Error in formatChunk(pkValuesInDb = env$primaryKeyValuesInDb, chunk = chunk) : concept_set_id is of type numeric which cannot be converted between data frames pkValuesInDb and chunk

I'm getting the following error when I run CohortDiagnostics::createMergedResultsFile(dataFolder = exportFolder, overwrite = TRUE)

Error in formatChunk(pkValuesInDb = env$primaryKeyValuesInDb, chunk = chunk) : 
  concept_set_id is of type numeric which cannot be converted between data frames pkValuesInDb and chunk

The issue seems to be with the concept_sets.csv table and coming from the fomatChunk in ResultsModelManger function.

I'm guessing that when the file is read in the column type for concept_set_id is numeric instead of integer but I don't really know yet where the issue is.

Here is the traceback

> traceback()
13: stop(errorMsg) at DataModel.R#824
12: formatChunk(pkValuesInDb = env$primaryKeyValuesInDb, chunk = chunk) at DataModel.R#350
11: uploadChunk(chunk, pos, env, specifications, resultsFolder, connection, 
        runCheckAndFixCommands, forceOverWriteOfSpecifications) at DataModel.R#481
10: private$callback(data, index) at callback.R#82
9: (function (data, index) 
   {
       result <- private$callback(data, index)
       private$cancel <- identical(result, FALSE)
   })(structure(list(cohort_id = 568, concept_set_id = 1, concept_set_sql = "SELECT 1 as codeset_id, c.concept_id FROM (select distinct I.concept_id ...... (deleted this for brevity)
8: read_tokens_chunked_(data, callback, chunk_size, tokenizer, col_specs, 
       col_names, locale_, spec, progress) at read_delim_chunked.R#41
7: read_tokens_chunked(ds, callback = callback, chunk_size = chunk_size, 
       spec = spec, tokenizer, spec$cols, names(spec$cols), locale_ = locale, 
       progress = progress)
6: read_delimited_chunked(file, callback = callback, chunk_size = chunk_size, 
       tokenizer = tokenizer, col_names = col_names, col_types = col_types, 
       locale = locale, skip = skip, skip_empty_rows = skip_empty_rows, 
       comment = comment, guess_max = guess_max, progress = progress, 
       show_col_types = show_col_types) at read_delim_chunked.R#101
5: readr::read_csv_chunked(file = file.path(resultsFolder, csvFileName), 
       callback = function(chunk, pos) uploadChunk(chunk, pos, env, 
           specifications, resultsFolder, connection, runCheckAndFixCommands, 
           forceOverWriteOfSpecifications), chunk_size = 1e+07, 
       col_types = readr::cols(), guess_max = 1e+06, progress = FALSE) at DataModel.R#481
4: uploadTable(tableName, connection, schema, tablePrefix, databaseId, 
       resultsFolder, specifications, runCheckAndFixCommands, forceOverWriteOfSpecifications, 
       purgeSiteDataBeforeUploading, warnOnMissingTable) at DataModel.R#609
3: ResultModelManager::uploadResults(connectionDetails = connectionDetails, 
       schema = schema, resultsFolder = unzipFolder, tablePrefix = tablePrefix, 
       forceOverWriteOfSpecifications = forceOverWriteOfSpecifications, 
       purgeSiteDataBeforeUploading = purgeSiteDataBeforeUploading, 
       runCheckAndFixCommands = TRUE, databaseIdentifierFile = "database.csv", 
       specifications = getResultsDataModelSpecifications(), warnOnMissingTable = FALSE, 
       ...) at ResultsDataModel.R#136
2: uploadResults(connectionDetails = connectionDetails, schema = "main", 
       zipFileName = zipFileName, tablePrefix = tablePrefix) at Shiny.R#202
1: CohortDiagnostics::createMergedResultsFile(dataFolder = exportFolder, 
       overwrite = TRUE)

OHDSI / CohortDiagnostics

Error in formatChunk(pkValuesInDb = env$primaryKeyValuesInDb, chunk = chunk) : concept_set_id is of type numeric which cannot be converted between data frames pkValuesInDb and chunk #1121