Mac: Difference between revisions
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* After I open the lid, the screen can not be unlocked. I only see the mouse cursor. | * After I open the lid, the screen can not be unlocked. I only see the mouse cursor. | ||
* The battery is drained out when I open the lid:( | * The battery is drained out when I open the lid:( | ||
* Wifi cannot automatically connect | |||
== [https://www.apple.com/imac-pro/specs/ iMac Pro] == | == [https://www.apple.com/imac-pro/specs/ iMac Pro] == |
Revision as of 07:21, 24 August 2018
macOS
https://en.wikipedia.org/wiki/MacOS
Darwin (operating system) and release history (first is September 30, 2015). Check the current machine's build number About this Mac > System Report > Software. I found after I installed the latest updates, the available disk space is increased.
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?
Darwin, MacOS, OpenSource?
http://superuser.com/questions/19492/is-mac-os-x-open-source. Darwin is like Linux, FreeBSD, etc... Mac OS X GUI is like KDE, GNome, etc...
Apple Open Source https://opensource.apple.com/. It includes Kernel, macOS, Developer Tools, etc.
Partition format
fdisk will show it is HFS/ HFS+. Ubuntu OS can read but can't write to it.
/dev/sdb1 * 64 250675199 250675136 119.5G af HFS / HFS+
However, I got a problem when I run cp command.
$ ls -l /media/brb/SamsungUSB/ -rw------- 1 99 99 10592270336 Feb 26 09:45 macSierra.ova -rw-r--r-- 1 99 99 6922018816 Feb 15 14:40 Sierra10.12.3.iso $ md5sum '/media/brb/SamsungUSB/macSierra.ova' md5sum: /media/brb/SamsungUSB/macSierra.ova: Permission denied $ sudo chown brb /media/brb/SamsungUSB/macSierra.ova chown: changing ownership of '/media/brb/SamsungUSB/macSierra.ova': Read-only file system
Some suggestion is to disable journaled file system as this.
But I found the problem should be resolved in macOS. That is, running 'sudo chmod 644' on the file from an Mac computer.
Beta version of macOS
How to get the new version of macOS 10.13
Preferences - Energy Saver
- https://support.apple.com/en-us/HT201714
- https://support.apple.com/en-us/HT202824
- Mine is greyed out. For a command line method, use the pmset command.
Multiple desktops
Mission Control 101: How to Use Multiple Desktops on a Mac
Split screen
https://support.apple.com/en-us/HT204948
- Hold down the full-screen button in the upper-left corner of a window.
- As you hold the button, the window shrinks and you can drag it to the left or right side of the screen.
- Release the button, then click another window to begin using both windows side by side.
Black screen with cursor
After I opened the lid to wake it up and type my password, the screen kept black with a cursor only. My solution: hold the power button for a few seconds and the screen will pop us a dialog asked me for a few options. I choose 'restart' and the desktop is back. Later it shows Your Mac hasn't restarted because RStudio failed to quit. To continue restarting, quit RStudio. If I clicked 'Try again', the Mac will re-start.
https://www.cnet.com/news/macbook-pro-blank-screen-on-wake-from-sleep-2-fixes/
Booting problem
How to Repair Your Mac’s Disk Using Safe Mode, fsck, and More
OS X File System
- https://developer.apple.com/library/content/documentation/FileManagement/Conceptual/FileSystemProgrammingGuide/FileSystemOverview/FileSystemOverview.html
- Mac OS X Directory Structure explained
- Directory structure between mac osx and linux
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
How to show hidden files and folders including ~/Library on a Mac
In MacOS Sierra, use CMD-Shift-. (dot).
Or follow Quickly Show/Hide Hidden Files on macOS Sierra, OS X El Capitan & Yosemite
/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
macOS Sierra: Share files with others who use your Mac
Format SD card as FAT
Use SD Memory Card Formatter. See https://www.raspberrypi.org/documentation/installation/noobs.md.
- Mac OS doesn't support writing to NTFS drives.
- Mac OS can't find ext3/ext4 partition. See some solutions How can I mount an ext4 file system on OS X?
- NTFS and REFS are a bad choice because Linux and Mac can't properly decode it
- exFAT doesn't support symlinks. So the Illumina igenomes data won't work on exFAT partitioned drive.
- 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.
- It is easy to create exfat partition format on Windows 7. When I move the USB drive to a Linux machine, fdisk -l shows
$ sudo fdisk -l /dev/sdc WARNING: GPT (GUID Partition Table) detected on '/dev/sdc'! The util fdisk doesn't support GPT. Use GNU Parted. Disk /dev/sdc: 123.6 GB, 123633401856 bytes 255 heads, 63 sectors/track, 15030 cylinders, total 241471488 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 512 bytes I/O size (minimum/optimal): 512 bytes / 512 bytes Disk identifier: 0x5b508967 Device Boot Start End Blocks Id System /dev/sdc1 2048 241469439 120733696 7 HPFS/NTFS/exFAT
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 # use bs=4000000 and skip count for an alternative diskutil partitionDisk disk2 GPT ExFat "toshiba" 0g
use dd command to burn an ubuntu image
The USB drive will not be able to start. It will give an error in GRUB step: illegal numeric value. This is tested on Ubuntu 18.04.
Find partition type
df -hT blkid /dev/sda1 mount sudo file -sL /dev/sd* sudo fdisk -l
rsync: mkstemp FILENAME failed: Function not implemented (38)
http://blog.marcelotmelo.com/linux/ubuntu/rsync-to-an-exfat-partition/
# Do not use 'rsync -av SRC DEST' # Use rsync -rltDv --info=progress2 SRC DEST
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
/bin/sh and /bin/bash differences
https://discussions.apple.com/thread/3177477?start=0&tstart=0
How to Auto-Hide the Dock With No Delay
http://www.makeuseof.com/tag/auto-hide-dock-no-delay-mac/
How can I list my open network ports with netstat?
http://apple.stackexchange.com/questions/117644/how-can-i-list-my-open-network-ports-with-netstat
sudo lsof -i -P | grep -i "listen"
Root account vs admin account
- https://discussions.apple.com/thread/3128749?start=0&tstart=0
- The Option "Allow User to Administer this Computer" option is Dimmed
- How to Enable the Root User in macOS
@ sign in file attributes
- https://apple.stackexchange.com/questions/97241/ls-command-what-does-the-in-file-mode-mean-and-how-to-get-rid-of-it
- Extended attributes https://en.wikipedia.org/wiki/Extended_file_attributes
- Use ls -l@ to see extended attributes. For example the file attributes can be different when SeqTools was downloaded from a browser and obtained by the scp command.
# seqtools-dl is a folder extracted from the SeqTools zip file. # Case 1. the zip file is downloaded through a browser brbs-iMac:~ brb$ ls -l@ Documents/seqtools-dl/SeqTools.app/Contents/MacOS/code total 176 -rwxr-xr-x 1 brb staff 18229 May 15 09:15 createGeneListSNPEFF.sh -rwxr-xr-x 1 brb staff 1550 Oct 24 2016 gdown.pl -rwxr-xr-x 1 brb staff 4214 May 15 09:15 gdown_mac.sh -rwxr-xr-x 1 brb staff 22264 May 15 09:15 statsVariantGeneAnno_Auto.sh ... # Case 2. the zip file is obtained through the scp command brbs-iMac:~ brb$ ls -l@ Downloads/seqtools-dl/SeqTools.app/Contents/MacOS/code total 176 -rwxr-xr-x@ 1 brb staff 18229 May 15 09:15 createGeneListSNPEFF.sh com.apple.quarantine 57 -rwxr-xr-x@ 1 brb staff 1550 Oct 24 2016 gdown.pl com.apple.quarantine 57 -rwxr-xr-x@ 1 brb staff 4214 May 15 09:15 gdown_mac.sh com.apple.quarantine 57 -rwxr-xr-x@ 1 brb staff 22264 May 15 09:15 statsVariantGeneAnno_Auto.sh com.apple.quarantine 57 ...
Create a Bootable macOS Installer
Make sure you use a USB flash drive or other removable media that has at least 12GB of available disk space.
- https://support.apple.com/en-us/HT201372
- http://osxdaily.com/2016/09/23/create-boot-macos-sierra-installer/
- http://osxdaily.com/2014/10/16/make-os-x-yosemite-boot-install-drive/
sudo /Applications/Install\ macOS\ Sierra.app/Contents/Resources/createinstallmedia \ --volume /Volumes/usb16g --applicationpath /Applications/Install\ macOS\ Sierra.app
Reboot, holding down the OPTION key and selecting the “Install OS X Sierra” drive upon boot..
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/
- http://www.makeuseof.com/tag/troubleshoot-mac-startup-keys/
Pressing the Option key on boot displays a list of your Mac’s bootable drives.
Terminal
Where is the terminal
Macintosh HD/Applications/Utilities/Terminal.
Mouse pointer
A temporary solution is to hold the 'Alt' key while moving the mouse in the terminal. This strategy also works on RStudio's code panel.
Another solution is to use iTerm2 instead.
Keyboard symbols
- ⌃ is the Control key (Caret notation. Widely used in Windows too, such as ^C for copy)
- ⌥ is the Option (alt) key
- ⇧ = Shift key
- http://osxdaily.com/2012/03/27/making-sense-of-mac-keyboard-symbols/
- http://tedwise.com/2009/04/28/what-do-those-weird-mac-symbols-mean/
Keyboard shortcuts
- Ctrl + a OR Cmd + left arrow = going to the beginning of the line
- Ctrl + e OR Cmd + right arrow = going to the end of the line
- Fn + Down arrow = page down
- Fn + Up arrow = page up
Rename terminal tabs
Click the “Shell” menu and select “Edit Title” to bring up the Terminal Inspector window
Terminal replacement
- iTerm2. GPL2 license. Source code is in github.
- (Update 5/14/2018) Copy from RStudio to iTerm2 R console may mess up. Don't find a solution yet.
- Save window/tabs on exit?. Works.
- The HOME/END keys work when I work in a virtual machine. To change font size, go to Preferences -> Profile -> Text -> Font or just use the keyboard shortcut Command + +/-.
- Copy won't include the background color.
- We can change the cursor color from grey to anything (Preferences -> Profile -> Colors -> Cursor Colors).
- It can display image on its terminal using their own utility imgcat. After downloading it, chmod +x and then move it to /usr/local/bin directory.
- iTerm2 Leaks Everything You Hover in Your Terminal via DNS Requests (9/20/2017)
- MacTerm
exit does not close a terminal/tab
You can change the setting by Preferences -> Profiles -> Shell. See https://superuser.com/questions/158375/how-do-i-close-the-terminal-in-osx-from-the-command-line.
Mac Terminal’s Hidden Task Manager to See Background Processes
terminal fun
- The Best “Just For Fun” Tricks Hidden in macOS’ Terminal:
- Make Your Mac Say Anything Out Loud,
- Play Simple Games Like Tetris, Pong, and Snake,
- caffeinate will prevent your Mac from falling asleep.
Recording the terminal
Keyboard shortcuts
How Not Using Keyboard Shortcuts Makes You Lose 64 Hours Every Year
Keyboard mappings using a PC keyboard on a Macintosh
Mac keyboard: Ctrl -> Option/Alt -> Cmd. Windows keyboard: Ctrl -> Windows -> Alt.
- https://support.microsoft.com/en-us/help/970299/keyboard-mappings-using-a-pc-keyboard-on-a-macintosh
- https://9to5mac.com/2016/03/17/how-to-remap-windows-keyboard-buttons-match-mac-layout/.
- Apple internal keyboard -> USB keyboard
- 'Option' -> 'Command'
- 'Command' -> 'Option'.
Lock screen
Shift + control + power
Cut and paste files
http://osxdaily.com/2011/07/29/cut-and-paste-mac-os-x-lion/
- Cmd + C
- Cmd + Opt + V
Minimize all windows
- Method 1: Cmd + F3 (min apps go to the RHS)
- Method 2: Opt + Cmd + H + M
Finder
Command + [: move back to the previous folder
See more.
- Command + up = go to the top of the document
- Command + down = go to the end of the document
- Command + f = search
- Fn + Down arrow = page down (or Spacebar in a web browser)
- Fn + Up arrow = page up (or Shift + Spacebar in a web browser)
- Fn + Left arrow = Home
- Fn + Right arrow = End
- Ctrl + TAB = switch tabs in browser
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
Switch input sources
Go to System Preferences -> Keyboard -> Shortcuts -> Input Sources. Check 'Select the previous input source ^Space'. Use Ctrl + Space to switch.
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
Switch between windows of the same application
Cmd + ` (backtick)
Hardware
MacBook Pro (Retina, 15-inch, Mid 2015) - Technical Specifications
2015 Macbook Pro model A1398, 15.4 inch.
9 Essential Details You Must Know About Your Mac
https://www.makeuseof.com/tag/essential-mac-details/
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 method 1: Use the normal three finger drag, leave two fingers on the trackpad while doing a flicking motion with the third finger (eg thumb). The more momentum you add to your motion, the further it drags.
- Drag and drop method 2:
- highlight the app first
- lightly click the app (you should only feel one click. Do not use too much force; if you do, you will hear two click sound and it will pop up a window to show the file information) with your thumb and then use your index to move the app to “Applications” directory.
CPU information
sysctl -n machdep.cpu.brand_string
My macbook Pro 2015 shows i7-4980HQ (see GeekBench 4 score) CPU @ 2.80GHz. Quad cores. Eight threads. Base Frequency 2.8GHz. Max Turbo Frequency 4.0GHz. Bus Speed: 5 GT/s DMI2.
CPU temperature
- https://apple.stackexchange.com/questions/54329/can-i-get-the-cpu-temperature-and-fan-speed-from-the-command-line-in-os-x. The istats works for me. 49.63°C on idle.
$ gem install iStats $ istats
- http://osxdaily.com/2016/03/13/monitor-system-stats-cpu-temp-fan-speed-in-mac-notification-center/
- https://beebom.com/how-check-cpu-temperature-mac/
RAM
Can you upgrade the ram in your Mac
Power Adapter
85W MagSafe 2 Power Adapter for MacBook Pro with Retina Display (MD506LL/A) $75
Battery diagnostic
About this Mac -> Overview -> System report -> Power.
Cycle count limits for my macbook pro 15inch Mid 2015 (shown from About This Mac) is 1000.
- The current cycle count currently is 175 cycle count (10/20/2017). Full charge capacity (mAh) is 8421.
- The current cycle count currently is 199 (Feb 7, 2017 -> Nov 29, 2017). Full charge capacity is 8076.
- The current cycle count is 263 (Mar 2, 2018). Full charge capacity is 8096.
The Chargeberry app shows the factory capacity is 8755 mAh.
Too hot: remove the cover, cleaning
How to Clean Dust Out of Your MacBook
Complaints
Macbook Pro 2015
- Even the lid is closed, the fan is turning loud (something is running?) parentalcontrolsd uses 248% cpu. Router showed the machine's wifi is still on.
- After I open the lid, the screen can not be unlocked. I only see the mouse cursor.
- The battery is drained out when I open the lid:(
- Wifi cannot automatically connect
iMac Pro
The new (2017) iMac Pro can be equipped with a 128 GB of memory and 4 TB SSD drive.
Finder - file manager
Copy file full path
This is important since RStudio cannot drag and drop a file to insert the file path.
- Navigate to the file or folder you wish to copy the path for
- Right-click (or Control+Click, or a Two-Finger click on trackpads) on the file or folder in the Mac Finder
- While in the right-click menu, hold down the OPTION key to reveal the “Copy (item name) as Pathname” option, it replaces the standard Copy option
- Once selected, the file or folders path is now in the clipboard, ready to be pasted anywhere
Enter key does not open the file
Use Command+Down instead of Enter key to open a file or go into a directory.
Enter key is only used to rename a file. See https://discussions.apple.com/thread/3140356?start=0&tstart=0.
Use Command+Down will immediately uncompress a tar.gz file.
Go to a folder
Use Cmd+Shift+o to go to a specific location by entering its full path. Unfortunately this option is not available in other applications in general.
Commander One
Free dual pane file manager for Mac.
- User Guide
- The bookmark is called 'Favorites' in Commander One. Click the 'star' icon and a Windows' style of a right click menu will pop up. You can select 'Add to Favorites' to add the current directory to the favorites. This bookmarked location will be shown when you click the 'star' icon next time.
- The icon (multiple horizontal lines) next to the 'star' shows the recent locations. This is useful too!
- By default, Commander One will send anonymous usage statistics to Eltima. Go to Preferences -> General to uncheck this option.
Screenshots
- Shift +Cmd + 4: select a rectangle
- http://www.howtogeek.com/278615/the-best-screenshot-apps-for-macos/
- How to Change Where Mac Screenshots Are Saved
Terminal
Use the screencapture command.
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
To view an image file, use the open command. See also Shell tricks: the OS X open command.
open test.jpg
To view the metadata of an image file, use the mdls command such as mdls XXX.png. See How to look up file metadata in OS X
Grab
Grab is a utility. Finder -> Go -> Applications -> Utilities -> Grab.
How To Use macOS & Mac OS X Grab Utility To Take Screenshots
Take a Timed Screenshot With the Grab (built-in) Application. Open Grab, select Capture -> Selection/Window/Screen/Timed screen.
Lightshot
Lightshot works like Shutter in Ubuntu - easy to use and can sit on the taskbar.
Note: to view an image resolution in Finder, right click an image and select Get Info -> More Info.
Its icon is a feather.
Feather has an advantage that the screenshot does not need to be saved. It can be copied to a clipboard and then discarded.
Screen cast
Quicktime player
We can record the screen (full screen or a selected region). The recorded file will be in a .mov format.
Screen cast o magic
http://screencast-o-matic.com/
Application
How to Install Applications
- http://www.howtogeek.com/177619/how-to-install-applications-on-a-mac-everything-you-need-to-know/
- Installing a .dmg and .pkg application from the command line
Keyboard shortcut to launch an application
- F4 key - LaunchPad
- Command + Space - Spotlight search
Messages when you launch an application
- Google Chrome
- iTerm
- SeqTools
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/
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 formats
app directory
Example: App Store.app, Atom editor, SourceTree
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.
To deliver the program in an app format, we can zip the app folder. If we use Safari browser, it will automatically decompress the zip file so the app program will appear in the Downloads directory.
For example, in SourceTree, the download file is called 'SourceTree_X.Y.zip'. When we click the zip file, it will be automatically extracted. And when I click SourceTree.app, it will have a dialog to help user to move the program to the application folder.
pkg file
Example: R-cran
- Extract PKG files on Mac and Windows
- How to Open .pkg Files to View What Will Install on Mac with Suspicious Package
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.
To install a pkg file from terminal, see this post
sudo installer -pkg R-3.3.3.pkg -target /
dmg (disk image) file
Example: Google chrome, JDK, FastQC, Sketchup, Commander One.
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
To install a dmg file from terminal, see this or this
MOUNTDIR=$(echo `hdiutil mount jdk-8u121-macosx-x64.dmg | tail -1 \ | awk '{$1=$2=""; print $0}'` | xargs -0 echo) \ && sudo installer -pkg "${MOUNTDIR}/"*.pkg -target / \ && sudo hdiutil detach "${MOUNTDIR}"
Explanation: The first command (hdiutil mount jdk-8u121-macosx-x64.dmg) will output
expected CRC32 $628D96B6 /dev/disk2 GUID_partition_scheme /dev/disk2s1 Apple_HFS /Volumes/JDK 8 Update 121
We like to grab the string "/Volumes/JDK 8 Update 121". This can be achieved by getting the last line of the output and replace the first and 2nd fields with empties and then output the whole line.
Package manage software
http://apple.stackexchange.com/questions/32724/what-are-pros-and-cons-for-macports-fink-and-homebrew & http://apple.stackexchange.com/questions/64690/macports-vs-fink-vs-homebrew
MacPorts
Different versions of Mac OS X has a different macport binary (in .pkg format).
MacPorts Brings the Best Open Source Software to Your Mac
Homebrew
# Install /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" # install some package brew install wget brew install htop brew install ruby # install a newer version of ruby & gem; overwrite the pre-installed one brew install cvs # Update brew brew update # Not add sudo # Uninstall homebrew ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall)"
brew tap command
How to uninstall / remove a Homebrew package including all its dependencies
Homebrew Cast extends Homebrew and brings its elegance, simplicity, and speed to macOS applications and large binaries alike. What is the difference between `brew` and `brew cask`?.
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.
Rudix
# 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
Extract files (Unzip)
Unarchiver. Mentioned by Raspbian.
Image editor
https://www.howtogeek.com/304677/the-best-free-photo-editors-for-macos/
Note when I use the 'Preview' program, it will automatically save the changes without any warnings when I exit the program.
Paintbrush
https://paintbrush.sourceforge.io/
Works fine. It does prompt to save for any changes when I quit the program.
Text editor
http://beebom.com/best-text-editors-for-mac/
For printing to pdf files with line numbers, I am using GEdit in Ubuntu VM. Some promising editors like BBEdit cannot even let me open rmd files.
Change the default text editor
Just right (or control) click a file of the type you want to change and: "Get Info" -> "Open with:" -> (Select your program) -> "Change All".
The above method can be used to change the default player too (iTune -> VLC).
If you use the open command in a terminal to open a text file, the default program will be used.
Atom editor from Github
Complains: too frequent updates. It makes multiple instances on the right click menu in Finder on macOS (seems it is only a problem on Mac). See a report here. A solution is
rm -rf ~/Library/Caches/com.github.atom.ShipIt killall Finder
and then launch Finder manually.
- The atom application requires no installation. So once it is downloaded (we actually download a zip file. After download has finished Safari browser will automatically decompress the zip file), we can drag it to the Application folder.
- Open atom from a terminal.
Method 1 (GUI). Atom -> Install Shell Commands. Two symbolic links (atom and apm) will be created in /usr/local/bin to point to the currently opened Atom application.
Method 2 (Manual):
ln -s /Applications/Atom.app/Contents/Resources/app/atom.sh /usr/local/bin/atom
- When you open the Atom the first time, it will split the screen into two panes: on the LHS it has a 'Welcome' and on the RHS it has a 'Welcome Guide'. You can choose to close any one of them by View -> Panes -> Close Pane. You may reopen the Welcome Guide by Help -> Welcome Guide.
- You can hide the directory on the left hand side by View -> Toggle Tree View.
- Command Palette: Press Cmd+Shift+P.
- You can search by any keyword to find the keyboard shortcut.
- You can use it to install the terminal commands atom and apm if they were not installed during installing Atom.
- Settings: Atom -> Preferences.
- Open a file: Cmd+o. Save a file: Cmd+s.
- If a file is modified and not saved yet, the changes are saved to a cache. Even we close Atom, the changes are there. The original file is still intact.
- Open a directory as a project. Open a folder will add a tree view to the editor where you can browse all the files. You can toggle the tree view on the side of the window by Cmd+\.
- Jump to a specific line: Ctrl+g.
- Find and replace: Cmd+f. To search the whole project, Cmd+Shift+f.
- Folding: Alt+Cmd+[ and Alt+Cmd+]
- Panes splitting: Cmd+K Up/Down/Left/Right
- Preview a markdown file (toggle): Ctrl+Shift+M
- R syntax highlight
$ apm install language-r Installing language-r to /Users/USERNAME/.atom/packages ✓ # Re-start Atom to enable it
Printing. No way!
Macdown- markdown editor
If I use macDown to open a text file, macDown will still assume the file is a markdown file and give a preview on the right panel.
Sublime
How do I open new files in a new tab?
TextMate
http://lifehacker.com/5817833/the-best-programming-text-editor-for-mac
For some reason when I open an old file, TextMate does not open it on a new tab; it opened the file in a new window??
gedit
http://macappstore.org/gedit/ Does not work. I got the same error.
Jekyll
http://idratherbewriting.com/documentation-theme-jekyll/mydoc_install_jekyll_on_mac.html
Text to speech
- In Chrome/Safari select a paragraph and right click -> Speech -> Start speaking.
- Dictater
- How to Make a Mac Talk: Text to Speech
Print to PDF from the print dialog
In the Print dialog, look for the “PDF” button in the lower left corner, click on that pull-down menu, and select “Save as PDF”. Click “Save” in the save dialogue box, and save the file to whatever location you want.
Command line to print a file to pdf
# Suppose we have an R file. We like to print it to PDF with line numbers. $ cat -n tmp.R > tmp.txt $ cupsfilter tmp.txt > tmp.pdf # OK. But how to control the font size? How to deal with indentation for line wrapping. Landscape orientation.
- text2pdf
- Use pandoc to convert it to docx (so we can control font size) and convert it again to PDF.
Convert a pptx to pdf
The 'Zoom' function is kind of slow to response with Office 2016. There is no this problem with converted PDF file.
- Use 'Save As...'
- Don't use print to PDF. The quality will reduced.
Delete/add/reorder page pages using Preview
http://osxdaily.com/2010/01/20/delete-pages-in-a-pdf-document/
There is no need to save the document. It will be saved automatically.
Crop pdf files
Preview. See a demonstration on youtube. This is very good and the crop experience is similar to briss.
- View → Thumbnails
- Select all pages by Cmd+a. Use Cmd+click to unselect any pages.
- Click the Show Markup Toolbar button from the RHS of the toolbar and click the Rectangular Selection button or directly click on Tools → Rectangular Selection
- Use mouse to select an area on the first page (or on a specific page). A rectangular area will show up on ALL pages.
- Adjust the width/height as you want from the 1st page (or from the specific page).
- Close the document and the changes will be automatically saved.
Edit by Preview
- How to use Preview on Mac (highlight/underline/strike through, crop, add signature,
- Use the Preview app to view and edit images and PDFs
Disk
Trash can
See its icon in the Dock.
Alternative to WinDirStat
https://alternativeto.net/software/windirstat/?license=free&platform=mac
- ncdu
brew install ncdu
- Disk Inventory X. It shows the sizes of files and folders in a special graphical way called "treemaps". The filename is DIX1.0Universal.dmg. It froze my Mac:(
- QDirStat based on Qt. No binary for macOS
- DaisyDisk $10.
Google Chrome browser
- https://en.wikipedia.org/wiki/Google_Chrome and Chrome stable updates
- What's the latest version of Chrome?
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/
Note: it seems there is no way to run this automatically without the alert box. Users need to agree the license.
xcode-select --install
The installed tools (like ar, gcc, g++, git, libtool, make, nm, otool, svn, et al) are located in /Library/Developer/CommandLineTools/usr/bin/ directory. If the command is run again, you will get a message
xcode-select: error: command line tools are already installed, use "Software update" to install updates
To check the Xcode version (if you have installed a full Xcode)
$ xcodebuild -version # if you have the full Xcode installed Xcode 8.2.1 Build version 8C1002 # if you only have the command line tool installed $ xcodebuild -version xcode-select: error: tool 'xcodebuild' requires Xcode, but active developer directory '/Library/Developer/CommandLineTools' is a command line tool instance
To check whether Xcode has been installed
$ xcode-select -p /Library/Developer/CommandLineTools # if you have installed the command line tool only # or /Applications/Xcode.app/Contents/Developer # if you have the full Xcode package installed # or xcode-select: error: unable to get active developer directory, use `sudo xcode-select --switch path/to/Xcode.app` to set one (or see `man xcode-select`)
To accept the XCode license through command line, follow the post Debugging macOS Kernel using VirtualBox:
$ sudo xcodebuild -license accept # it seems not working. A dialog is still popped up.
The df command shows installing the command line developer tools takes about 600MB space.
Uninstall Xcode
http://osxdaily.com/2012/02/20/uninstall-xcode/
Header file location
- /usr/include
- /usr/local/include (e.g. from "sudo make install" command)
- /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/ (if you have installed a full Xcode)
Lib location
- /usr/lib
- /usr/local/lib
- /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/lib/ (if you have installed a full Xcode)
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
- http://apple.stackexchange.com/questions/221587/how-to-make-a-clean-install-of-openssl-on-el-capitan
- http://mac-dev-env.patrickbougie.com/openssl/
Python packages
http://www.scipy.org/install.html
Install macOS on a PC
http://www.makeuseof.com/tag/how-to-install-mac-os-x-on-a-pc-without-using-a-mac/ (7/17/2017)
VirtualBox
Touchpad
The direction of scrolling up and down in guest machine is opposite to the host machine.
Keyboard shortcuts (macOS + Windows keyboard)
Since there is no Command key on Windows keyboards, we need to modify preferences.
Copy and paste: go to preferences -> keyboard -> Modifier keys. Change 'Option' key to 'Command' key and 'Command' key to 'Option' key. Since the 'Option' key is 'Alt' on Windows keyboards, the layout will be very similar to using Mac keyboards. This is consistent with Logitech K780 multi-device keyboard where 'Alt' key shares with the 'Command' key.
Do not use Ctrl to replace Command; you will not able to use the Ctrl key in nano and you are missing Ctrl + a to move mouse to HOME in Terminals. NOTE: iTerm2 is a good replacement for macOS's built-in Terminal program; HOME/END works.
Keyboard shortcuts (Windows OS + mac keyboard)
- Left CMD is used by VirtualBox to switch to full screen (at least on VirtualBox)
- Right CMD = Windows key
- fn + delete = DEL/Backspace key
Guest additions
VirtualBox doesn't have guest additions for OSX. http://askubuntu.com/questions/372982/virtualbox-4-3-guest-additions-on-osx-guest
In order to share files between the host and guest machine, we need to 1. add 'host-only' network adapter to the guest machine and 2. enable 'Remote Login' by going to the System Preferences -> Sharing.
For example, from the host machine, I can use the following on the host machine to access the guest machine
$ ssh [email protected]
However, it is unsuccessfully to do access the host machine from the guest machine??
$ ssh [email protected]
Smart card reader
If USB is enabled in the guest machine, the Smart Card reader will not be available on the host machine. That is, we cannot use the smart card in Mac. So it is necessary to uncheck the USB from the USB setting in the guest machine.
Screen resolution
https://forums.virtualbox.org/viewtopic.php?f=22&t=54030 works.
$ VBoxManage setextradata "vm_name" VBoxInternal2/EfiGopMode 4
The number '3' corresponds to a resolution of 1280x1024 (5:4) and '4' corresponds to 1440x900 (8:5). On lenovo laptop (1600 x 900, 16:9), the height will fill the screen but there are little black spaces on both sides. See Display resolution and aspect ratio.
Note that I need to enable Full Screen for the guest machine b/c the desktop is too large.
El Capitan (10.11)
- http://www.wikigain.com/install-mac-os-x-el-capitan-virtualbox/
- http://www.wikigain.com/complete-guide-fix-virtualbox-errors-installing-mac-os-x/
It works on my VirtualBox 5.1.14 and Macbook Pro 2015.
Note: if I skip the following commands, the macOS booting will keep re-run again and again.
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)
- The official image (e.g. Install macOS Sierra.app) we downloaded from Apple Store is saved under /Applications folder.
- We can follow the instruction https://github.com/geerlingguy/macos-virtualbox-vm to convert the app folder into an iso file. The prepare-iso.sh script seems to always put the iso file onto the Desktop folder; i.e. output folder and name is not taken.
- When we want to create a virtual machine in VirtualBox
- video memory change from 16GB to 128MB
- increase memory to 4096MB
- turn off audio
VBoxManage modifyvm "{vmname}" --cpuidset 00000001 000306a9 00020800 80000201 178bfbff
Another instruction is to run (this seems to be necessary even we uses 'import Appliance' method)
VBoxManage modifyvm "Sierra10.14" --cpuidset 00000001 000106e5 00100800 0098e3fd bfebfbff VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/efi/0/Config/DmiSystemProduct" "iMac11,3" VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/efi/0/Config/DmiSystemVersion" "1.0" VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/efi/0/Config/DmiBoardProduct" "Iloveapple" VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/smc/0/Config/DeviceKey" "ourhardworkbythesewordsguardedpleasedontsteal(c)AppleComputerInc" VBoxManage setextradata "Sierra10.14" "VBoxInternal/Devices/smc/0/Config/GetKeyFromRealSMC" 1
After booting, select the preferred language and (before click the 'Continue' button) go to Utilities > Disk Utility. Select the VirtualBox disk and choose Erase to format it as a Mac OS Extended (Journaled) drive. Installing macOS took about 15 minutes on my Dell T3600 Desktop running Ubuntu/Mint.
After a successful login, the 'df -h' command shows macOS uses 8.6 GB space.
Unfortunately, the Mac guest machine cannot install guest additions.
I get a 'Guru meditation' error when I test the iso on an old non-mac machine (intel core 2 duo CPU).
Note there is an error (IOConsoleUsers: gIOScreenLockState 3, hs 0, bs 0, now 0, sm 0x0) to install Sierra 10.12.4 as a guest machine. See https://benlimmer.com/2017/04/23/macos-sierra-virtualbox-10-12-4/.
Create an ISO from the Sierra install app obtained from the Mac app store
https://klue.github.io/blog/2017/04/macos_kernel_debugging_vbox/
How to Run Your Mac’s Boot Camp Partition as a Virtual Machine
https://www.howtogeek.com/315083/how-to-run-your-macs-boot-camp-partition-as-a-virtual-machine/
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
- http://apple.stackexchange.com/questions/237038/os-x-terminal-command-to-turn-on-off-ssh-server
- http://osxdaily.com/2016/08/16/enable-ssh-mac-command-line/
- http://superuser.com/questions/416096/enabling-ssh-daemon-from-terminal-os-x-lion
ssh key
Remote/Virtual machine: go to system preferences -> sharing and enable remote login. Suppose the user name is 'brb' and the hostname is 'brbs-MacBook-Pro.local'.
Host machine:
ssh-keygen -t rsa -f ~/.ssh/virtmac # press 'Enter' 3 times cat ~/.ssh/virtmac.pub | ssh [email protected] "mkdir -p ~/.ssh && cat >> ~/.ssh/authorized_keys" ssh -i ~/.ssh/virtmac [email protected]
When I run testings, I need to restore the virtual machine to its initial status. I can use this method in order to avoid the message "WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!" when I use the 'ssh' command.
Remote Desktop Connection to Mac
On Mac, go to system preferences -> System Preferences -> Sharing -> Screen Sharing. It will show the vnc address of the Mac computer.
On my Ubuntu, see AppleRemoteDesktop
- The built-in program Remmina Remote Desktop Client does not work. After clicking the 'connect' button & entering username/password, the screen flashed and disappeared.
- RealVNC. I download the tarball (VNC Connect 6.0.3, Generic x64, default). Extract it to the Download folder and run vncviewer program. Yes, I can connect to Mac. But since the Mac has a very high resolution, I need to adjust the resolution setting in my connection. To do that: close the connection, right click a connection icon (created from last connection), choose Properties. In 'Options' tab, select Scaling -> Scale to fit window.
- After connection, a toolbar will appear on the top of screen. It has a series of icons: Full screen mode, No scaling, Ctrl Alt Del, Info, Properties, Disconnect.
- Even Mac screen lid is closed, VNC still works.
- The connection speed is not ideal. You can see the screen refresh slowly.
- Vinagre. It has to be installed from Ubuntu Software. Unfortunately it does not even allow me to enter a long password:(
Remote Desktop Connection from Mac
When I try to use the Screen Sharing (1.7) program in Mac to connect to Ubuntu 16.04 (type 'vnc://192.168.1.188'), I get an error 'The software on the remote computer appears to be incompatible with this version of Screen Sharing.'
Another remote desktop program is called Remote Desktop Connection for iMac. It appears to be used to connect to a Windows-based computer.
Tips
Got a New Mac? Do This First!
http://www.makeuseof.com/tag/new-mac-setup/
Forget a wifi network
http://osxdaily.com/2014/03/09/forget-wifi-network-mac-os-x/. Go to 'Advanced' and click '-' to remove.
List DNS servers
How do I check what DNS server I'm using (on Mac OS X)
$ scutil --dns | grep 'nameserver\[[0-9]*\]'
To change the DNS settings, follow this.
How to Keep an iPad From Dropping Wi-Fi Signals
Renew the iPad's DHCP lease.
Change the channel on your wireless channel (pick the channel has the lowest signals).
PS1
If I give PS1="\[\w$ " it will change my prompt from
NCI-12345678-ML:bdge USERNAME$
to
~/github/bdge$
where the new one is probably better. We can replace \w with \W to get the directory basename instead of the full path.
The default PS1='\h:\W \u\$ ' is defined in /etc/bashrc.
My El Capitan, I need to create a new file ~/.profile (not in ~/.bash_profile) and put the command there.
export PS1="\w (\!)\$ "
See
- Bash prompt tips and tricks
- https://www.askdavetaylor.com/how_to_set_linux_mac_terminal_shell_ps1_prompt/
- Where to find the .bashrc file on Mac OS X
app Store
- Need a credit card information. The 'None' option is not available. Some tricks.
- Cannot log in my account. Activity clock just keeps spinning and spinning
- If macOS has been downloaded, the 'Download' button will be changed to 'Open' button in 'App Store' application.
- If my macOS is already Sierra, we don't need to sign into 'App Store' in order to download a newer version Sierra image.
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 download macOS update using the terminal
https://www.howtogeek.com/347920/how-to-download-macos-updates-using-the-terminal/
Console/All Messages
This is like the system log application in Linux/
Does not sleep when the lid is closed
$ syslog | grep 'Wake reason' | grep 'Mar 22' ... processWakeReason Wake reason: Host (0x01) ... Wake reason: ? ... processWakeReason Wake reason: Host (0x01) ... Wake reason: RTC (Alarm) ... processWakeReason Wake reason: Host (0x01) ... Wake reason: EC.LidOpen (User) $ pmset -g assertions 2018-03-22 19:45:03 -0400 Assertion status system-wide: BackgroundTask 0 ApplePushServiceTask 0 UserIsActive 1 PreventUserIdleDisplaySleep 0 PreventSystemSleep 0 ExternalMedia 0 PreventUserIdleSystemSleep 1 NetworkClientActive 0 Listed by owning process: pid 120(hidd): [0x00050da000090379] 00:16:13 UserIsActive named: "com.apple.iohideventsystem.queue.tickle" Timeout will fire in 1189 secs Action=TimeoutActionRelease pid 2903(RStudio): [0x0004b27a000124c2] 08:02:10 PreventUserIdleSystemSleep named: "R Computation" pid 2903(RStudio): [0x0004b27a000124ba] 08:02:10 PreventUserIdleSystemSleep named: "R Computation" No kernel assertions. Idle sleep preventers: IODisplayWrangler
- It seems mac wakes up every 2 hours according to the syslog output. This issue is indeed caused by the discoveryd process.
- Turn Off in Power management "Wake up by Wifi"
- iMac randomly wakes up from sleep. In my case, I see Rstudio and hidd processes show 'Yes'.
Prevent ssh from sleep
http://osxdaily.com/2011/03/21/temporarily-prevent-a-mac-from-sleeping/
pmset noidle
This method does not prevent Mac from displaying screensaver & locking the screen. But it seems to fix the problem of broken pipe in ssh connection.
A better way is to modify .ssh/config file. See Way to prevent ssh connection timeout.
How to Configure a Proxy Server
https://www.howtogeek.com/293444/how-to-configure-a-proxy-server-on-a-mac/
Open a chm file
iChm program works fine. Chmox is too old (power pc) and not works.
CHM Reader from Mac App Store is not different from iChm.
Back up
Record sound
Use 'QuickTime player'.
The build-in microphone is located inside the left speaker. The recording sound is weak. Go to System Preferences -> Sound. Select 'Input' tab and increase the 'input volume' from the smallest to the loudest.
If we want to use an external mic, make sure the headphone connector has 4 sections.
XXX can't be opened because it is from an unidentified developer
- http://osxdaily.com/2012/07/27/app-cant-be-opened-because-it-is-from-an-unidentified-developer/
- Enroll in the Apple's OS X developer program. The yearly fee is $99. https://forum.qt.io/topic/38876/solved-running-app-on-mac-osx-app-structure/5
/private/var/folders
https://discussions.apple.com/thread/1933443?start=0&tstart=0
If SeqTools was downloaded through a browser, then when we launch it the R script folder in <run_variantannose.sh> becomes something like /private/var/folders/1h/kcm8vkdx6nl00z5wjm5bqlw00000gp/T/AppTranslocation/051E078E-7C2D-4C6C-90FF-F651985EC9C0/d/SeqTools.app/Contents/MacOS/SeqTools/code
Extreme NAC Assessment Agent
https://isdp.nih.gov/isdp/version.action?prodid=220
'Please enter the host name or IP address of the Extreme NAC Assessment Agent server' 137.187.64.22.
Uninstall inSync
https://www.insynchq.com/uninstall
How to Add an AirDrop Icon to Your macOS Dock
Digital color meter
Discover the DigitalColor Meter tool on your Mac Very useful when you want to know the color's RGB value from any dot on your screen.
Git GUI Client
https://git-scm.com/download/gui/mac
SourceTree
sourcetree. See also Happy Git and Gihub for the useR from Jenny Bryan.
Unfortunately it requires a Bitbucket account in order to finish its installation.
Github Desktop
Looks good. It is OK to bypass to login a Github account in the installation process.
Useful Apps
The Ultimate List of Mac Menu Bar Apps
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
- http://thenubbyadmin.com/2014/01/29/solving-wget-error-cannot-verify-site-certificate-unable-to-locally-verify-the-issuers-authority/
- https://finkers.wordpress.com/2009/10/06/wget-and-https/ (fink solution)
- http://stackoverflow.com/questions/9224298/how-do-i-fix-certificate-errors-when-running-wget-on-an-https-url-in-cygwin (cygwin solution)
- http://stackoverflow.com/questions/30105376/error-cannot-verify-www-youtube-coms-certificate-with-wget-http-www-yout (brew has the same problem)
watch
http://stackoverflow.com/questions/9574089/osx-bash-watch-command
while :; do clear; your_command; sleep 2; done
top command
To sort by CPU
top -u
To sort by Memory
top -o mem
htop
http://unix.stackexchange.com/questions/98253/how-do-i-install-htop-inside-mac-os-x
It seems the result is not accurate. For example when the fan is working (esets_daemon is running), htop does not show much CPU from eset_daemon but Activity Monitor shows esets_daemon is on the top cpu usage list.
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
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)
zcat
macOS always adds .Z to the .gz filename. A more portable solution is to use gunzip -c such as gunzip -c XXX.gz.
See zcat on OS X is running in POSIX mode and will always append .Z to all filenames.
R
failed to load cairo DLL
I got an error when I use svg() command.
svg("~/Downloads/3dPiePlot.svg") Warning messages: 1: In svg("~/Downloads/3dPiePlot.svg") : unable to load shared object '/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so': dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so, 6): Library not loaded: /opt/X11/lib/libXrender.1.dylib Referenced from: /Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so Reason: image not found 2: In svg("~/Downloads/3dPiePlot.svg") : failed to load cairo DLL
http://r.789695.n4.nabble.com/Cairo-package-error-quot-unable-to-load-quot-td4694453.html
you don't have X11 installed and it no longer ships with OS X 10.9 - you need to get it from
At the end of installation, it will ask you to log out and log in again to make xquartz a default X11 server.
Tex/Latex
- http://tug.org/mactex/ and http://tug.org/mactex/mactex-download.html
- http://mactex-wiki.tug.org/wiki/index.php?title=TeX_Live_Manager
- http://ctan.org/mirrors
- http://dante.ctan.org/mirmon/
Download failure
The error seems to be related to a new release (6/7/2017). The download link for basicTex is http://tug.org/cgi-bin/mactex-download/BasicTeX.pkg. It downloaded the file mactex-basictex-20161009.pkg. But the new release is mactex-basictex-20170607.pkg. The download works fine on 6/8/2017.
http://ctan.org/pkg/mactex-basic website is working fine but the downloaded file name is <BasicTex.pkg> so it is not clear about the release date.
tlmgr error
- https://tex.stackexchange.com/questions/64261/updating-tlmgr-2011-to-2012
- https://tex.stackexchange.com/questions/253599/repository-and-local-installation
$ tlmgr update --self tlmgr: The Tex Live versions supported by the repository http://ctan.sharelatex.com/tex-archive/systems/texlive/tlnet (2016-2016) do not include the version of the local installation (2017).
Install a new package through tlmgr
When I try to knitr an R markdown file in RStudio, an error was popped up complaining about missing 'framed.sty' file. The solution is to install the framed package on macOS or texlive-latex-extra package on Ubuntu/Debian.
sudo tlmgr update --self sudo tlmgr install framed
Microsoft Outlook
Encrypted emails
Unable to read encrypted emails.
Go to Preferences > Account > Advanced > Security.
- Digital signing Certificate: XXXX-S
- Encryption Certificate: XXX-E
- Certificate authentication Authentication: XXX-S
Rebooting computer helps.
To check PIV card is inserted: open the 'Keychain Access' app.
Save an email
The file format is *.eml.
Apple Server
- Mac Pro server (up to 64 GB DDR3 memory)
- Why Apple Will Never Offer Another Server Again
OS Server
Hackintosh
How to Triple Boot Your Hackintosh with Windows and Linux
http://lifehacker.com/5698205/how-to-triple-boot-your-hackintosh-with-windows-and-linux
How To Install macOS Sierra Hackintosh On PC
http://www.redmondpie.com/how-to-install-macos-sierra-hackintosh-on-pc-guide/
Building a GTX 1080 Ti-powered Hackintosh: Installing macOS Sierra step-by-step
iOS
iPad Pro 10.5 vs iPad 9.7 (2017)
- Apple iPad Pro 10.5 vs iPad 9.7 (2017): What's the difference?
- How to Find Out Which iPad Model You Own
Screen shut off automatically
Settings -> Display & Brightness -> Auto-Lock. If you select 'Never', the screen will never turn it off by itself.
Firefox Focus
Feel quite fast on my iPad. The 'setting' (gear symbol) on the top right hand side cannot be seen unless we click 'Erase' first. On the setting, we can change the search engine, Send usage data, etc.
But the regular Firefox has an option called "Tracking Protection" which is doing the same thing.
File manager
https://www.makeuseof.com/tag/file-manager-apps-iphone-ipad/
Documents by Readdle is a file manager with an integrated web browser, which makes it easy to download and transfer YouTube videos. See How to Download and Save YouTube Videos on iPhone.
Split screen
How to Split Screen on iPad (And the Best Tips and Tricks When Doing It)
MiniKeePass
Dropbox -> KeePass file -> "..." -> Export -> Open in -> Copy to MiniKeePass.
Voice recorder
https://www.makeuseof.com/tag/iphone-voice-recorder-apps/
Take a screenshot
- Press and hold the Sleep/Wake (on/off) button on the top of your iPad.
- Quickly click the Home button at the bottom of the screen.
- Release both buttons.
When you successfully trigger a screen shot, you'll see a white flash and, if audio is on, hear the camera shutter sound.
HDR photo
How to Shoot in HDR on Your iPhone
The best use cases for HDR photography are landscapes, objects in direct sunlight, and low-light or backlit scenes.
How to Take Better Fireworks Photos
https://lifehacker.com/how-to-take-better-fireworks-photos-with-your-iphone-1827324154
Procreate
GoodNotes
Replace desktop?
- How to download pdf files?
- How to search on pdf files?
AirDrop
Use AirDrop on your iPhone, iPad, or iPod touch
Portal: wifi transfer files
How to Quickly Transfer Files from a Computer to Your Phone with Portal
Turn off passcode
https://appsliced.co/ask/how-do-i-disable-the-passcode-lock-on-my-ipad
Under Settings -> Touch ID &N Passcode
Turn off auto-lock
http://www.solveyourtech.com/disable-auto-lock-ipad-2/
Under Settings -> Display & Brightness
iCloud
6 Nifty Uses for Spare iCloud Storage
Music
Learn the Basics of Beatmaking with This Open-Source Synthesizer App