Frequently Asked Questions (FAQs)

[wjchulme]

This issue lists some common, stereotyped queries that many users face when using the OpenSAFELY platform. Please check here first before posting a new question on the Q&A forum

I have a bug/error/problem with my study definition

Please read the study definition pages in the documentation thoroughly. If something is not clear, please tell us. If you're still struggling, search the Q&A forum for similar issues, and if there's nothing there, ask.

I have a bug/error/problem with my analysis code

This is most likely a problem with your analysis scripts rather than with OpenSAFELY itself, so we recommend following your usual de-bugging routine to get to the bottom of the issue. If you are certain it’s an issue with OpenSAFELY itself, then use the Q&A forum to ask for help.

My analysis code works when I run it using my local R/Stata/python installation, but not when I run within an OpenSAFELY docker container

This is a common occurrence. The docker container replicates the environment in which your code will be run on the server. This environment will in some ways be different to that on your local machine. Most of the time this isn't a problem, but sometimes it is. Candidate culprits are:
* Your local R or Stata session contains functions or data that are not available when run inside docker.
* Restart the session (for example with session > Restart R in RStudio) to clear all objects in the environment that may have been created by running other scripts or commands during the same session. Then re-run locally to see if you get the same error that occurs in the docker container. If you do, fix the bug locally, then re-run again using OpenSAFELY.
* Check that the action used to run the script in the project.yaml is importing all the relevant files that it needs to run, with the needs: option.
* Differences in software or package versions. You can see what versions are installed on the Requesting new libraries page.

I have a git / GitHub problem

You should be familiar with the basics of the git workflow in OpenSAFELY. However, git can still be difficult for the most seasoned developers. If you've run into difficulties, search online to try to fix the problem. If you're still struggling, you can ask for help in the Q&A forum.

I have a problem with the opensafely command-line tool

If you want to report bugs or request features in the opensafely command-line tool, you can do so in its own dedicated issue tracker.

I want to extract [patient characteristic / feature / attribute] from the database but I’m not sure if it is possible

See the request new variables page to check that the variable doesn't already exist or hasn't already been requested, and if not, how to make a request.

I want to use a library / package that isn't available

See the requesting new libraries page to see what current versions are installed and how to make a request.

I want to use OpenSAFELY, how do I start?

You can get pretty far with OpenSAFELY on your own. Read our getting started guide to get started! If you want to run code against the real data, there is an approvals and onboarding process to follow.