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OHDSI / CohortGenerator

An R package for instantiating cohorts using data in the CDM.
https://ohdsi.github.io/CohortGenerator/
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Released version currently failing unit tests #70

Closed schuemie closed 1 year ago

schuemie commented 1 year ago

I see this error:

* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘CohortGenerator’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building ‘GeneratingCohorts.Rmd’ using rmarkdown
Quitting from lines 43-48 (GeneratingCohorts.Rmd) 
Error: Error: processing vignette 'GeneratingCohorts.Rmd' failed with diagnostics:
http error 500: Internal server error.

(note: I've added a new GA workflow that will run R check on the main branch every weekend)

anthonysena commented 1 year ago

I've re-run the GA workflow and now the R check is passing. The error is related to this block of code which is attempting to use the public OHDSI WebAPI:

https://github.com/OHDSI/CohortGenerator/blob/f170a5085aa729dc9fd03491e9b653ac7439dd5c/vignettes/GeneratingCohorts.Rmd#L42-L48

The vignette should probably not evaluate this block of code but instead should load the cohortDefinitionSet from the package inst folder instead. I'll fix this in a future release.