Full installation guide
(table of content)
In this section, you'll install R, RStudio, devtools and all other dependencies.
R is a functional programming language that RAVE uses. Devtools are necessary for R to enable advanced features. RStudio is an IDE (Intergrated Development Environment) for easy and better code management especially designed for R. If you are hosting a server in RAVE, or prefer to using command lines, RStudio is not necessary. However, it's highly recommended that you have RStudio installed for RAVE.
Before installation, you might want to check you system:
RAVE is developed on both MacOS and Windows.
Hardware Requirement
(Recommended)
- Intel 4th Gen Core i5 CPU
- 64 GB RAM
(Minimum Requirement)
- Intel i3 CPU
- 8 GB RAM
RAVE is developed and built in R, therefore, you need to install R as its environment.
Here I tested installations on these operating systems: (as of 03/03/2018)
- MacOS (El-Captain or higher)
-
Windows (10 or higher,
SUMAwill be disabled on Windows) - Linux (To be tested)
(Tested on El-Captain and High-Sierra)
- First, go to Cran-R official website and download install the latest R:
https://cran.r-project.org/bin/macosx/
- After installing R, make sure that you install Xcode from the Mac App Store:
The best way is to google How to install Xcode. Moncef Belyamani has a great article here.
Or if you have AFNI installed, you must have Xcode installed, then you need xcode command line tool. Open terminal (from Application), enter
xcode-select --install
- RStudio
https://www.rstudio.com/products/rstudio/download/
On Windows, RAVE is limited because AFNI doesn't support windows. However, most of RAVE functions should work. To install RAVE, you need to have bash enabled on Windows 10.
It's easy to install on Windows.
- First, go to Cran-R official website and download install the latest R:
https://cran.r-project.org/bin/windows/base/
- After installing R, download and install Rtools. Please install the latest version:
https://cran.r-project.org/bin/windows/Rtools/
- RStudio
https://www.rstudio.com/products/rstudio/download/
If you have installed RStudio, open it, or if you are using terminal/command line, type R to enter R.
There are two ways to install RAVE. The first method install RAVE with a script, if you are not familiar with R, this could be a good choice. The second one is recommended for those who has written scripts in R before.
I have written a very simple and easy script for you. Open R, or RStudio, enter:
source('https://raw.githubusercontent.com/dipterix/instrave/master/R/hello.R')
If you fail, don't worry, try it several times, since there are so many packages to be installed and "turn R off and on again" is the easiest way to clean the installation environment :) However, if you try more than five times and still get errors, this might be an issue. Please report the issue on Github or contact me via my email.
* You might see the following message several times. Press "Yes". After restarted, run the command above again.
If you see console having the following output, then RAVE is installed
Loading required package: rave
--------------------
Active modules:
- Condition Explorer
Please edit [~/rave_modules/modules.csv]
...
Then you will see that RAVE is installed and attached. Type
require(rave)
init_app()
Enjoy :)
Inside of R, install devtools and rhdf5 by typing the following commands:
(Install devtools)
install.packages('devtools')
(Install rhdf5 and HDF5Array from Bioconductor)
source("https://bioconductor.org/biocLite.R")
biocLite(c("rhdf5", "HDF5Array"), suppressUpdates = T, suppressAutoUpdate = T)
(Install RAVE)
devtools::install_github('beauchamplab/rave', ref = 'rave-dipterix')
After installing RAVE, type the following command to test it.
require(rave)
init_app()
Here listed some common questions that might answer your questions.
Q: When I install RAVE from script that you wrote, R keeps asking me to restart before installing new packages. What should I do?
A: Press YES, and R will re-launch and install dependencies with clean environment. This might occur several times depending on the number of packages to update (usually two to four). However, after re-launching your R, you need to run the following code again to continue installing RAVE.
source('https://raw.githubusercontent.com/dipterix/instrave/master/R/hello.R')