R Under development (unstable) (2024-04-23 r86473 ucrt) -- "Unsuffered Consequences"
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> 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\RtmpsBrCn9/GiBleed_5.3.zip to: D:\temp\RtmpsBrCn9/GiBleed_5.3.sqlite
Connecting using SQLite driver
Executing SQL took 0.0289 secs
Cohorts created in table main.cohort
Constructing features on server
Fetching data from server
Fetching data took 0.446 secs
Aggregating covariates took 0.725 secs
Aggregating covariates took 0.702 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.181 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 0.144 secs
Constructing features on server
Fetching data from server
Fetching data took 0.208 secs
Constructing features on server
Fetching data from server
Fetching data took 0.195 secs
Constructing features on server
Fetching data from server
Fetching data took 0.223 secs
Constructing features on server
Fetching data from server
Fetching data took 0.228 secs
# CovariateData object

Cohorts of interest IDs: 1, 2

Inherits from Andromeda:
# Andromeda object
# Physical location:  D:\temp\RtmpsBrCn9\file5ff02151db2.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 0.214 secs
Constructing length of observation covariates
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.138 secs
Constructing features on server
Fetching data from server
Fetching data took 0.146 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.181 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.217 secs
Constructing features on server
Fetching data from server
Fetching data took 0.182 secs
Constructing features on server
Fetching data from server
Fetching data took 0.155 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.19 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.182 secs
Constructing features on server
Fetching data from server
Fetching data took 0.165 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.202 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.166 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.168 secs
Constructing features on server
Fetching data from server
Fetching data took 0.168 secs
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.193 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 0.151 secs
Constructing covariates from cohort attributes table
Loading took 0.0803 secs
Constructing covariates from cohort attributes table
Loading took 0.0802 secs
Constructing covariates from cohort attributes table
Loading took 0.0661 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 0.191 secs
Constructing features on server
Fetching data from server
Fetching data took 0.148 secs
Aggregating covariates took 0.773 secs
Constructing features on server
Fetching data from server
Fetching data took 0.198 secs
Constructing features on server
Fetching data from server
Fetching data took 0.123 secs
Constructing features on server
Fetching data from server
Fetching data took 0.156 secs
Constructing features on server
Fetching data from server
Fetching data took 0.134 secs
Constructing features on server
Fetching data from server
Fetching data took 0.212 secs
Constructing features on server
Fetching data from server
Fetching data took 0.169 secs
Constructing features on server
Fetching data from server
Fetching data took 0.138 secs
Constructing features on server
Fetching data from server
Fetching data took 0.176 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 0.229 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.229 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.276 secs
Sending temp tables to server
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 0.188 secs
Tidying covariates took 0.263 secs
Removing 1 redundant covariates
Removing 1 infrequent covariates
Normalizing covariates
Tidying covariates took 1.43 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.187 secs
Removing 0 redundant covariate ID - time ID combinations
Removing 0 infrequent covariates
Normalizing covariates
Tidying covariates took 1.65 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 0.00694 secs
> 
> proc.time()
   user  system elapsed 
 442.50   12.46  437.76