R Under development (unstable) (2024-04-23 r86473 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> options(dbms = "sqlite")
> runTestsOnEunomia <- TRUE
> if (runTestsOnEunomia) {
+   test_check("FeatureExtraction")
+ }
Loading required package: FeatureExtraction
Loading required package: DatabaseConnector
Loading required package: Andromeda
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

************* Testing on sqlite *************

attempting to download GiBleed
trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
Content type 'application/zip' length 6861852 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

attempting to extract and load: D:\temp\RtmpoV1jsF/GiBleed_5.3.zip to: D:\temp\RtmpoV1jsF/GiBleed_5.3.sqlite
Connecting using SQLite driver
Executing SQL took 0.0258 secs
Cohorts created in table main.cohort
Constructing features on server
Fetching data from server
Fetching data took 0.315 secs
Aggregating covariates took 0.793 secs
Aggregating covariates took 0.602 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.156 secs
trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
Content type 'application/zip' length 6861852 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

Cohorts created in table main.cohort
Constructing features on server
Fetching data from server
Fetching data took 0.152 secs
Constructing features on server
Fetching data from server
Fetching data took 0.178 secs
Constructing features on server
Fetching data from server
Fetching data took 0.179 secs
Constructing features on server
Fetching data from server
Fetching data took 0.211 secs
Constructing features on server
Fetching data from server
Fetching data took 0.262 secs
# CovariateData object

Cohorts of interest IDs: 1, 2

Inherits from Andromeda:
# Andromeda object
# Physical location:  D:\temp\RtmpoV1jsF\file1b6bc8952a73.sqlite

Tables:
$analysisRef (analysisId, analysisName, domainId, startDay, endDay, isBinary, missingMeansZero)
$covariateRef (covariateId, covariateName, analysisId, conceptId)
$covariates (covariateId, covariateValue, rowId)
Constructing features on server
Fetching data from server
Fetching data took 0.186 secs
Constructing length of observation covariates
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.154 secs
Constructing features on server
Fetching data from server
Fetching data took 0.148 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.183 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.185 secs
Constructing features on server
Fetching data from server
Fetching data took 0.125 secs
Constructing features on server
Fetching data from server
Fetching data took 0.135 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.159 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.231 secs
Constructing features on server
Fetching data from server
Fetching data took 0.127 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.214 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.152 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.201 secs
Constructing features on server
Fetching data from server
Fetching data took 0.231 secs
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.183 secs
Constructing features on server
Fetching data from server
Fetching data took 0.163 secs
Constructing features on server
Fetching data from server
Fetching data took 0.157 secs
Constructing covariates from cohort attributes table
Loading took 0.089 secs
Constructing covariates from cohort attributes table
Loading took 0.0914 secs
Constructing covariates from cohort attributes table
Loading took 0.0841 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.237 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.249 secs
Constructing features on server
Fetching data from server
Fetching data took 0.118 secs
Aggregating covariates took 0.655 secs
Constructing features on server
Fetching data from server
Fetching data took 0.161 secs
Constructing features on server
Fetching data from server
Fetching data took 0.158 secs
Constructing features on server
Fetching data from server
Fetching data took 0.162 secs
Constructing features on server
Fetching data from server
Fetching data took 0.124 secs
Constructing features on server
Fetching data from server
Fetching data took 0.172 secs
Constructing features on server
Fetching data from server
Fetching data took 0.183 secs
Constructing features on server
Fetching data from server
Fetching data took 0.124 secs
Constructing features on server
Fetching data from server
Fetching data took 0.155 secs
Constructing features on server
Fetching data from server
Fetching data took 0.143 secs
Constructing features on server
Fetching data from server
Fetching data took 0.195 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.311 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.256 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.173 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.196 secs
Tidying covariates took 0.261 secs
Removing 1 redundant covariates
Removing 1 infrequent covariates
Normalizing covariates
Tidying covariates took 1.3 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.165 secs
Removing 0 redundant covariate ID - time ID combinations
Removing 0 infrequent covariates
Normalizing covariates
Tidying covariates took 1.62 secs
[ FAIL 0 | WARN 5 | SKIP 57 | PASS 168 ]

══ Skipped tests (57) ══════════════════════════════════════════════════════════
• dbms == "oracle" is not TRUE (14): 'test-GetCohortBasedCovariates.R:788:3',
  'test-GetCohortBasedCovariates.R:800:3',
  'test-GetCohortBasedCovariates.R:812:3',
  'test-GetCohortBasedCovariates.R:824:3',
  'test-GetCohortBasedCovariates.R:836:3',
  'test-GetCohortBasedCovariates.R:848:3',
  'test-GetCohortBasedCovariates.R:860:3',
  'test-GetCohortBasedCovariates.R:872:3',
  'test-GetCohortBasedCovariates.R:884:3', 'test-query-no-fail.R:154:3',
  'test-query-no-fail.R:327:3', 'test-query-no-fail.R:431:3',
  'test-query-no-fail.R:536:3', 'test-spot-checks.R:204:3'
• dbms == "postgresql" is not TRUE (14):
  'test-GetCohortBasedCovariates.R:570:3',
  'test-GetCohortBasedCovariates.R:582:3',
  'test-GetCohortBasedCovariates.R:594:3',
  'test-GetCohortBasedCovariates.R:606:3',
  'test-GetCohortBasedCovariates.R:618:3',
  'test-GetCohortBasedCovariates.R:630:3',
  'test-GetCohortBasedCovariates.R:642:3',
  'test-GetCohortBasedCovariates.R:654:3',
  'test-GetCohortBasedCovariates.R:666:3', 'test-query-no-fail.R:138:3',
  'test-query-no-fail.R:311:3', 'test-query-no-fail.R:415:3',
  'test-query-no-fail.R:520:3', 'test-spot-checks.R:190:3'
• dbms == "redshift" is not TRUE (14): 'test-GetCohortBasedCovariates.R:897:3',
  'test-GetCohortBasedCovariates.R:909:3',
  'test-GetCohortBasedCovariates.R:921:3',
  'test-GetCohortBasedCovariates.R:933:3',
  'test-GetCohortBasedCovariates.R:945:3',
  'test-GetCohortBasedCovariates.R:957:3',
  'test-GetCohortBasedCovariates.R:969:3',
  'test-GetCohortBasedCovariates.R:981:3',
  'test-GetCohortBasedCovariates.R:993:3', 'test-query-no-fail.R:162:3',
  'test-query-no-fail.R:335:3', 'test-query-no-fail.R:439:3',
  'test-query-no-fail.R:544:3', 'test-spot-checks.R:211:3'
• dbms == "sql server" is not TRUE (14):
  'test-GetCohortBasedCovariates.R:679:3',
  'test-GetCohortBasedCovariates.R:691:3',
  'test-GetCohortBasedCovariates.R:703:3',
  'test-GetCohortBasedCovariates.R:715:3',
  'test-GetCohortBasedCovariates.R:727:3',
  'test-GetCohortBasedCovariates.R:739:3',
  'test-GetCohortBasedCovariates.R:751:3',
  'test-GetCohortBasedCovariates.R:763:3',
  'test-GetCohortBasedCovariates.R:775:3', 'test-query-no-fail.R:146:3',
  'test-query-no-fail.R:319:3', 'test-query-no-fail.R:423:3',
  'test-query-no-fail.R:528:3', 'test-spot-checks.R:197:3'
• empty test (1): 'test-GetCovariates.R:109:1'

[ FAIL 0 | WARN 5 | SKIP 57 | PASS 168 ]
Executing SQL took 0.00819 secs
> 
> proc.time()
   user  system elapsed 
 441.28   10.71  436.76