Macbook-setup-2022
Setting up a new Macbook
MacBook Pro (14-inch, 2021)
Apple M1 Pro
16 GB
500 GB
Settings
Settings > Trackpad, turn on Tap to click.
Chrome
Download Chrome, launch it and set as default browser.
Git and SSH keys
Launch the Terminal.
Set up git config:
git config --global user.name "John Doe"
If they aren't already installed you'll be prompted now to install developer tools... which can take an hour or so.
git config --global user.email johndoe@example.com
Confirm:
git config --list
Create SSH key:
ls -al ~/.ssh
# Lists the files in your .ssh directory, if they exist
If none exist:
ssh-keygen -t rsa -b 4096 -C "your_email@example.com"
Show contents of public SSH key to copy to add to web git service:
cat ~/.ssh/id_rsa.pub
Add SSH key to git web service and then clone repo using SSH in the area you want it on your computer (for example into a version-controlled folder in your home directory):
e.g. with Gitlab
git clone git@gitlab.com:YOURGITUSERNAME/YOURREPO.git
Add public key to any servers you need to access:
ssh-copy-id -i ~/.ssh/id_rsa.pub YOUR_USER_NAME@IP_ADDRESS_OF_THE_SERVER
Homebrew
Install homebrew as a package manager:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
I followed the post-install instructions shown in the terminal to add to the default shell's path which was probably not needed as I am going to change that next.
bash
Using bash so can use same scripts as on Linux box. Default is version 3.2.57(1)-release over 10 years old, update with:
brew install bash
Verify installation (should see install in /opt/homebrew/bin/bash):
which -a bash
Allow new shell:
sudo vim /etc/shells and add /opt/homebrew/bin/bash to the file (/bin/bash is already there - this is the old version).
Set as default shell:
chsh -s /opt/homebrew/bin/bash
Change for root user:
sudo chsh -s /opt/homebrew/bin/bash
Also check in System Preferences > Users & Groups by clicking the lock icon and entering your password. Hold the Ctrl key, click the user account name in the left pane, and select “Advanced Options." Make sure the shell is /opt/homebrew/bin/bash.
Add homebrew to bash path:
echo "export PATH=/opt/homebrew/bin:$PATH" >> ~/.bash_profile && source ~/.bash_profile
check shell with:
echo $SHELL
Add some aliases to short cut commands, e.g.:
vim .bash_profile
and for example add:
alias work='ssh YOURUSERNAME@SERVERIPADDRESS'
Vim
Default Vim is version 8.2.3489, update with:
brew install vim
Add alias to ~/.bash_profile file so homebrew version loads instead of system version:
which -a vim
alias vim=/opt/homebrew/bin/vim
Then let's install VimPlug:
curl -fLo ~/.vim/autoload/plug.vim --create-dirs \
https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
Then copy .vimrc which I store in a git repository to home folder:
e.g. navigate to folder and then
cp .vimrc ~/
And then install the plug ins from within the .vimrc file in Vim by typing:
:PlugInstall
LaTeX and Ghostscript
MacTex 2021 comes with ghostscript 9.53.3 to compress pdfs. So head to:
https://www.tug.org/mactex/mactex-download.html
and download and install MacTeX.
Open Texshop which will be installed via GUI and check Preferences > Engine for location Path, in my case /Library/TeX/texbin, so...
Add to Path:
echo "export PATH=/Library/TeX/texbin:$PATH" >> ~/.bash_profile && source ~/.bash_profile
Poppler
For PDF tools such as pdftotext:
brew install poppler
Pandoc
To convert document formats:
brew install pandoc
OCRmyPDF
To OCR PDFs example: ocrmypdf -l eng input.pdf output.pdf
brew install ocrmypdf
Latex diff
To show diffs in LaTeX:
brew install latexdiff
Rename
For flexible tools to rename file in BASH:
brew install rename
Mosh
For more persistent remote terminal access.
brew install mosh
XQuartz
Replace X11 with Xquartz which is required by some R packages.
brew install --cask xquartz
Node
brew install node
R and R Studio
Download and install R - be sure to choose the Apple silicon arm64 version:
Enter R via the terminal as superuser:
sudo R
Let's see how many CPUs we are using:
getOption("Ncpus", 1L)
Just 1. So how many can we use?
parallel::detectCores()
8, so let's use 6 to speed up install of packages:
options(Ncpus = 6)
Confirm:
getOption("Ncpus", 1L)
And then:
install.packages(c("ggplot2","tidyverse","knitr","ggthemes","scales","ggmap","plotly","ggfortify","leaflet","leaflet.extras","rgdal","forecast","treemapify","dbscan","survival","googleVis","rmarkdown","flexdashboard","highcharter","devtools","maptools","mapview","treemap","networkD3","visNetwork","DiagrammeR","DT","ggcorrplot","Hmisc","anomalize", "fpp2", "h2o", "sweep", "timetk", "xgboost", "prophet", "survminer","ggwordcloud", "ggsn", "formattable", "IMD", "car", "maps", "this.path", "triangle", "fuzzyjoin", "waterfalls"))
This will take about 30 minutes.
After it completes, to enable mapshot to work:
webshot::install_phantomjs()
q() to exit R
Troubleshooting R install
However we got an unexpected error on our big install of packages:
Warning message:
In install.packages(c("ggplot2", "tidyverse", "knitr", "ggthemes", :
installation of one or more packages failed,
probably ‘rgdal’
This may be a compilation issue so downloaded gnu fortran for arm as linked from https://cran.r-project.org/ in case that is the reason.
copied to /opt/R/arm64 and then add to PATH with:
echo "export PATH=/opt/R/arm64:$PATH" >> ~/.bash_profile && source ~/.bash_profile
Then attempting to install rgdal package from within R, and we get a different error message:
configure: error: gdal-config not found or not executable.
So next trying to install gdal, quit R and:
brew install gdal
and also
brew install proj
And then back to R to install rgdal which will now work.
Also:
install.packages("gpclib", type = "source")
install.packages("rgeos")
install.packages("mapproj")
test if all packages can be loaded.
mapview errors on load (requires terra?), as do h2o and ggsn (requires sf?)
solution for sf from: r-spatial/sf#1317 (comment)
remotes::install_github("RcppCore/Rcpp")
install.packages('sf', configure.args = '--with-gdal-config=/usr/local/bin/gdal-config --with-geos-config=/usr/local/bin/geos-config --with-proj-include=/usr/local/include/ --with-proj-lib=/usr/local/lib/', configure.vars = 'GDAL_DATA=/usr/local/opt/gdal/share/gdal/')
I am not sure why this worked as the files this seems to point to don't seem to exist but it did work so ¯_(ツ)_/¯
Everything now works
Download and install R Studio:
https://rstudio.com/products/rstudio/download/
add gruvbox theme: https://github.com/tallguyjenks/gruvboxr
Python - additionals
Python 3 will have already been installed in this process through brew.
python3 -m pip install --upgrade pip
and
pip3 install openpyxl
and
pip3 install xlsx2csv
and so available in Python 2 just in case I occassionally fail to reference python3:
sudo easy_install xlsx2csv
To work with password protected Excel files:
pip3 install msoffcrypto-tool
Java
Required for example for R package xlsx to write xlsx files. Just manually download and install from:
https://www.oracle.com/java/technologies/downloads/
brew install java
EPS2PGF
The usual link is dead: https://sourceforge.net/projects/eps2pgf/files/latest/download
This one works though:
https://www.onworks.net/software/windows/app-eps2pgf
Acorn
Nice commercial graphics editor:
Sublime Text
Keynote
Pre-installed.
Microsoft Office
https://account.microsoft.com/services/office/install
AWS Command Line Interface
Download from: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html
aws configure
Input access key id, access key and region (eu-west-2).
Mermaid filter
https://github.com/raghur/mermaid-filter
npm install --global mermaid-filter
Additional Fonts
Fira Sans - download and batch install by unpacking, and selecting all files with Finder and dragging into Font Book:
https://fonts.google.com/specimen/Fira+Sans?selection.family=Fira+Sans
Tex Gyre Heroes - download and batch install by unpacking, and selecting all files with Finder and dragging into Font Book:
https://www.fontsquirrel.com/fonts/tex-gyre-heros
Open Font Book. Some fonts may be greyed-out and this caused me some issues with the hc_theme in gg_themes (the error message was "polygon edge not found"). So download missing fonts as needed.
Copy non-backed up files from old machine
In my case, two folders:
r-resources - contains R functions I use a lot.
shapefiles - contains large shapefiles that I point to from other R scripts.