New Mac setup

We are a Mac lab. Basic info when setting up a new one (modifying from here):

  • Turn on, create initial account, register with UTK.
  • Create temporary account with admin privileges.
  • Restart in this account, then use Migration Assistant to copy existing lab accounts and files from existing computer.
  • Install homebrew
  • brew install svn
  • brew install git
  • brew tap homebrew/science
  • brew install r
  • brew install svn
    brew install git
    brew tap caskroom/cask
    brew install brew-cask
    brew install Caskroom/cask/xquartz
    brew cask install java
    brew tap homebrew/science
    brew install R --with-openblas 
    brew install Caskroom/cask/rstudio
    brew cask install mactex
    brew install libsvg curl libxml2 gdal geos boost
    R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers
    brew tap caskroom/fonts
    brew cask install font-fira-code
    brew cask install iterm2
    brew install r-gui
    brew linkapps
    brew cask install gitup
  • In R: install.packages(“ctv”,repos=””)
  • In R: library(“ctv”)
  • In R: install.views(c(“Phylogenetics”, “Optimization”, “HighPerformanceComputing”),repos=””)
  • If you want to install ALL CRAN packages:
  • availablePackages <- available.packages("")[,1]