RAVE:Install

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RAVE logo R Analysis and Visualization of iEEG

RAVE


Install RAVE

Native Installation (Recommended)

1. Install the prerequisites. The most common installation problem is that the prerequisites are not installed. RAVE is written in the programming language "R", so before installing RAVE, "R" must be installed along with RStudio, an integrated development environment for "R". RAVE requires the latest versions of R and RStudio. Trying to install RAVE on older versions of R and RStudio will lead to unpredictable error messages.

2. Open the RStudio application if it is not already open. In Windows, you should open RStudio as an administrator so that you have the appropriate permissions to install the required libraries. Copy and paste the following commands (one at a time) into the RStudio console to install RAVE. In the case of errors, relaunch RStudio and repeat the commands.

 install.packages("remotes")
 remotes::install_github('beauchamplab/rave')
 remotes::install_github('beauchamplab/ravebuiltins@migrate2')

You may be asked questions.

 Do you want to install from sources the package which needs compilation? (Yes/no/cancel)

Answer "no".

 These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

Answer "2".

3. Once everything gets installed, RAVE needs to download and compile some internal configuration files. In your RStudio console, type the following command:

 rave::check_dependencies(nightly = TRUE)

If you see in the console window:

 Package `raveio` has been successfully loaded. 
 However, BioConductor package `rhdf5` has not been installed. 
 Please run the following command:
   
 BiocManager::install('rhdf5', update = FALSE, type = 'source')

Then, once the check_dependencies command finishes, run the install command for rhdf5:

 BiocManager::install('rhdf5', update = FALSE, type = 'source')

4. Finalize installation and install demo data.

 rave::finalize_installation(upgrade = 'ask')

Downloading data will take minutes. To check on progress, click on the "Jobs" tab. When a single job finishes, click the small left blue arrow in the top left to see the screen with all jobs. When all downloads are shown as complete, click on the "Console" tab and launch RAVE.

Docker (special-purpose containerized installation)

Docker creates a "virtual machine" within which other software, such as RAVE, runs. This can be useful if you wish to distribute or create archival copies of RAVE, for instance to create a snapshot of software+data for uploading to a repository when a manuscript is published.For more information, see the GitHub Rave Docker page.

RAVE-within-Docker is not recommended for day-to-day (production) usage as performance is worse and usage is more complex. For most use case, we recommend installing RAVE using the steps above.

Deprecated methods for installing RAVE.

OSX Installer (Experimental)

For Mac users, the following command will install brew, R, RStudio, and RAVE bundle. This is an experimental script.

Warning: the script will REMOVE currently installed R, RStudio and install the latest version according to your system architecture (for example, both R and RStudio will be ARM build on Apple M1 chip). Please use the default installation guide if you have already got R for other projects.

Please open termina.app at /Applications/Utilities folder, copy-paste the following command, and hit return. The terminal will prompt for password. This is because some installations require administrator privilege. Please enter your password (it won't show up on the screen), and hit return key.

 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/dipterix/instrave/master/brew/osx-patch.sh)"

Ubuntu Installer (Experimental)

For Ubuntu users, the following command will install R and RAVE bundle. This is an experimental script.

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:

 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/dipterix/instrave/master/brew/ubuntu-patch.sh)"

The terminal will prompt for password. This is because some installations require administrator privilege. Please enter your password (it won't show up on the screen), and hit return key.

Checking installation

After installing or updating RAVE, quit and restart RStudio before continuing. To start RAVE, type (or copy and paste) the following command into the RStudio console:

 rave::start_rave()

A new web browser window should open showing the RAVE splash screen and the current version number (e.g. 1.0). If RAVE data is not in the default location, point RAVE to it with

rave::rave_options()

Updating RAVE

To update existing installations of RAVE, first check for newer versions of RStudio (start RStudio, "Help"/"Check for Updates") and R (start R, "R"/"Check For R Updates"). Enter this command into the RStudio console:

 rave::check_dependencies(nightly = TRUE)

After this command completes, quit and restart RStudio. Then restart your brand new RAVE:

 rave::start_rave()

If this fails, the fallback is to completely reinstall RAVE.