R Under development (unstable) (2024-04-27 r86487 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\Rtmpk17brH/GiBleed_5.3.zip to: D:\temp\Rtmpk17brH/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 0.236 secs
Aggregating covariates took 0.514 secs
Aggregating covariates took 0.438 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.12 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 0.105 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 0.154 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 0.163 secs
# CovariateData object

Cohorts of interest IDs: 1, 2

Inherits from Andromeda:
# Andromeda object
# Physical location:  D:\temp\Rtmpk17brH\file27db47a2eb5.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 0.12 secs
Constructing length of observation covariates
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.0869 secs
Constructing features on server
Fetching data from server
Fetching data took 0.091 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.114 secs
Sending temp tables to server
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 0.0931 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0859 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 0.108 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0921 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.115 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.109 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.105 secs
Constructing features on server
Fetching data from server
Fetching data took 0.114 secs
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.0926 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0952 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0939 secs
Constructing covariates from cohort attributes table
Loading took 0.0453 secs
Constructing covariates from cohort attributes table
Loading took 0.0841 secs
Constructing covariates from cohort attributes table
Loading took 0.0793 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.176 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.157 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0924 secs
Aggregating covariates took 0.44 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 0.0974 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0902 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0672 secs
Constructing features on server
Fetching data from server
Fetching data took 0.12 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 0.0851 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 0.114 secs
Constructing features on server
Fetching data from server
Fetching data took 0.133 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.123 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.247 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.12 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.141 secs
Tidying covariates took 0.158 secs
Removing 1 redundant covariates
Removing 1 infrequent covariates
Normalizing covariates
Tidying covariates took 0.934 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.153 secs
Removing 0 redundant covariate ID - time ID combinations
Removing 0 infrequent covariates
Normalizing covariates
Tidying covariates took 1.42 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 0.0089 secs
> 
> proc.time()
   user  system elapsed 
 263.07    5.92  256.86