Starting Sid

In all cases you need to start Sid

• In the browser go to https://sid.hmdc.harvard.edu​

• Launch Sid

• Click Run An Interactive Application

Running RStudio

• Select RStudio

• Select Version

• Click Google drive (login if necessary)

• Select CPU/RAM

• Click Launch Application

• Wait until URL is visible. The status will change from Initializing to Running

• Click on the URL

You can now create a RStudio Project.

Accessing Google Drive

Upon launching RStudio, your Google drive will be accessible from the file browser pane, located in the lower, right-hand corner of the window.

Installing and Using R Libraries

Using R libraries in RStudio is easy. Run the library command in the Console tab:

library(tidyverse) 
library(gridExtra)

If a library is not available and get an error like this. In this case the `dslabs` library is missing:

Error in library(dslabs): there is no package called ‘dslabs’

Install the package from within your notebook with:

install.packages("dslabs")

Installing System Libraries

Some R libraries require additional system libraries. If the required system libraries are not installed, install.packages() will report an error like this:

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------

To install additional system libraries, use the R function system() to run sudo apt-get update and sudo apt-get install to install the Debian packages:

system("sudo apt-get update")
system("sudo apt-get install -y libxml2-dev")

If you are comfortable with programming external service calls, you can also use the https://sysreqs.r-hub.io/ service to automatically detect which system libraries are needed. (example)