pages tagged configuration

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 Docker

Sun, 02 Jul 2017 01:09:02 +0000

macOS

Homebrew

brew cask install docker
brew cask install docker-toolbox

Create a virtual machine

bash$ docker-machine create default

Start the virtual machine

Start the virtual machine default:

bash$ docker-machine start
bash$ docker-machine env
export DOCKER_TLS_VERIFY="1"
export DOCKER_HOST="tcp://192.168.99.100:2376"
export DOCKER_CERT_PATH="/Users/meng/.docker/machine/machines/default"
export DOCKER_MACHINE_NAME="default"
# Run this command to configure your shell:
# eval $(docker-machine env)
bash$ eval "$(docker-machine env default)"

Verify that the docker machine is working

bash$ docker run hello-world
Unable to find image 'hello-world:latest' locally
latest: Pulling from library/hello-world
b04784fba78d: Pull complete
Digest: sha256:f3b3b28a45160805bb16542c9531888519430e9e6d6ffc09d72261b0d26ff74f
Status: Downloaded newer image for hello-world:latest

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://cloud.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/engine/userguide/

Run and test the 'tensorflow/tensorflow' Docker image

bash$ docker run -it tensorflow/tensorflow:1.1.0 bash
Unable to find image 'tensorflow/tensorflow:1.1.0' locally
1.1.0: Pulling from tensorflow/tensorflow
c62795f78da9: Pull complete
d4fceeeb758e: Pull complete
5c9125a401ae: Pull complete
0062f774e994: Pull complete
6b33fd031fac: Pull complete
353b34ef0a98: Pull complete
4f6aefc14b68: Pull complete
ce066374c6ca: Pull complete
c0755a91ab3a: Pull complete
f03279b52d25: Pull complete
d1c27c29b7e3: Pull complete
23807c5f4b3e: Pull complete
Digest: sha256:27bd43f1cf71c45eb48cb6e067b7cef47b168ac11c685d55a3495d27f0d59543
Status: Downloaded newer image for tensorflow/tensorflow:1.1.0
root@d000fef7e8dc:/notebooks#
root@d000fef7e8dc:/notebooks# python
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 
>>> import tensorflow as tf
>>> hello = tf.constant('Hello, TensorFlow!')
>>> sess = tf.Session() # It will print some warnings here.
2017-06-29 06:08:55.848559: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.1 instructions, but these are available on your machine and could speed up CPU computations.
2017-06-29 06:08:55.848626: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.2 instructions, but these are available on your machine and could speed up CPU computations.
2017-06-29 06:08:55.848663: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use AVX instructions, but these are available on your machine and could speed up CPU computations.
>>> print(sess.run(hello))
Hello, TensorFlow!
>>>

List all virtual machines

$ docker-machine ls                                                
NAME      ACTIVE   DRIVER       STATE     URL   SWARM   DOCKER    ERRORS
default   -        virtualbox   Stopped                 Unknown

Delete a virtual machine

$ docker-machine rm default
About to remove default
WARNING: This action will delete both local reference and remote instance.
Are you sure? (y/n): y
Successfully removed default

References

https://stackoverflow.com/questions/21871479/docker-cant-connect-to-docker-daemon

Installing and configuring TensorFlow

Sat, 01 Jul 2017 21:23:24 +0000

Install TensorFlow using 'tensorflow/tensorflow' Docker image

Start the Docker virtual machine

Create a virtual machine if not already

bash$ docker-machine create default

Start the virtual machine default:

bash$ docker-machine start
Starting "default"...
(default) Check network to re-create if needed...
(default) Waiting for an IP...
Machine "default" was started.
Waiting for SSH to be available...
Detecting the provisioner...
Started machines may have new IP addresses. You may need to re-run the `docker-machine env` command.
>>> elapsed time 35s
bash$ docker-machine env
export DOCKER_TLS_VERIFY="1"
export DOCKER_HOST="tcp://192.168.99.100:2376"
export DOCKER_CERT_PATH="/Users/meng/.docker/machine/machines/default"
export DOCKER_MACHINE_NAME="default"
# Run this command to configure your shell:
# eval $(docker-machine env)
bash$ eval "$(docker-machine env default)"

Start 'tensorflow/tensorflow' Docker image

$ export MY_WORKSPACE_DIR='/Users/meng/workspace'
$ docker run -it \
--net=host \
--publish 6006:6006 \
--volume ${MY_WORKSPACE_DIR}/tensorflow_test:/tensorflow_test \
--workdir /tensorflow_test \
tensorflow/tensorflow:1.1.0 bash
root@30d79c2e5fc3:/tensorflow_test# pwd
/tensorflow_test

Start TensorBoard

root@30d79c2e5fc3:/tensorflow_test# tensorboard --logdir training_summaries &
[1] 12
root@30d79c2e5fc3:/tensorflow_test# Starting TensorBoard 47 at http://0.0.0.0:6006
(Press CTRL+C to quit)

root@30d79c2e5fc3:/tensorflow_test#

Open TensorBoard at

http://192.168.99.100:6006

in a Web browser, where the IP is the same as DOCKER_HOST in the output of docker-machine env.

Download training data

# curl -O http://download.tensorflow.org/example_images/flower_photos.tgz
# tar xzf flower_photos.tgz
# find flower_photos -type f | wc -l
3671
# cp -R flower_photos flower_photos_subset
# rm flower_photos_subset/*/[2-9]*
# find flower_photos_subset/ -type f | wc -l
1202

Download training script

# curl -O https://raw.githubusercontent.com/tensorflow/tensorflow/r1.1/tensorflow/examples/image_retraining/retrain.py

Training

# python retrain.py \
      --bottleneck_dir=bottlenecks \
      --how_many_training_steps=500 \
      --model_dir=inception \
      --summaries_dir=training_summaries/basic \
      --output_graph=retrained_graph.pb \
      --output_labels=retrained_labels.txt \
      --image_dir=flower_photos_subset

Python script to classify new images of flowers

Create a new file label_image.py:

import os, sys

import tensorflow as tf

os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'

# change this as you see fit
image_path = sys.argv[1]

# Read in the image_data
image_data = tf.gfile.FastGFile(image_path, 'rb').read()

# Loads label file, strips off carriage return
label_lines = [line.rstrip() for line 
                   in tf.gfile.GFile("retrained_labels.txt")]

# Unpersists graph from file
with tf.gfile.FastGFile("retrained_graph.pb", 'rb') as f:
    graph_def = tf.GraphDef()
    graph_def.ParseFromString(f.read())
    tf.import_graph_def(graph_def, name='')

with tf.Session() as sess:
    # Feed the image_data as input to the graph and get first prediction
    softmax_tensor = sess.graph.get_tensor_by_name('final_result:0')

    predictions = sess.run(softmax_tensor, \
             {'DecodeJpeg/contents:0': image_data})

    # Sort to show labels of first prediction in order of confidence
    top_k = predictions[0].argsort()[-len(predictions[0]):][::-1]

    for node_id in top_k:
        human_string = label_lines[node_id]
        score = predictions[0][node_id]
        print('%s (score = %.5f)' % (human_string, score))

Classify a new image:

# python label_image.py flower_photos/daisy/99306615_739eb94b9e_m.jpg
daisy (score = 0.47996)
dandelion (score = 0.24667)
sunflowers (score = 0.24508)
tulips (score = 0.02018)
roses (score = 0.00811)

Exit the Docker image and stop the Docker virtual machine

Ctrl+D to exit Docker image and then run

$ docker-machine stop

References

https://codelabs.developers.google.com/codelabs/tensorflow-for-poets

Fix Adobe Connect for Google Chrome 42

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

Adobe Connect, which is the teleconference software I use for work, stopped working in Google Chrome 42.0.\<some version\>. After ignoring it for a while and several failed attempts to fix it, I finally figured out how to resurrect it.

Open chrome://flags/ in Chrome, enable the plug-in under 'Enable NPAPI Mac, Windows';
Install Adobe NPAPI Flash plug-in: http://get.adobe.com/flashplayer;
Open chrome://plugins in Chrome, under the section 'Adobe Flash Player', disable PPAPI and enable NPAPI.

References

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 Apache2

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

Uninstalling Apache server

If Apache server has been installed, you may want to remove it and re-install it.

Update packages:

sudo apt-get update
sudo apt-get autoremove

Uninstall Apache2 and its configuration files:

sudo apt-get purge apache2
sudo apt-get autoremove

Installing

Reinstall Apache2 and PHP5 packages:

sudo apt-get install apache2 php5

Setting up `~/public_html/`

Create public_html directory for storing Web site files:

mkdir $HOME/public_html

Configure Apache2 server to use $HOME/public_html as the Web site root path:

cd /etc/apache2/mods-enabled
sudo ln -s ../mods-available/userdir.conf userdir.conf
sudo ln -s ../mods-available/userdir.load userdir.load

Restarting Apache2 server

sudo /etc/init.d/apache2 restart

sudo service apache2 restart

Installing PHP

sudo apt-get install php5 libapache2-mod-php5 php5-mcrypt

Installing MySQL

See "Installing and configuring MySQL."

References

How To Install Linux, Apache, MySQL, PHP (LAMP) stack on Ubuntu 14.04

Installing and configuring Haskell

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

`cabal` VS. `stack`

cabal and stack are two tools one can use to install Glasgow Haskell Compiler (GHC), i.e. the binaries ghc and ghci, and Haskell software packages. stack installs Haskell programs in ~/.stack and cabal installs in ~/.cabal. Using both cabal and stack, or either one of them is possible, but it seems the current general wisdom is that stack is more user friendly especially for beginners. So I chose to uninstall cabal and delete ~/.cabal, and use stack only.

Install Haskell compiler and softwares using `stack`

stack is built on top of cabal (which in turn relies on ghc-pkg), the package management system for Haskell softwares, but is more user friendly in some ways.

Uninstall the ghc installed using the system's package management system

macOS:

    brew uninstall --force cabal-install
    brew uninstall --force ghc

Linux:

    sudo apt-get remove ghc
    sudo apt-get remove cabal-install

Install stack
- macOS:
```
    brew install haskell-stack
```
- Linux: Follow the instruction about installation in the official documentation. Don't just do sudo apt-get install haskell-stack.
Install ghc
```
  stack setup
```
If you want to use binaries installed via stack regularly, put them on path. Run stack path and append the paths of form ~/.stack/.../bin in the output to $PATH in ~/.bashrc.

Install packages using stack:

  stack install ghc-mod
  stack install cabal-install
  stack install hlint
  stack install pandoc
  stack install purescript
  stack install wreq
  stack install lens
  stack install ihaskell        
  stack install projectile
  stack install use-package
  stack install which-key

  stack install apply-refact
  stack install codex
  stack install hasktags

ihaskell: IHaskell, Haskell kernel for Jupyter notebooks.

Install Haskell compiler and softwares using `cabal`

Install ghc and cabal
```
  brew install cabal-install ghc
```

Install packages via cabal

  cabal update
  cabal install happy # 2016-3-5: prerequisite for ghc-mod
  cabal install ghc-mod hlint haskell-docs

Verifying the stack and Haskell installation

cd $HOME
# Assume 'stack setup' has been run.
stack init
stack build --dependencies-only --test

Configure Emacs for Haskell development

Install the following Emacs packages, ideally using the GNU Emacs Lisp Package Archive (see also EmacsWiki: ELPA):

Emacs packages specifically relevant for Haskell:
- haskell-mode
- haskell-snippets
- flycheck-hlint
- intero
Other Emacs packages generally helpful.

Configure a Haskell project using `stack`

Create a project

cd path/to/workspace/
stack new haskell-stack-test-project
cd haskell-stack-test-project
stack setup
stack build --dependencies-only --test

This creates a new project using template ~/.stack/templates/new-template.hsfiles. The project directory structure:

$ tree
.
├── LICENSE
├── Setup.hs
├── app
│   └── Main.hs
├── haskell-stack-test-project.cabal
├── src
│   └── Lib.hs
├── stack.yaml
└── test
    └── Spec.hs

Remarks:

app/ contains the source file(s) for more application-specific logic, including a app/Main.hs.
src/ contains the source file(s) for more shareable and general-purpose code.

Build

$ cd path/to/haskell-stack-test-project
$ stack build
haskell-stack-test-project-0.1.0.0: configure
Configuring haskell-stack-test-project-0.1.0.0...
haskell-stack-test-project-0.1.0.0: build
Preprocessing library haskell-stack-test-project-0.1.0.0...
[1 of 1] Compiling Lib              ( src/Lib.hs, .stack-work/dist/x86_64-osx/Cabal-1.22.5.0/build/Lib.o )
In-place registering haskell-stack-test-project-0.1.0.0...
Preprocessing executable 'haskell-stack-test-project-exe' for
haskell-stack-test-project-0.1.0.0...
[1 of 1] Compiling Main             ( app/Main.hs, .stack-work/dist/x86_64-osx/Cabal-1.22.5.0/build/haskell-stack-test-project-exe/haskell-stack-test-project-exe-tmp/Main.o )
Linking .stack-work/dist/x86_64-osx/Cabal-1.22.5.0/build/haskell-stack-test-project-exe/haskell-stack-test-project-exe ...
haskell-stack-test-project-0.1.0.0: copy/register
Installing library in
/Users/meng/Dropbox/WorkSpace-Dropbox/Computing/repo-meng-lib/Haskell/haskell-stack-test-project/.stack-work/install/x86_64-osx/lts-5.5/7.10.3/lib/x86_64-osx-ghc-7.10.3/haskell-stack-test-project-0.1.0.0-BCjrGi4SAkj4MdkT4tD42y
Installing executable(s) in
/Users/meng/Dropbox/WorkSpace-Dropbox/Computing/repo-meng-lib/Haskell/haskell-stack-test-project/.stack-work/install/x86_64-osx/lts-5.5/7.10.3/bin
Registering haskell-stack-test-project-0.1.0.0...

The path to the built executable is contained in the line starting with Linking: Linking .stack-work/dist/x86_64-osx/Cabal-1.22.5.0/build/haskell-stack-test-project-exe/haskell-stack-test-project-exe ....

$ .stack-work/dist/x86_64-osx/Cabal-1.22.5.0/build/haskell-stack-test-project-exe/haskell-stack-test-project-exe
someFunc

Configure a Haskell project using IntelliJ IDEA

Install JetBrains' Haskell plug-in.
Configure Languages & Frameworks | Haskell:

If using binaries installed via cabal:

Create a Haskell project and its first component.

Use menu File | New | Project and select 'Haskell', click 'next', and choose name for the project and the name for the first module and its sub-directory:

Set GHC (ghc) as the platform SDK: use menu File | Project Structure, and select '+' and navigate to the installation path of the desired version of ghc, e.g. /Users/meng/.stack/programs/x86_64-osx/ghc-7.10.3 which is installed via stack or /usr/local/Cellar/ghc/7.10.3, which is installed via brew.

Optionally, create additional modules in the project: use menu File | New | Module, select 'Haskell', and choose name for the module and directory.

References

A 2-hour long video tutorial on setting up Haskell environment using stack by Christopher Allen and Julie Moronuki: https://www.youtube.com/watch?v=sRonIB8ZStw.
https://www.stackage.org/
The Haskell Tool Stack documentation, http://docs.haskellstack.org/en/stable/README/
- guide: http://docs.haskellstack.org/en/stable/GUIDE/

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

Installing and configuring LaTeX

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

Last verified as of
- macOS: 2020-5-14 and macOS 10.14.6 and MacTex 2020.0407;
- Linux: 2015-9 and Ubuntu.

Linux

Tested on Ubuntu Linux 14 as of 2015-9.

sudo apt-get install texlive-full

Install extensions using `apt-get`

How to search the package that contains file standalone.sty and install it:

$ sudo apt-get install apt-file
$ apt-file update
$ apt-file search standalone.sty
texlive-latex-extra: /usr/share/texlive/texmf-dist/tex/latex/standalone/standalone.sty
$ sudo apt-get install texlive-latex-extra

macOS

Veify if you already have LaTeX and needs an update

As of May 14, 2020, the latest 'tex-live' release is 'Tex Live 2020'.

I verified on my computer that I have an older version installed:

$ which latex
/Library/TeX/texbin/latex

$ latex --version
pdfTeX 3.14159265-2.6-1.40.16 (TeX Live 2015)
kpathsea version 6.2.1
Copyright 2015 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Compiled with libpng 1.6.17; using libpng 1.6.17
Compiled with zlib 1.2.8; using zlib 1.2.8
Compiled with xpdf version 3.04

I no longer remember how I installed it or if I used homebrew or 'MacTeX'. But I will just re-install it using Homebrew assuming I don't really need to carefully uninstall the current files.

Uninstalling previous versions of MacTeX

Uninstall previous versions of MacTeX[^mactexuninstalling]:

$ ls -la /usr/local/texlive/                                                                     drwxr-xr-x  20 root  wheel   640B May  8  2019 2015/
drwxr-xr-x  20 root  wheel   640B May  8  2019 2017/
drwxr-xr-x  20 root  wheel   640B May  8  2019 2019/
drwxr-xr-x   9 meng  admin   288B Oct 27  2017 texmf-local/
$ du -hs /usr/local/texlive/2015
4.3G
$ du -hs /usr/local/texlive/2017
5G
$ du -hs /usr/local/texlive/2019
6.3G
$ sudo rm -rf /usr/local/texlive/2015 /usr/local/texlive/2017 /usr/local/texlive/2019

Remove the GUI application
```
  rm -rf /Applications/TeX
```
Re-install MacTeX
```
  brew cask install mactex
```

Installing MacTex using homebrew

Homebrew tells you to install MacTeX if you simply search for the keyword 'tex':

$ brew search tex
asciitex        blahtexml       itex2mml        latexila        libtextcat      rtf2latex2e     texinfo         vilistextum
bibtex2html     gettext ✔       latex2html      latexml         opendetex       texapp          texmath
bibtexconv      html2text       latex2rtf       libdrawtext     ptex            texi2html ✔     textql
caskroom/cask/tex-live-utility             caskroom/fonts/font-tex-gyre-adventor      caskroom/fonts/font-tex-gyre-heros
caskroom/fonts/font-tex-gyre-cursor        caskroom/fonts/font-tex-gyre-termes        caskroom/fonts/font-tex-gyre-pagella-math
caskroom/fonts/font-tex-gyre-chorus        caskroom/fonts/font-tex-gyre-schola
caskroom/fonts/font-tex-gyre-bonum         caskroom/fonts/font-tex-gyre-pagella

If you meant "tex" specifically:
Installing TeX from source is weird and gross, requires a lot of patches,
and only builds 32-bit (and thus can't use Homebrew dependencies)

We recommend using a MacTeX distribution: https://www.tug.org/mactex/

You can install it with Homebrew-Cask:
  brew cask install mactex

I will just install using

$ brew cask install mactex
==> Downloading http://mirror.ctan.org/systems/mac/mactex/mactex-20170524.pkg
Already downloaded: /Users/meng/Library/Caches/Homebrew/Cask/mactex--20170524.pkg
==> Verifying checksum for Cask mactex
==> Installing Cask mactex
==> Running installer for mactex; your password may be necessary.
==> Package installers may write to any location; options such as --appdir are ignored.
Password:
==> installer: Package name is MacTeX-2017
==> installer: Upgrading at base path /
==> installer: The upgrade was successful.
🍺  mactex was successfully installed!
>>> elapsed time 9m39s

$ which latex                                                                        
/Library/TeX/texbin/latex

$ latex --version                                                                        
pdfTeX 3.14159265-2.6-1.40.18 (TeX Live 2017)
kpathsea version 6.2.3
Copyright 2017 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.29; using libpng 1.6.29
Compiled with zlib 1.2.11; using zlib 1.2.11
Compiled with xpdf version 3.04

Installing extensions using `tlmgr`

Alternatively, if the TeX system is not installed via Ubuntu Linux's package management system and apt-get, one can use tlmgr to install and update the TeX extensions:

tlmgr update --self --all
tlmgr install standalone
tlmgr update standalone

Linux

The TeX package management tool tlmgr itself is part of texlive-base and can be installed via

sudo apt-get install texlive-base

macOS

On macOS, installing MacTeX using homebrew will install tlmgr as well.

References

[^mactexuninstalling] tug.org/mactex. "Uninstalling". https://www.tug.org/mactex/uninstalling.html.

pages tagged configuration

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 Docker

macOS

Homebrew

Create a virtual machine

Start the virtual machine

Verify that the docker machine is working

Run and test the 'tensorflow/tensorflow' Docker image

List all virtual machines

Delete a virtual machine

References

Installing and configuring TensorFlow

Install TensorFlow using 'tensorflow/tensorflow' Docker image

Start the Docker virtual machine

Start 'tensorflow/tensorflow' Docker image

Start TensorBoard

Download training data

Download training script

Training

Python script to classify new images of flowers

Exit the Docker image and stop the Docker virtual machine

References

Fix Adobe Connect for Google Chrome 42

References

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 Apache2

Uninstalling Apache server

Installing

Setting up ~/public_html/

Restarting Apache2 server

Installing PHP

Installing MySQL

References

Installing and configuring Haskell

cabal VS. stack

Install Haskell compiler and softwares using stack

Install Haskell compiler and softwares using cabal

Verifying the stack and Haskell installation

Configure Emacs for Haskell development

Configure a Haskell project using stack

Create a project

Build

Configure a Haskell project using IntelliJ IDEA

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

Installing `mutt`

Installing `getmail`

`/etc/apache2/httpd.conf`

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

Setting up `~/public_html/`

`cabal` VS. `stack`

Install Haskell compiler and softwares using `stack`

Install Haskell compiler and softwares using `cabal`

Configure a Haskell project using `stack`

`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

Install extensions using `apt-get`

Installing extensions using `tlmgr`