$ operator is invalid for atomic vectors

[ablack3]

I'm running cohort diagnostics (current OHDSI main branch) and getting the following error.

Thread: Main
Message: $ operator is invalid for atomic vectors
Level: FATAL
Time: 2024-06-06 12:36:18

Stack trace:
4: RunDiagnostics.R#807: executeCohortRelationshipDiagnostics(connection = connection, databaseId = databaseId, exportFolder = exportFolder, cohortDatabaseSchema = cohortDatabaseSchema, cdmDatabase
3: Private.R#326: eval(expr)
2: RunDiagnostics.R#801: timeExecution(exportFolder, "executeCohortRelationshipDiagnostics", cohortIds, parent = "executeDiagnostics", expr = {
executeCohortRelationshipDiagnostics(connection =
1: CohortDiagnostics::executeDiagnostics(cohortDefinitionSet = cohortDefinitionSet, connectionDetails = connectionDetails, cdmDatabaseSchema = cdmSchema, cohortDatabaseSchema = writeSchema, databas

R version:
R version 4.4.0 (2024-04-24)

Platform:
x86_64-pc-linux-gnu

Attached base packages:

• stats
• graphics
• grDevices
• datasets
• utils
• methods
• base

Some cohorts have zero counts in my database.

[ablack3]

CohortDiagnostics/R/RunDiagnostics.R

Line 816 in 03c40ab

temporalCovariateSettings = temporalCovariateSettings[[1]],

temporalCovariateSettings is a covariateSettings object but when executeCohortRelationshipDiagnostics is called only the first element of the list is passed in. So inside executeCohortRelationshipDiagnostics the temporalCovariateSettings is a length one logical vector.

Then inside executeCohortRelationshipDiagnostics it seems as if temporalCovariateSettings is expected to be a
covariate settings object.

CohortDiagnostics/R/CohortRelationship.R

Line 266 in 03c40ab

temporalStartDays <- temporalCovariateSettings$temporalStartDays

So I think

CohortDiagnostics/R/RunDiagnostics.R

Line 816 in 03c40ab

temporalCovariateSettings = temporalCovariateSettings[[1]],

should not include the subsetting.

temporalCovariateSettings = temporalCovariateSettings,
Has anyone else experienced this issue?

[azimov]

I think this issue is caused by a check occuring only when running temporal characterization is false:

CohortDiagnostics/R/RunDiagnostics.R

Line 357 in 03c40ab

temporalCovariateSettings <- list(temporalCovariateSettings)

I should be able to resolve this in the develop branch today