Running RStudio

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.

Your RStudio home directory is on ephemeral storage. This means that when the container is deleted all the files will be lost. Store your files on Google Drive to save your work.

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)

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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.

Your RStudio home directory is on ephemeral storage. This means that when the container is deleted all the files will be lost. Store your files on Google Drive to save your work.

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)