R Under development (unstable) (2024-04-29 r86495 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\RtmpMLwWyk/GiBleed_5.3.zip to: D:\temp\RtmpMLwWyk/GiBleed_5.3.sqlite
Connecting using SQLite driver
Executing SQL took 0.0185 secs
Cohorts created in table main.cohort
Constructing features on server
Fetching data from server
Fetching data took 0.234 secs
Aggregating covariates took 0.531 secs
Aggregating covariates took 0.442 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.119 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 0.0964 secs
Constructing features on server
Fetching data from server
Fetching data took 0.121 secs
Constructing features on server
Fetching data from server
Fetching data took 0.119 secs
Constructing features on server
Fetching data from server
Fetching data took 0.129 secs
Constructing features on server
Fetching data from server
Fetching data took 0.167 secs
# CovariateData object

Cohorts of interest IDs: 1, 2

Inherits from Andromeda:
# Andromeda object
# Physical location:  D:\temp\RtmpMLwWyk\file23ab4380f50a3.sqlite

Tables:
$analysisRef (analysisId, analysisName, domainId, startDay, endDay, isBinary, missingMeansZero)
$covariateRef (covariateId, covariateName, analysisId, conceptId)
$covariates (cohortDefinitionId, covariateId, covariateValue, rowId)
Constructing features on server
Fetching data from server
Fetching data took 0.116 secs
Constructing length of observation covariates
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.0884 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0948 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.111 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.116 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0911 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0847 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.11 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.104 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0894 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.11 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.129 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.13 secs
Constructing features on server
Fetching data from server
Fetching data took 0.129 secs
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.107 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0916 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0994 secs
Constructing covariates from cohort attributes table
Loading took 0.054 secs
Constructing covariates from cohort attributes table
Loading took 0.0762 secs
Constructing covariates from cohort attributes table
Loading took 0.058 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 0.153 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0979 secs
Aggregating covariates took 0.451 secs
Constructing features on server
Fetching data from server
Fetching data took 0.146 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0963 secs
Constructing features on server
Fetching data from server
Fetching data took 0.13 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0931 secs
Constructing features on server
Fetching data from server
Fetching data took 0.14 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 0.0936 secs
Constructing features on server
Fetching data from server
Fetching data took 0.107 secs
Constructing features on server
Fetching data from server
Fetching data took 0.117 secs
Constructing features on server
Fetching data from server
Fetching data took 0.137 secs
Sending temp tables to server
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 0.102 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.122 secs
Tidying covariates took 0.157 secs
Removing 1 redundant covariates
Removing 1 infrequent covariates
Normalizing covariates
Tidying covariates took 0.874 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.163 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 0.00664 secs
> 
> proc.time()
   user  system elapsed 
 258.09    6.35  250.71