Mac

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macOS

https://en.wikipedia.org/wiki/MacOS

Darwin (operating system) and release history

Find OS version by command line

$ sw_vers
ProductName:	Mac OS X
ProductVersion:	10.11.6
BuildVersion:	15G1004

$ sw_vers -productVersion
10.11.6

How to differentiate Linux and Mac

Use uname (unix name) with -s (system name) flag 

# Mac
$ uname -s
Darwin

# Linux
$ uname -s
Linux

BSD and Linux

What’s the Difference Between Linux and BSD?

OS X File System

Home directory

/Users/USERNAME

The following is the default directories under $HOME. 

$ ls ~/
Applications	Documents	Library		Music		Public	
Desktop		Downloads	Movies		Pictures

See also How to reclaim the /home directory.

/ (root) directory

Some directory may be hidden. See http://www.westwind.com/reference/OS-X/invisibles.html 

$ ls -l /
total 45
drwxrwxr-x+ 62 root  admin  2108 Feb 15 12:41 Applications
drwxr-xr-x+ 69 root  wheel  2346 Feb  9 11:02 Library
drwxr-xr-x@  3 root  wheel   102 Feb  9 08:47 Network
drwxr-xr-x@  4 root  wheel   136 Sep 16 17:07 System
drwxr-xr-x   7 root  admin   238 Feb  7 15:32 Users
drwxrwxrwt@  4 root  admin   136 Feb 15 13:32 Volumes
drwxr-xr-x@ 39 root  wheel  1326 Jul  8  2016 bin
drwxrwxr-t@  2 root  admin    68 Sep 16 16:59 cores
dr-xr-xr-x   3 root  wheel  4311 Feb  9 08:47 dev
lrwxr-xr-x@  1 root  wheel    11 Sep 16 16:59 etc -> private/etc
dr-xr-xr-x   2 root  wheel     1 Feb 14 15:31 home
-rw-r--r--@  1 root  wheel   313 Aug  2  2015 installer.failurerequests
dr-xr-xr-x   2 root  wheel     1 Feb 14 15:31 net
drwxr-xr-x@  3 root  wheel   102 Feb  9 14:58 opt
drwxr-xr-x@  6 root  wheel   204 Sep 16 16:59 private
drwxr-xr-x@ 59 root  wheel  2006 Sep 16 16:59 sbin
lrwxr-xr-x@  1 root  wheel    11 Sep 16 16:59 tmp -> private/tmp
drwxr-xr-x@ 12 root  wheel   408 Feb  9 11:02 usr
lrwxr-xr-x@  1 root  wheel    11 Sep 16 16:59 var -> private/var

/Volumes and Machintosh HD directory

Macintosh HD is just a symbolic link to / (root) on your system; that is done in /Volumes. 

$ ls -l /Volumes/
total 8
lrwxr-xr-x  1 root  admin    1 Feb  9 08:47 Macintosh HD -> /
drwxrwxr-t  8 root  admin  340 Jan 18 14:06 OS X Install ESD

Best drive/partition format to share data between Mac, Linux and OS X

ExFAT. See http://superuser.com/questions/398190/what-is-the-best-drive-format-to-share-data-between-mac-linux-and-os-x

  • Mac OS doesn't support writing to NTFS drives.
  • NTFS and REFS are a bad choice because Linux and Mac can't properly decode it
  • exFAT doesn't support symlinks
  • Fat32 has a 4GB single file limit and 2TB partition size.
  • In one case when my NTFS partition (USB drive) is broken, it becomes a format called 'RAW' shown on Windows Disk Management utility.

For some reason using Disk Utility to erase/format a 16GB USB drive to ExFat failed (Media kit reports not enough space on device). Fortunately the command line method works (and fast at least for the 16GB space case). 

diskutil list     # get the name to the disk you're trying to format
diskutil unmountDisk force disk2
sudo dd if=/dev/zero of=/dev/disk2 bs=1024 count=1024
diskutil partitionDisk disk2 GPT ExFat "toshiba" 0g

What is the “wheel” user in OS X?

wheel is the system administrator group in BSD, much like root is the system administrator user. See http://superuser.com/questions/191955/what-is-the-wheel-user-in-os-x

Install to a USB drive

To boot from your external Sierra drive, plug it into the Mac in question, press the power button, and hold the Option key until the recovery disk screen appears. From there, you can select your external drive and click the arrow to boot into it for that session.

How to Install and Use macOS Sierra on an External Drive

https://www.howtogeek.com/293476/how-to-install-and-use-macos-sierra-on-an-external-drive/

How to Burn OS X El Capitan to a USB Flash Drive

http://lifehacker.com/how-to-burn-os-x-el-capitan-to-a-usb-flash-drive-1733425133

Install, Boot, and Run Mac OS X From an External Hard Drive

http://www.online-tech-tips.com/mac-os-x/install-boot-and-run-mac-os-x-from-an-external-hard-drive/

Terminal

Where is the terminal

Macintosh HD/Applications/Utilities/Terminal.

Keyboard shortcuts

  • Ctrl + a - going to the beginning of the line
  • Ctrl + e - going to the end of the line

More

Keyboard shortcuts

Navigation in a browser or document

  • Command + up = go to the top of the document
  • Command + down = go to the end of the document
  • Command + f = search

Text navigation and selection

12 Keyboard Shortcuts for Navigating & Selecting Text in Mac OS X

  • Select text to beginning of a line – Shift+Command+Left Arrow
  • Select text to end of a line – Shift+Command+Right Arrow
  • Select text to beginning of current word – Shift+Option+Right Arrow
  • Select text to end of current word – Shift+Option+Right Arrow
  • Select text to beginning of all text – Shift+Command+Up Arrow
  • Select text to end of all text – Shift+Command+Down Arrow

Compare to Windows/Linux

  • Use Command + q to close an application instead of "Alt+F4" on Windows/Linux.
  • System Activity tool:
    • Windows: Task Manager
    • Linux: System Monitor
    • Mac: Activity Monitor

Hardware

2015 Macbook Pro model A1398, 15.4 inch.

Display resolution

2880x1800 on my 15-Inch Retina Display MacBook Pro. According to the Retina Display page on Wikipedia, its PPI (pixels per inch) is 220. To achieve the same PPI on 21.5 inch display, it has to be 4K and the display has to be 5K if it is 27 inch display.

Unfortunately Virtualbox (5.1.14) can only give 1440x900 (tested on Ubuntu & Windows). See a workout http://tusharm.com/articles/win7-on-retina-display-with-virtual-box/.

Touchpad

Need to press a little bit (instead of touch) for the left-click effect. If we want to use 'tap' for the click (like other OS), go to the System Preferences to change it.

The right click is called secondary click in OS X. By default it is click with two fingers. We can change the setting by going to System Preferences/Touchpad/Secondary click.

Scroll: two fingers move up/down. The direction is like moving a paper; i.e. scrolling up will gradually show the next part of the content.

Zoom in/out: pinch with two fingers.

Smart zoom: double-tap with two fingers.

Drag and drop: use your thumb to click on the lower part of the track and the index finger to move

CPU information

sysctl -n machdep.cpu.brand_string

My macbook Pro 2015 shows i7-4980HQ CPU @ 2.80GHz.

Power Adapter

85W MagSafe 2 Power Adapter for MacBook Pro with Retina Display (MD506LL/A) $75

Finder - file manager

Keyboard

Use Command+Down instead of Enter key to open a binary file.

Use Command+Down will immediately uncompress a tar.gz file.

'Enter' key is not used to launch a program or open a file. It is used to rename a file. We can use Command + Down key to open a file.

Alternatives

Commander One Free dual pane file manager for Mac

Screenshots

http://www.howtogeek.com/278615/the-best-screenshot-apps-for-macos/

Terminal

screencapture test.jpg

screencapture -c    # send to the clipboard

screencapture -T 10 timedshot.jpg # timer 

screencapture -w test.jpg
# OR
screencapture -W

screencapture -h     # help

Grab

Take a Timed Screenshot With the Grab (built-in) Application. Open Grab, select Capture -> Selection/Window/Screen/Timed screen.

Lightshot

An easy-to-use app Lightshot which sits on the taskbar.

Note: to view an image resolution in Finder, right click an image and select Get Info -> More Info.

Application

How to Install Applications

Install pkg file from command line

http://apple.stackexchange.com/questions/15658/how-can-i-open-a-pkg-file-manually 

sudo installer -pkg ~/Downloads/packagename.pkg -target ~/Applications/
# OR
installer -pkg ~/Downloads/packagename.pkg -target ~/Applications/

Launch an application

  • F4 key - LaunchPad
  • Command + Space - Spotlight search

Close an application

Clicking the red button does close/quit an application/a program. You need to use Command-Q.

Another answer: The red close button just closes the window. It is up to the application whether it quits or not - typically if the application uses documents or it has other windows that can be opened it will not quit. Applications with a single window (System Preferences, for example), will usually quit when the window is closed, since there isn't anything else it does.

Package

app file

Example: App Store.app, Qt application.

http://apple.stackexchange.com/questions/112197/what-does-a-app-file-actually-do

apps are "Package Bundles" is Apple jargon. These are actually Unix directories, in a special format. The actual Unix Executable File is in a subdirectory named MacOS, which you can see using the "Show Package Contents" menu in Finder.

dmg (disk image) file

Example: Google chrome, FastQC.

A DMG file is a disk image, which is sort of like an archive file. When you download one, you can double-click it to “mount” it (under Devices in the Finder), allowing you to extract the application from inside it.

After the app is dragged to your Applications folder, you can run it normally — from the Finder, Launchpad, Spotlight, dock, or anything else.

We can mount or eject a dmg file by 

# mount
hdiutil mount fastqc_v0.11.5.dmg
# copy its content
mkdir -p ~/FastQC
cp -r /Volumes/FastQC/FastQC.app/Contents/MacOS/* ~/FastQC/
# eject
hdiutil eject /Volumes/FastQC/

To create a dmg file (see command line or here and GUI) 

hdiutil create -volname WhatYouWantTheDiskToBeNamed \
    -srcfolder /path/to/the/folder/you/want/to/create \
    -ov -format UDZO name.dmg

To convert a dmg file to iso 

hdiutil convert imagefile.dmg -format UDTO -o imagefile.iso
mv imagefile.iso.cdr imagefile.iso

pkg file

Example: R-cran

PKG files are Mac OS X installation (setup) packages that contain installer scripts ('Scripts' file) and compressed installation files ('Payload' file) that are used to install Mac software applications onto a user's hard drive.

On the case of R-x.y.z.pkg, it contains R framework, R.app GUI, Tcl/Tk X11 and TexInfo.

MacPorts, Fink and Homebrew

http://apple.stackexchange.com/questions/32724/what-are-pros-and-cons-for-macports-fink-and-homebrew & http://apple.stackexchange.com/questions/64690/macports-vs-fink-vs-homebrew

  • MacPorts. Different versions of Mac OS X has a different macport binary (in .pkg format).
# Install
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
# install some package
brew install wget
# Uninstall homebrew
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall)"
  • Fink. No binary installer for recent versions of OS X (good to me). You will need to install the proper Command Line Tools for Xcode for your system.
# install
curl -s https://raw.githubusercontent.com/rudix-mac/rpm/2016.12.13/rudix.py | sudo python - install rudix
# install some package
sudo rudix install wget
sudo rudix install python-pip
# remove a package
sudo rudix remove python-pip
# uninstall
sudo rudix -R

Developer

Macs (unlike Linux) don’t come with a package manager, but there are a couple of popular package managers you can install. See SciPy.

Install Xcode

http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/ 

xcode-select --install

The installed tools are located in /Library/Developer/CommandLineTools/usr/bin/ directory.

To check the Xcode version 

xcodebuild -version

ldd on Mac

otool -L  <exec>

openssl

Method 1: brew 

brew doctor
brew update
brew upgrade
brew install openssl  # the opposite operation is 'uninstall'
cd /usr/local/include
ln -s ../opt/openssl/include/openssl .

Method 2: compile yourself

Python packages

http://www.scipy.org/install.html

VirtualBox

Touchpad

The direction of scrolling up and down in guest machine is opposite to the host machine.

El Capitan (10.11)

It works on my VirtualBox 5.1.14 and Macbook Pro 2015. 

VBoxManage modifyvm macElcapitan --cpuidset 00000001 000106e5 00100800 0098e3fd bfebfbff
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/efi/0/Config/DmiSystemProduct" "iMac11,3"
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/efi/0/Config/DmiSystemVersion" "1.0"
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/efi/0/Config/DmiBoardProduct" "Iloveapple"
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/smc/0/Config/DeviceKey" "ourhardworkbythesewordsguardedpleasedontsteal(c)AppleComputerInc"
VBoxManage setextradata macElcapitan "VBoxInternal/Devices/smc/0/Config/GetKeyFromRealSMC" 1

Con: The image downloaded there is already a virtual machine image format.

If I try to use the iso file downloaded from internet, I saw an error "Missing Bluetooth Controller Transport" (https://gist.github.com/frdmn/de12c894a385bc8e6bff).

Sierra (10.12)

Note the official image (e.g. Install macOS Sierra.app) we downloaded from Apple Store is saved under /Applications folder.

https://github.com/geerlingguy/macos-virtualbox-vm

  • video memory change from 16GB to 128MB
  • increase memory to 4096MB
  • turn off audio
VBoxManage modifyvm "{vmname}" --cpuidset 00000001 000306a9 00020800 80000201 178bfbff

After booting, select the preferred language and go to Utilities > Disk Utility. Select the VirtualBox disk and choose Erase to format it as a Mac OS Extended (Journaled) drive.

Unfortunately, the Mac guest machine cannot install guest additions.

I get a 'Guru meditation' error when I test the iso on a non-mac machine (intel core 2 duo CPU).

Remote connection (ssh)

Use Preferences -> Sharing -> Select Remote Login. http://osxdaily.com/2011/09/30/remote-login-ssh-server-mac-os-x/

To uses a command line to enable it, see

Tips

Got a New Mac? Do This First!

http://www.makeuseof.com/tag/new-mac-setup/

Upgrading to macOS Sierra (nee OSX) for R users

http://www.win-vector.com/blog/2017/01/upgrading-to-macos-sierra-nee-osx-for-r-users/

Access the Root Directory

http://osxdaily.com/2013/01/17/access-root-directory-mac-os-x/

Disable update notification

http://news.softpedia.com/news/how-to-disable-os-x-update-notifications-493961.shtml

How to Configure a Proxy Server

https://www.howtogeek.com/293444/how-to-configure-a-proxy-server-on-a-mac/

Missing Linux commands

wget

Method 1: Rudix 

curl -O https://raw.githubusercontent.com/rudix-mac/rpm/2016.12.13/rudix.py
python rudix.py install rudix
sudo rudix install wget
which wget
# /usr/local/bin/wget

$ wget https://raw.githubusercontent.com/arraytools/bdge/master/install_rnaseq.sh
--2017-02-26 08:41:09--  https://raw.githubusercontent.com/arraytools/bdge/master/install_rnaseq.sh
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.192.133, 151.101.128.133, 151.101.0.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.192.133|:443... connected.
ERROR: cannot verify raw.githubusercontent.com's certificate, issued by ‘CN=DigiCert SHA2 High Assurance Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’:
  Unable to locally verify the issuer's authority.
To connect to raw.githubusercontent.com insecurely, use `--no-check-certificate'.
$ wget https://raw.githubusercontent.com/arraytools/bdge/master/install_rnaseq.sh --no-check-certificate
--2017-02-26 08:41:26--  https://raw.githubusercontent.com/arraytools/bdge/master/install_rnaseq.sh
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.192.133, 151.101.128.133, 151.101.0.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.192.133|:443... connected.
WARNING: cannot verify raw.githubusercontent.com's certificate, issued by ‘CN=DigiCert SHA2 High Assurance Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’:
  Unable to locally verify the issuer's authority.
HTTP request sent, awaiting response... 200 OK
Length: 8502 (8.3K) [text/plain]
Saving to: ‘install_rnaseq.sh’

install_rnaseq.sh                        100%[===============================================================================>]   8.30K  --.-KB/s    in 0.001s  

2017-02-26 08:41:26 (15.7 MB/s) - ‘install_rnaseq.sh’ saved [8502/8502]

Method 2: homebrew 

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install wget --with-libressl

Method 3: Build from source (require Xcode, works on my OS X 10.12 Sierra w/ Xcode 8.2.1) 

xcode-select --install
cd ~/Downloads

curl -O https://www.openssl.org/source/openssl-1.0.2h.tar.gz
tar xzvf openssl-1.0.2h.tar.gz
cd openssl-1.0.2h
./configure darwin64-x86_64-cc 
make
sudo make install

curl -O http://ftp.gnu.org/gnu/wget/wget-1.18.tar.gz # version 1.19 won't work at the 'make' step
tar -zxvf wget-1.18.tar.gz
cd wget-1.15/
./configure –with-ssl=openssl –with-libssl-prefix=/usr/local/ssl
make
sudo make install

For some reason, when I use wget to download files from https server, I will get a message: ERROR: cannot verify site certificate. Unable to locally verify the issuer’s authority. See

watch

http://stackoverflow.com/questions/9574089/osx-bash-watch-command 

while :; do clear; your_command; sleep 2; done

htop

http://unix.stackexchange.com/questions/98253/how-do-i-install-htop-inside-mac-os-x

md5sum

It is called md5 instead of md5sum in Linux.

For SHA-1 and SHA-256 use 

shasum filename
# OR
shasum -a 1 filename

shasum -a 256 filename

tar

If we run the following command 

tar xzvf filename.tar.gz -C directory 2> error.log

we will get a non-empty file in <error.log> even the extraction is successful.

Therefore it is better to use the following way 

tar xzvf filename.tar.gz -C directory
if [ $? -eq 0 ]; then
    echo OK
else
    echo FAIL
fi

Git client

sourcetree. See also Happy Git and Gihub for the useR from Jenny Bryan.

Diff tools

  • Diff Tools on macOS
  • FileMerge - part of XCode from Apple. Too un-intuitive compared to WinMerge on Windows or Meld on Linux:(
  • DiffMerge. Still not intuitive.
  • Meld for OSX - BEST!
  • Beyond Compare (commercial)
  • Araxis Merge (commercial)
  • DeltaWalker (commercial)
  • Kaleidoscope (commercial)
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