Never confuse education with intelligence, you can have a PhD and still be an idiot.
- Richard Feynman -



Homebrew and Macports

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MacOS is missing a couple of programs we're using in our courses/books. You can get around this by installing either Homebrew or The MacPorts Project. Both of them require that xcode is installed. Once you have these installed you can use our download script (see Software used) to prepare your computer for using our material. Some course may require you to install additional software.

Install required packages

XCode Installation

Install xcode

Note: after installation you need to accept the license terms. Read them and execute the following command in a terminal window sudo xcodebuild -license

Install extra package manager

Apple ships MacOS with a couple of useful programs, such as bash. The problem for us is that the programs shipped are far from enough and that some of them are old to say the least. As an example the bash version installed in MacOs is from 2007, so it's kind of old. You can download additional software using the apple store (or what ever it's called today) but the packages here are not enough and it will soon become cumbersome to install all the packages we need without someone making sure the versions work together. So we need an additional package manager taking care of our packages. We know of two ones:

You will find installation hints and some useful tricks per package manager below.

Quick guide to using Homebrew and MacPorts

Homebrew

  • Installs in directory: /usr/local
  • Searching for a package (e g wget): brew search wget
  • Install a package (e g wget): brew install wget

MacPorts

  • Installs in directory: /opt/local/
  • Searching for a package (e g wget): port search wget
  • Install a package (e g wget): sudo port install wget

Homebrew

Installation

Follow the instructions on this page: Homebrew (installation)

Here are some samples from our bash session when we installed Homebrew on our mac. 

$ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
==> This script will install:
/usr/local/bin/brew
/usr/local/share/doc/homebrew
/usr/local/share/man/man1/brew.1
/usr/local/share/zsh/site-functions/_brew
/usr/local/etc/bash_completion.d/brew
/usr/local/Homebrew
==> The following existing directories will be made group writable:
/usr/local/bin
/usr/local/lib
==> The following existing directories will have their owner set to juneday:
/usr/local/bin
/usr/local/lib
==> The following existing directories will have their group set to admin:
/usr/local/bin
/usr/local/lib
==> The following new directories will be created:
/usr/local/Cellar
/usr/local/Homebrew
/usr/local/Frameworks
/usr/local/etc
/usr/local/include

..... 

Tapped 4479 formulae (4,759 files, 12MB)
==> Cleaning up /Library/Caches/Homebrew...
==> Migrating /Library/Caches/Homebrew to /Users/juneday/Library/Caches/Homebrew...
==> Deleting /Library/Caches/Homebrew...
Already up-to-date.
==> Installation successful!

==> Homebrew has enabled anonymous aggregate user behaviour analytics.
Read the analytics documentation (and how to opt-out) here:
  https://docs.brew.sh/Analytics.html

==> Next steps:
- Run `brew help` to get started
- Further documentation: 
    https://docs.brew.sh

Install packages

Since some time during 2019, they changed homebrew so that it doesn't come with Bash installed. So the first thing you should do after installing homebrew is to install Bash: 

$ brew install bash

Let's say you want to install the program wget. All you need to do now is to type the following in a terminal: 

$ brew install wget

and after this simple procedure you can use wget, e g like this: 

$ brew install wget
==> Installing dependencies for wget: gettext, libunistring, libidn2, openssl@1.1
==> Installing wget dependency: gettext
==> Downloading https://homebrew.bintray.com/bottles/gettext-0.19.8.1.sierra.bot
==> Downloading from https://akamai.bintray.com/83/8368522242c5fe33acd5c80b5f132
######################################################################## 100.0%
==> Pouring gettext-0.19.8.1.sierra.bottle.tar.gz
==> Caveats
This formula is keg-only, which means it was not symlinked into /usr/local,
because macOS provides the BSD gettext library & some software gets confused if both are in the library path.

If you need to have this software first in your PATH run:
  echo 'export PATH="/usr/local/opt/gettext/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set:
    LDFLAGS:  -L/usr/local/opt/gettext/lib
    CPPFLAGS: -I/usr/local/opt/gettext/include

==> Summary
🍺  /usr/local/Cellar/gettext/0.19.8.1: 1,934 files, 16.9MB
==> Installing wget dependency: libunistring
==> Downloading https://homebrew.bintray.com/bottles/libunistring-0.9.8.sierra.b
==> Downloading from https://akamai.bintray.com/b6/b685813e92dbd3a4eedcaac4b1a87
######################################################################## 100.0%
==> Pouring libunistring-0.9.8.sierra.bottle.tar.gz
🍺  /usr/local/Cellar/libunistring/0.9.8: 53 files, 4.4MB
==> Installing wget dependency: libidn2
==> Downloading https://homebrew.bintray.com/bottles/libidn2-2.0.4.sierra.bottle
######################################################################## 100.0%
==> Pouring libidn2-2.0.4.sierra.bottle.tar.gz
🍺  /usr/local/Cellar/libidn2/2.0.4: 46 files, 580.8KB
==> Installing wget dependency: openssl@1.1
==> Downloading https://homebrew.bintray.com/bottles/openssl@1.1-1.1.0g_1.sierra
==> Downloading from https://akamai.bintray.com/b0/b0d78618e300fd5fceb5bf98001d4
######################################################################## 100.0%
==> Pouring openssl@1.1-1.1.0g_1.sierra.bottle.tar.gz
==> Caveats
A CA file has been bootstrapped using certificates from the system
keychain. To add additional certificates, place .pem files in
  /usr/local/etc/openssl@1.1/certs

and run
  /usr/local/opt/openssl@1.1/bin/c_rehash

This formula is keg-only, which means it was not symlinked into /usr/local,
because this is an alternate version of another formula.

If you need to have this software first in your PATH run:
  echo 'export PATH="/usr/local/opt/openssl@1.1/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set:
    LDFLAGS:  -L/usr/local/opt/openssl@1.1/lib
    CPPFLAGS: -I/usr/local/opt/openssl@1.1/include

==> Summary
🍺  /usr/local/Cellar/openssl@1.1/1.1.0g_1: 6,585 files, 15.6MB
==> Installing wget
==> Downloading https://homebrew.bintray.com/bottles/wget-1.19.2_1.sierra.bottle
==> Downloading from https://akamai.bintray.com/38/381e209d4c0af56747f2a4ae4671d
######################################################################## 100.0%
==> Pouring wget-1.19.2_1.sierra.bottle.tar.gz
🍺  /usr/local/Cellar/wget/1.19.2_1: 50 files, 3.8MB
$

Search for packages

A program we know the name of

Let's say we want to install the program tree. We can use the search function in Homebrew: 

$ brew search tree
==> Searching local taps...
mvptree               pstree                tree                  treecc                treefrog
==> Searching taps on GitHub...
==> Searching blacklisted, migrated and deleted formulae...

We can see that there are a couple of different programs matching tree. It's hard for us give general rule of which program to chose but we suggest you read a bit more about each program using brew search: 

$ brew info tree
tree: stable 1.7.0 (bottled)
Display directories as trees (with optional color/HTML output)
http://mama.indstate.edu/users/ice/tree/
Not installed
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/tree.rb

This seems like a good choice so let's install it using brew install: 

$ brew install tree
==> Downloading https://homebrew.bintray.com/bottles/tree-1.7.0.sierra.bottle.1.tar.gz
######################################################################## 100.0%
==> Pouring tree-1.7.0.sierra.bottle.1.tar.gz
🍺  /usr/local/Cellar/tree/1.7.0: 7 files, 113.3KB
A program we know parts of the name of

Let's say we want to search for a program which we only remember parts of the name of, let's say ls 

$ brew search ls
==> Searching local taps...
aardvark_shell_utils       ebook-tools                libxlsxwriter              psutils
adr-tools                  ec2-ami-tools              libxmlsec1                 pulseaudio
appscale-tools             ec2-api-tools              lsdvd                      pwntools
avro-tools                 eiffelstudio               lsh                        rails-completion
aws-cfn-tools              elb-tools                  lsof                       rds-command-line-tools
b2-tools                   eot-utils                  lsyncd                     recutils
bamtools                   euca2ools                  ltc-tools                  renameutils
bcftools                   findutils                  lwtools                    rom-tools
bedtools                   flow-tools                 mailutils                  samtools
bibutils                   fonttools                  mbedtls                    scummvm-tools
binutils                   fsevents-tools             mdbtools                   shellshare
bpm-tools                  garmintools                megatools                  skktools
bzr-externals              genometools                mjpegtools                 smartmontools
bzrtools                   gerrit-tools               moreutils                  somagic-tools
cctools                    git-utils                  moz-git-tools              spatialite-tools
cctools-headers            glslang                    msitools                   speech-tools
cdrtools                   glslviewer                 mtools                     sslscan
charm-tools                gnome-doc-utils            mupdf-tools                sslsplit
coreutils                  gnutls                     muttils                    sundials
cpmtools                   gperftools                 mvtools                    swftools
crush-tools                gputils                    nfcutils                   t1utils
cuetools                   grails                     num-utils                  tlsdate
cvsutils                   grails@2.5                 objc-codegenutils          u-boot-tools
daemontools                gupnp-tools                ocamlsdl                   uniutils
dateutils                  hfsutils                   ogmtools                   vcftools
debianutils                hopenpgp-tools             olsrd                      vorbis-tools
desktop-file-utils         html-xml-utils             opus-tools                 wireguard-tools
diffutils                  icon-naming-utils          orc-tools                  xlslib
dmtx-utils                 icoutils                   osslsigncode               xml-coreutils
docker-ls                  idutils                    osxutils                   xmlsectool
docker-machine-parallels   inetutils                  parquet-tools              xmlsh
docutils                   irrtoolset                 patchutils                 xmlstarlet
dosfstools                 jdnssec-tools              pdf-redact-tools           yelp-tools
dvd+rw-tools               lcdf-typetools             picard-tools               zsh-navigation-tools
dvdrtools                  librealsense               plotutils
dwarfutils                 librealsense@1             proctools
e2tools                    librtlsdr                  psftools
==> Searching taps on GitHub...
==> Searching blacklisted, migrated and deleted formulae...

This gives us a bit too many programs, but you'll get the point.

Using the bash from Homebrew

Homebrew ships a new and fresh bash. You can us this in (at least) two ways:

  • manually - by starting bash manually (in bash)
  • automatically - using a settings file

Read more about bash versions at Bash_version.

Using the bash from Homebrew - manually

When you start a terminal in MacOS bash is started along with the terminal. The version of bash is the old one. If you want t fresher bash you can simply type 

$ bash

Using the bash from Homebrew - automatically

Homebrew installs bash in /usr/local/bin/ and adds this directory to your PATH. You can check that the path is set by 1) print the PATH variable and 2) see what bash will be started: 

$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
$ which bash
/usr/local/bin/bash

If you want, which we assume since you're reading this, to make the Homebrew version of bash the default you need to do execute a few commands, see below. This means that this version of bash will be started when you start a new terminal window. 

1 $ sudo -s 
2 bash-3.2# which bash >> /etc/shells
3 bash-3.2# exit
4 $ chsh -s $(which bash)
5 Changing shell for juneday.
6 Password for juneday: 
7 $

Explaining what's going on above:

  1. sudo -s - start a new shell as superuser (root)
  2. which bash >> /etc/shells - add the Homebrew version of bash to a list of acceptable shells
  3. exit - leave the bash running as superuser
  4. chsh -s $(which bash) - Change the default shell using chsh (try man chsh
  5. printout from chsh
  6. chsh asking for your password - type it in
  7. normal prompt

The next terminal you start should be running the Homebrew version of bash.

MacPorts

Installation

The MacPorts Project (installation).

Note: make sure that the command port can be found using the PATH variable. Try typing port version. If you see something like Version: 2.3.5 you're fine. If not add read this page MacPorts and the Shell

When using port you might see a warning like this: 

Warning: xcodebuild exists but failed to execute
Warning: Xcode does not appear to be installed; most ports will likely fail to build.

Fix this by executing the following command: 

sudo xcode-select -switch /Applications/Xcode.app/Contents/Developer

Read more about problems using MacPorts here: ProblemHotlist

Install packages

Search for packages

A program we know the name of

Let's again say we want to install the program tree. We can use the search function in MacPorts: 

$ port search tree
bact @0.13 (math)
a Boosting Algorithm for Classification of Trees

castxml @20171013 (lang)
CastXML is a C-family abstract syntax tree XML output tool.

cvsgraph @1.7.0_2 (devel)
utility for graphical representation of CVS/RCS revision tree

etree-scripts @1.4 (audio)
utilities useful to people who use the etree network

ftpsync @1.3.04_5 (net)
Synchronizes a local and a remote ftp directory tree

... 

tree @1.7.0 (sysutils)
display tree-view of directories with optional color/HTML output

tree-puzzle @5.2 (science)
a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood

treecc @0.3.10_1 (devel)
Manages generation of code to handle syntax trees.

treehh @2.65_1 (science)
Data Analysis and Scientific Plotting

treeline @1.4.1 (office, pim, python)
Advanced outliner and personal information manager

X-MasTree @1.4 (aqua, amusements)
Christmas tree

xom @1.2.10 (java, devel, textproc)
A tree-based API for XML processing

Found 148 ports.

We got so many hits we had to snip the printout. We can see that there is a tool cooled tree which most likely is the program we want. Let's install it: 

$ port install tree 
Error: Insufficient privileges to write to MacPorts install prefix.

Ah, ok. We need to be superuser when using MacPorts. Let's execute the installation command as superuser. 

$ sudo port install tree 
Password:
Warning: xcodebuild exists but failed to execute
Warning: Xcode does not appear to be installed; most ports will likely fail to build.
--->  Fetching archive for tree
--->  Attempting to fetch tree-1.7.0_0.darwin_16.x86_64.tbz2 from https://packages.macports.org/tree
--->  Attempting to fetch tree-1.7.0_0.darwin_16.x86_64.tbz2.rmd160 from https://packages.macports.org/tree
--->  Installing tree @1.7.0_0
--->  Activating tree @1.7.0_0
--->  Cleaning tree
--->  Updating database of binaries
--->  Scanning binaries for linking errors
--->  No broken files found.

Do you see the warning? Let's fix it: 

sudo xcode-select -switch /Applications/Xcode.app/Contents/Developer
A program we know parts of the name of

Let's again say we want to search for a program which we only remember parts of the name of, let's say ls 

$ port search ls
2Pong @1.0.1a (games)
Pong game with 2 balls, 2 and 4 player support

alliance @5.0-20110203_2 (science)
Alliance, CAD and libraries for VLSI design

am-utils @6.1.5_1 (sysutils)
The Berkeley Automounter Suite of Utilities

amttools @1.4_2 (sysutils)
Intel AMT® Serial-over-LAN client and tools

angelscript @2.31.2 (devel)
Flexible cross-platform scripting library

aolserver @4.5.1 (www)
America Online's open-source web server

ap-utils @1.3.3 (net)
Utilities for AMTEL, NWN, ME102 wireless access points

.... 

xz @5.2.3 (archivers)
    XZ Utils

yelp-tools @3.18.0 (gnome)
    Tools to help create Yelp documentation.

yorick-yutils @1.5.2 (science, yorick)
    Various utilities for the Yorick language

yum-utils @1.1.17_1 (sysutils)
    Utilities based around the yum package manager

Found 1281 ports.
$

This gives us a bit too many programs, but you'll get the point just as you did when reading about Homebrew.

Using the bash from MacPorts

MacPorts ships a new and fresh bash. You can us this in (at least) two ways:

  • manually - by starting bash manually (in bash)
  • automatically - using a settings file

Read more about bash versions at Bash_version.

Using the bash from MacPorts - manually

When you start a terminal in MacOS bash is started along with the terminal. The version of bash is the old one. If you want t fresher bash you can simply type 

$ bash

Using the bash from MacPorts - automatically

MacPorts installs bash in /usr/local/bin/ and adds this directory to your PATH. You can check that the path is set by 1) print the PATH variable and 2) see what bash will be started: 

$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
$ which bash
/opt/local/bin/bash
$

If you want, which we assume since you're reading this, to make the Homebrew version of bash the default you need to do execute a few commands, see below. This means that this version of bash will be started when you start a new terminal window. 

1 $ sudo -s 
2 bash-3.2# which bash >> /etc/shells
3 bash-3.2# exit
4 $ chsh -s $(which bash)
5 Changing shell for juneday.
6 Password for juneday: 
7 $

Explaining what's going on above:

  1. sudo -s - start a new shell as superuser (root)
  2. which bash >> /etc/shells - add the Homebrew version of bash to a list of acceptable shells
  3. exit - leave the bash running as superuser
  4. chsh -s $(which bash) - Change the default shell using chsh (try man chsh
  5. printout from chsh
  6. chsh asking for your password - type it in
  7. normal prompt

The next terminal you start should be running the MacPorts version of bash.

Using both Homebrew and MacPorts

While this is not something we se very useful, but if you're brave and beautiful you might do this in order to test which is best (Homebrew or MacPorts) or simply because it is possible. The latter is btw a great reason.

When having bot Homebrew and MacPorts installed you will end up with (at least) three versions of bash:

  • Homebrew's version
  • MacPorts's version
  • Apple's version (again, this version is from year 2007!!)

You know by now (otherwise check out the following section in our FAQ: xxx: command not found) that you need to set the PATH to point our your favorite package manager's path as the first path in your PATH. Here are examples of how to adjust your PATH variable. Depending on the package manager you should add the following to your ~/.bashrc file:

  • Homebrew: export PATH=/usr/local/bin:$PATH
  • MacPorts: export PATH=/opt/local/bin:/opt/local/sbin:$PATH
  • Apple: export PATH=/bin:/usr/bin:/usr/sbin:$PATH

Links

Package managers for MacOS:

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