. This step is optional, and requires gpg.

  curl -O https://pkgsrc.joyent.com/packages/Darwin/bootstrap/${BOOTSTRAP_TAR}.asc
  gpg --recv-keys 0x1F32A9AD
  gpg --verify ${BOOTSTRAP_TAR}{.asc,}

Install bootstrap kit to /opt/pkg
```
  sudo tar -zxpf ${BOOTSTRAP_TAR} -C /
```
Reload PATH/MANPATH (pkgsrc installs /etc/paths.d/10-pkgsrc for new sessions)
```
  eval $(/usr/libexec/path_helper)
```

Installing pkgsrc on Ubuntu Linux

TODO

Installing softwares

There are three ways of installing softwares using pkgsrc:

The most typical method is to build a software from source files, a.k.a. "bootstrapping";
Another possibly easier method is to install and uninstall pre-built softwares using commands pkg_add and pkg_delete, respectively;
Install softwares using the high-level tool pkgin. It's the facsimile of Ubuntu and Debian Linux's apt-get in pkgsrc.

Use pkgsrc to install softwares

Use pkgsrc to install some softwares that Homebrew can't.

Refresh the pkgin database with the latest version
```
  $ sudo pkgin -y update
```

Search for a package. Regular expressions are supported.

  $ pkgin search "^ffmpeg[0-9]$"
  ffmpeg3-3.0.1   Decoding, encoding and streaming software (v3.x)
  ffmpeg2-2.8.6   Decoding, encoding and streaming software (v2.x)
  ffmpeg1-1.2.12  Decoding, encoding and streaming software (v1.x)

Install a package without prompting
```
  $ sudo pkgin -y install ffmpeg3
```
List all available packages
```
  $ pkgin avail
```
Upgrade all out-of-date packages
```
  $ sudo pkgin -y full-upgrade
```
Remove a package
```
  $ sudo pkgin -y remove ffmpeg2
```
Automatically remove orphaned dependencies
```
  $ sudo pkgin -y autoremove
```

Use pkg_* tools to manage packages

See what packages are installed.
```
  $ pkg_info
```

See what package a file belongs to.

  $ pkg_info -Fe /opt/pkg/bin/node
  nodejs-4.4.3

List the contents of a package.

  $ pkg_info -qL nodejs
  /opt/pkg/bin/node
  /opt/pkg/bin/npm
  [...]

Perform an audit of all currently installed packages.

  $ sudo pkg_admin fetch-pkg-vulnerabilities
  $ pkg_admin audit
  Package jasper-1.900.1nb11 has a integer-overflow vulnerability, see http://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2008-3520
  Package samba-3.6.25nb3 has a privilege-escalation vulnerability, see https://www.samba.org/samba/security/CVE-2015-5299.html
  Package tiff-4.0.6 has a arbitrary-memory-access vulnerability, see http://www.securityfocus.com/archive/1/537205
  [...]

Create a binary package from some metadata files and package directory.

  $ pkg_create -B build-info -c comment -d description -f packlist -I /opt/pkg -p files/ -U foo-1.0.tgz

Configuration file `mk.conf` for "bootstrapping"

After running

pkgsrc/bootstrap

it creates a example configuration file ../pkgsrc/bootstrap/work/mk.conf.example:

# Example /usr/pkg/etc/mk.conf file produced by bootstrap-pkgsrc
# Sat Feb  7 20:20:18 PST 2015

.ifdef BSD_PKG_MK   # begin pkgsrc settings

PKGSRC_COMPILER=    clang
CC=         clang
CXX=            clang++
CPP=            ${CC} -E
CLANGBASE=      /usr

PKG_DBDIR=      /var/db/pkg
LOCALBASE=      /usr/pkg
VARBASE=        /var
PKG_TOOLS_BIN=      /usr/pkg/sbin
PKGINFODIR=     info
PKGMANDIR=      man

TOOLS_PLATFORM.awk?=        /usr/pkg/bin/nawk
TOOLS_PLATFORM.sed?=        /usr/pkg/bin/nbsed

.endif          # end pkgsrc settings

Here is a version that is customized and installed at /usr/pkg/etc/mk.conf:

.ifdef BSD_PKG_MK       # begin pkgsrc settings

ABI=                    64
PKGSRC_COMPILER=        clang
CC=                     clang
CXX=                    clang++
CPP=                    ${CC} -E
CLANGBASE=              /usr

PKG_DBDIR=              /usr/pkg/.pkgdb
LOCALBASE=              /usr/pkg
VARBASE=                /var
PKG_TOOLS_BIN=          /usr/pkg/sbin
PKGINFODIR=             info
PKGMANDIR=              man

TOOLS_PLATFORM.awk?=    /usr/pkg/bin/nawk
TOOLS_PLATFORM.sed?=    /usr/pkg/bin/nbsed

MULTILIB_SUPPORTED=     no

PREFER.openssl=         pkgsrc

X11_TYPE=               native
X11BASE=                /opt/X11

.if !empty(PKGPATH:Mmail/mutt-devel)
PKG_OPTIONS.mutt+=      mutt-hcache mutt-smtp ncursesw sasl
.endif

.endif                  # end pkgsrc settings

Uninstalling pkgsrc and softwares installed by it

Delete the following directories:

sudo rm -rf /usr/pkg
sudo rm -rf /var/db/pkg*

and possibly also the source files if you used the first method:

sudo rm -rf /path/to/pkgsrc

References

Wikipedia, Pkgsrc.
Tony Fischetti, The state of package management on macOS, Oct. 14, 2013
pkgsrc: http://pkgsrc.org/
pkgsrc.se: http://pkgsrc.se/
pkgin: http://pkgin.net/
http://www.perkin.org.uk/pages/pkgsrc-binary-packages-for-osx.html
http://www.onthelambda.com/2013/10/14/the-state-of-package-management-on-mac-os-x/
pkgsrc binary packages for Mac OSX.

pages tagged macOS

Installing and configuring mutt

Intro to Mutt

Installing mutt

Installing getmail

Installing and configuring Homebrew

Topics

How to upgrade if Homebrew stuck at an old version?

Installing and configuring Apache HTTP Server on macOS

previous version of Apache configuration files

Apache configuration file

/etc/apache2/httpd.conf

/etc/apache2/extra/httpd-userdir.conf

Restarting Apache server

References

Installing and configuring Java on macOS

macOS's system Java

The 'java' executable and Java Virtual Machines

JAVA_HOME environment variable

(Re-)install macOS's system Java

Preventing future macOS update to Java

Installing Oracle's Java

The path /Library/Java/

Installing Oracle's JDK

Making Oracle Java binaries available at command line

Managing JAVA_HOME for different environments

Setting JAVA_HOME for Bash

Setting JAVA_HOME for Mathematica

JAVA_HOME

CommandLine -> "java"

Methods for starting Mathematica

open -a Mathematica

Double clicking "/Applications/Mathematica.app"

Wrapper application OpenMathematicaAppFromCLIWithJava1.6.app made with Automator

Configuring IDEs (virtually Eclipse and IntelliJ IDEA)

IntelliJ IDEA

Eclipse

Method 1: -vm <Oracle JDK 1.7 Home/ path> in Eclipse.ini

Method 2: shell script + Automator application

Installing Oracle JDK from command-line

References

Key bindings of macOS

Installing and configuring pkgsrc

Intro to pkgsrc

Install, configure, manage pkgsrc and software packages in it

Installing and configuring pkgsrc on macOS (64-bit, version 10.9 or later)

Installing pkgsrc on Ubuntu Linux

Installing softwares

Use pkgsrc to install softwares

Use pkg_* tools to manage packages

Configuration file mk.conf for "bootstrapping"

Uninstalling pkgsrc and softwares installed by it

References

Installing `mutt`

Installing `getmail`

`/etc/apache2/httpd.conf`

`/etc/apache2/extra/httpd-userdir.conf`

`JAVA_HOME` environment variable

The path `/Library/Java/`

Managing `JAVA_HOME` for different environments

Setting `JAVA_HOME` for Bash

Setting `JAVA_HOME` for Mathematica

`JAVA_HOME`

`CommandLine -> "java"`

`open -a Mathematica`

Method 1: `-vm <Oracle JDK 1.7 Home/ path>` in Eclipse.ini

Configuration file `mk.conf` for "bootstrapping"