Installation.md

In beauchamplab/rave: R Analysis and Visualization of 'ECOG/iEEG' Data

Prerequisite Installation Guide for RAVE for Mac, Windows and Linux

Click on your operating system.

• Mac OS
• Windows (Windows 10, with Bash enabled)
• Ubuntu 16.04+

MacOS

1. First, go to Cran-R official website and download install the latest version of R:

https://cran.r-project.org/bin/macosx/

1. After installing R, make sure that you install Xcode from the Mac App Store: ( here is a helpful article in case of errors)

Open Terminal (in the Applications folder), enter

xcode-select --install

Click yes to proceed installing command-line tools. On first use, you will br required to read and accept the Apple license.

Don't worry if the following error occurs. It just means you have already installed xcode command line tools.

// xcode-select: error: command line tools are already installed, use "Software Update" to install updates

1. Install the free version of RStudio Desktop here:

https://www.rstudio.com/products/rstudio/download/

Windows

You will be asked many questions by the installers; the default response is fine for all of them. 1. Install the latest version of R

https://cran.r-project.org/bin/windows/base/

1. Install the latest version of RTools. The version of RTools must match your version of R.

https://cran.r-project.org/bin/windows/Rtools/

1. Download and install the free version of RStudio Desktop for Windows.

https://www.rstudio.com/products/rstudio/download/

Ubuntu

1. Add R-Cran repository to your app list:

Open terminal (if you don't know how, look at your sidebar in ubuntu, search your computer enter "terminal", and open it), type the following code:

sudo gedit /etc/apt/sources.list

Then there will be a text editor with lots of "deb"s in it. Append the following line at the end of this file

deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/

IMPORTANT Based on you system, you might want to enter different repositories (https://cran.r-project.org/bin/linux/). However, this line should be with a format of deb + [repository URL] + xenial (or xenial-cran35) + /. The difference between xenial and xenial-cran35 will affect the version of R to be installed.

Save the file and close text editor.

1. In your terminal, update apt-get repository:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update

The first line gives you access to the new repository (it adds keys to your computer so that you can safely download R).

1. Install R

Copy the following command line by line into your terminal and run

sudo apt-get install r-base

sudo apt-get install r-base-dev

1. Install compiling tools and system dependencies

After installing R, copy the following command to your terminal and run:

sudo apt-get install libssl-dev libcurl4-openssl-dev libssh2-1-dev libv8-3.14-dev libxml2-dev libfftw3-dev libtiff5-dev libhdf5-dev

The first three packages libssl-dev libcurl4-openssl-dev libssh2-1-dev are necessary for devtools (compilers). libv8-3.14-dev is for V8 package to enable JavaScript. libxml2-dev is for xml2. libfftw3-dev libtiff5-dev are necessary for fast-fourier transformations and libhdf5-dev is for reading and writing data in open data format HDF5.

1. Install the free version of RStudio Desktop here:

Go to https://www.rstudio.com/products/rstudio/download/#download and download one with keywords "Ubuntu 16.04+/Debian 9+ (64-bit)", move the downloaded file to your desktop, rename it "rstudio.deb".

Open terminal, type the folloing command in your terminal

cd ~/Desktop
sudo apt-get install libjpeg62

Then you can install RStudio.

sudo dpkg -i ./rstudio.deb 

and RStudio should be in your application list. Again, if you don't know where it is, look at your sidebar in ubuntu, click search your computer and enter "RStudio".

Other linux systems might need to check recommended system packages

beauchamplab/rave documentation built on Feb. 23, 2024, 7:20 a.m.