Some how T2DM is built with
Sys.unsetenv("R_PROFILE_USER")
devtools::check()
i do not know why it worked.
now the problem is
Connecting using PostgreSQL driver
Creating cohort table
Creating cohort table took 0.195 secs
Error: '' does not exist in current working directory ('D:/OHDSI-LegendT2DM/LegendT2dm').
In addition: Warning message:
In dir.create(outputFolder, recursive = TRUE) :
'D:\OHDSI-LegendT2DM\results' already exists
An error report has been created at D:/OHDSI-LegendT2DM/results//errorReportR.txt
Thread: Main
Message: Error: '' does not exist in current working directory ('D:/OHDSI-LegendT2DM/LegendT2dm').
Level: FATAL
Time: 2021-11-12 18:08:46
Stack trace:
13: stop("'", path, "' does not exist", if (!is_absolute_path(path)) paste0(" in current working directory ('", getwd
12: check_path(path)
11: standardise_path(file)
10: datasource(file, skip = skip, skip_empty_rows = FALSE, skip_quote = FALSE)
9: read_lines_raw(file, n_max = n_max)
8: unlist(read_lines_raw(file, n_max = n_max))
7: readr::guess_encoding(file = fileName, n_max = min(1e+07))
6: checkInputFileEncoding(pathToCsv)
5: getCohortsJsonAndSqlFromPackage(packageName = packageName, cohortToCreateFile = cohortToCreateFile, cohortIds = c
4: getCohortsJsonAndSql(packageName = packageName, cohortToCreateFile = cohortToCreateFile, baseUrl = baseUrl, cohor
3: CreateAllCohorts.R#63: CohortDiagnostics::instantiateCohortSet(connectionDetails = connectionDetails, cdmDatabase
2: Assessment.R#75: createExposureCohorts(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSche
1: assessPhenotypes(connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSchema, oracleTempSchema =
R version:
R version 4.0.5 (2021-03-31)
looks like
was the last place it can ever produce a good log.
What is cohortToCreateFile = cohortToCreateFile?
extra log that might be helpful
2021-11-12 18:44:25 [Main thread] INFO LegendT2dm assessPhenotypes Starting assessPhenotypes() for LEGEND-T2DM class-vs-class studies
2021-11-12 18:44:25 [Main thread] INFO LegendT2dm createExposureCohorts Creating class exposure cohorts
2021-11-12 18:44:25 [Main thread] INFO LegendT2dm createExposureCohorts - Populating table legendt2dm_study_class_cohort
2021-11-12 18:44:25 [Main thread] WARN CohortDiagnostics instantiateCohortSet OracleTempSchema has been deprecated by DatabaseConnector
2021-11-12 18:44:25 [Main thread] INFO CohortDiagnostics createCohortTable Creating cohort table
2021-11-12 18:44:25 [Main thread] DEBUG CohortDiagnostics createCohortTable Created table temp_renv.legendt2dm_study_class_cohort
2021-11-12 18:44:25 [Main thread] DEBUG CohortDiagnostics getCohortsJsonAndSqlFromPackage Executing on cohorts specified in package - LegendT2dm
2021-11-12 18:44:25 [Main thread] FATAL readr check_path Error: '' does not exist in current working directory ('D:/OHDSI-LegendT2DM/LegendT2dm').
Where is the “’” ?