Add R CMD check GitHub Action

[katy-sadowski]

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Added a GitHub Action to run R CMD check upon push & PR to the repo.

Some notes:

• I used the Hades R CMD check GH Action template here. I removed the "Release" section of this template because I wasn't sure if it was needed/relevant for DQD, and added a couple env variables needed to enable installation of the Eunomia package from GitHub (it's not available on CRAN at the moment)
• I removed the Travis badge from the README and added one for the GH Action. The Action also should run codecov and populate that badge accordingly
• I added some packages to Suggests & Remotes in the DESCRIPTION file so that GH Actions can install them as dependencies for running R CMD check

Regarding the checks themselves:

• There are 4 warnings, which I can address if needed but am leaving out-of-scope for this PR
• The Ubuntu R devel check is failing on an error which I believe might be the same issue someone reported here. Sounds like we might need to update the yaml file to the latest versions of some of the standard actions in order to solve this; I also left this out of scope for this PR
• I haven't yet run the unit test that queries the 3 remote OHDSI databases (they're skipped when the creds aren't available). In a follow-up PR I will look into these; I just received the DB creds from Adam

[ablack3]

@katy-sadowski Will you target the "develop" branch instead of "main"?

[katy-sadowski]

Done!

[ablack3]

@katy-sadowski You should see actions running successfully in your fork here: https://github.com/katy-sadowski/DataQualityDashboard/actions

I created a PR on your fork that I think fixes the problems when running tests: https://github.com/katy-sadowski/DataQualityDashboard/pull/3

[katy-sadowski]

@clairblacketer @ablack3 - i just merged in @ablack3 's changes which resolve all of the R CMD check failures except for the following one which i think we can address separately:

The Ubuntu R devel check is failing on an error which I believe might be the same issue someone reported here. Sounds like we might need to update the yaml file to the latest versions of some of the standard actions in order to solve this; I also left this out of scope for this PR

[katy-sadowski]

FYI @ablack3 @clairblacketer I was able to get the remote DB creds set up and working locally. Similar to Adam, I found that the executeDqChecks test for the remote DBs took ages to run when configured to run all checks at all levels. In order to get these tests in use, I propose we change the remote DB test just to run 1 DQ check. This way the tests at least verify that the DQD can run at all against each remote DB. My most recent commit (bf3c6e6) includes this change.

I'm thinking at this stage we can get this PR merged to get the automated checks + tests off the ground, and then take our time to develop a robust unit testing strategy. Let me know if you agree!

PS - @clairblacketer looks like we need your approval in order for the GH Actions to run in this repo :) also, let me know if I should add you and/or another maintainer as a reviewer for the "official" review of this PR. Thanks!

[katy-sadowski]

Oh and one more thing - now that I've added back the remote DB test, once the GH Actions run in this repo we will see if the secrets you added are working correctly @clairblacketer :)

[ablack3]

Hi @clairblacketer, will you review this PR and approve the workflow run? I see a lot of PRs on DQD. Should we have a DQD merge-a-thon? 😃