Here are the steps for installing the required environment to run the OHDSI R packages. Four things needs to be installed:
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- R is a statistical computing environment. It comes with a basic user interface that is primarily a command-line interface.
- RTools is a set of programs that is required on Windows to build R packages from source.
- RStudio is an IDE (Integrated Development Environment) that makes R easier to use. It includes a code editor, debugging and visualization tools. Please use it to obtain a nice R experience.
- Java is a computing environment that is needed to run some of the components in the OHDSI R packages, for example those needed to connect to a database.
These instructions are also demonstrated in this video, showing a step-by-step guide to installing the required software.
In Windows, both R and Java come in 32-bit and 64-bits architectures. If you install R in both architectures, you must also install Java in both architectures. It is recommended to only install the 64-bit version of R.
Installing R
- Go to https://cran.r-project.org/, click on ‘Download R for Windows’, then ‘base’, then click the Download link indicated in the screenshot below.
- After the download has completed, run the installer. Use the default options everywhere, with two exceptions: First, it is better not to install into program files. Instead, just make R a subfolder of your C drive as shown below. Second, to avoid problems due to differing architectures between R and Java, disable the 32-bit architecture as also shown below.
Once completed, you should be able to select R from your Start Menu.
Installing RTools
- Go to https://cran.r-project.org/, click on ‘Download R for Windows’, then ‘Rtools’, and select the very latest version of RTools to download.
- After downloading has completed run the installer. Select the default options everywhere.
- Since R v4.0.0 you also need to add the following line to your .Renviron file, as described on the RTools page:
Installing RStudio
- Go to https://www.rstudio.com/, select ‘Download RStudio’ (or the ‘Download’ button under ‘RStudio’), opt for the free version, and download the installer for Windows as highlighted below.
- After downloading, start the installer, and use the default options everywhere.
Installing Java
- Go to https://java.com/en/download/manual.jsp, and select the Windows 64-bit installer as highlighted below. If you also installed the 32-bit version of R, you must also install the other (32-bit) version of Java.
- After downloading just run the installer.
Installing R
- Go to https://cran.r-project.org/, click on ‘Download R for (Mac) OS X’, then ‘base’, then click the Download link indicated in the screenshot below.
- After the download has completed, run the installer and accept all of the default options. You should see a screen indicating that the installation was successful.
Installing R build tools
We will need to install C and Fortran compilers in order to build R packages from source code. These are included with Xcode which can be downloaded from the Mac App store.
- Open the App Store in Mac OS and install Xcode. Xcode is a large program. If disk space is scarce you could also try only installing Xcode command line tools by following the instructions here. Verify that the C compiler gcc is installed by opening the terminal and running the command
clang
. You should see an error that says “no input files”. - Download and install the gfortran compiler .dmg from https://github.com/fxcoudert/gfortran-for-macOS/releases. Choose the latest version that is compatible with your operating system. Verify the installation by opening the terminal and running the command
gfortran
. You should see an error that says “no input files”. - Go to https://www.xquartz.org/, download the .dmg and run the installer.
- Verify that build tools are installed and available by opening an R console and running
Installing RStudio
- Go to https://www.rstudio.com/, select ‘Download RStudio’ (or the ‘Download’ button under ‘RStudio’), opt for the free version, and download the installer for Mac as highlighted below.
Installing Java
- Go to https://www.oracle.com/java/technologies/javase-jdk15-downloads.html, and select the Mac OS installer for the Oracle JDK as highlighted below.
- After downloading just run the installer. Check that java is installed by opening the terminal and running the command
java
. If you see some helpful output about usage then the installation was successful.
You should now be ready to go, but we should make sure. Start R-studio, and type
Hades Ios
This function uses Java, so if all goes well we know both R and Java have been installed correctly!
Another test is to see if source packages can be built. Run the following R code to install the
CohortMethod
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