Citrix Biostat Desktop

We currently house SAS and R on a server that is available for use by anyone with Lifespan credentials. This page will contain details on how to acquire access to this server and other useful resources related to using the server for data management and analyses.

Requesting Access to the Citrix Biostat Desktop

Access to the Citrix Biostat Desktop is granted by Lifespan Information Services when interested parties complete the following steps:

  1. Go to https://intranet.lifespan.org/ and select the “IS Self-Service” tab located on the top of the page
  2. From the “Request an IS Service – Need something new” menu, select “System Access Request”
  3. Provide requested details regarding who needs access, who approves access, and provide your contact information as an “alternate contact”
  4. Under “Request Details”, check the box for “Access not listed”
  5. In the “Please describe in detail the unlisted Access” notes box, indicate that you are requesting access to the “Citrix Biostat Desktop”
  6. In the “Why is Access needed?” notes box, indicate that you will be performing data management and/or analyses as a function of your role with Lifespan.
  7. Click “Review & Submit”
  8. Review and submit!
  9. Once access has been APPROVED and FULFILLED (Note: the access has to be approved before the work can be done. When the work is completed, you will be notified it has been fulfilled.)
    • If you have a lifespan computer, this icon will appear on your desktop. Double click and sign in using your lifespan user name and password.

    • If you do not have a lifespan computer, go to connect.lifespan.org, login with your lifespan username and password. The citrix biostat desktop will be available under the “Desktops” tab.

Setting up R to install and load packages on the biostats desktop

Background: R packages can trigger security policies. To avoid this issue we have a designated directory on the biostats server to run library packages out of. Packages run from the designated library are automatically cleared by our security policies. Instructions to update your package library are below.

https://rstats.wtf/r-startup.html#renviron

  • Load the usethis package:
    • library(usethis, lib.loc = “D:/Program Files/R/4.1”)
  • Edit .Renviron file (this only needs to be done once or when the version of R is updated):
    • Run this code within R: usethis::edit_r_environ()
    • This opens the .Renviron file
    • Type: R_LIBS_USER=D:/Program Files/R/4.1
    • Save the .Renviron file and close it
    • Restart R

TROUBLESHOOTING

* If you receive a pop-up for ‘Security Notification – Unapproved File’ after running the code, usethis::edit_r_environ(), check to see if the .Renviron file was opened.  If the .Renviron file is opened, continue following the instructions above and ignore the error message.

* If you receive the error: Error in loadNamespace(x) : there is no package called ‘packagename’, Install the package causing the error, install.packages(“packagename”).  Once installed, restart R and continue following the instructions

*If you receive an error for a commonly used package such as: Error in library(dplyr) : there is no package called ‘dplyr’, this is likely an indication that the R version has been updated and you’ll need to update the .Renviron file to reflect the new version.

  • To install the usethis package in the new location, run the following code
    • install.packages(“usethis”, lib = “D:/Program Files/R/4.X”)