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\Rtmpawr5H2/GiBleed_5.3.zip to: D:\temp\Rtmpawr5H2/GiBleed_5.3.sqlite
Connecting using SQLite driver
Executing SQL took 0.0184 secs
Cohorts created in table main.cohort
Constructing features on server
Fetching data from server
Fetching data took 0.231 secs
Aggregating covariates took 0.508 secs
Aggregating covariates took 0.439 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.13 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 0.122 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 0.117 secs
Constructing features on server
Fetching data from server
Fetching data took 0.132 secs
Constructing features on server
Fetching data from server
Fetching data took 0.165 secs
# CovariateData object

Cohorts of interest IDs: 1, 2

Inherits from Andromeda:
# Andromeda object
# Physical location:  D:\temp\Rtmpawr5H2\file283e057e02e2d.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 0.162 secs
Constructing length of observation covariates
Constructing length of observation covariates
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 0.107 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 0.129 secs
Constructing features on server
Fetching data from server
Fetching data took 0.131 secs
Constructing features on server
Fetching data from server
Fetching data took 0.118 secs
Sending temp tables to server
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 0.129 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0873 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 0.106 secs
Sending temp tables to server
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 length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.0955 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0961 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0953 secs
Constructing covariates from cohort attributes table
Loading took 0.0444 secs
Constructing covariates from cohort attributes table
Loading took 0.0571 secs
Constructing covariates from cohort attributes table
Loading took 0.0622 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 0.153 secs
Constructing features on server
Fetching data from server
Fetching data took 0.093 secs
Aggregating covariates took 0.646 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 0.141 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 0.131 secs
Constructing features on server
Fetching data from server
Fetching data took 0.159 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 0.0882 secs
Constructing features on server
Fetching data from server
Fetching data took 0.122 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0833 secs
Constructing features on server
Fetching data from server
Fetching data took 0.098 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.139 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.153 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.0751 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.0913 secs
Tidying covariates took 0.115 secs
Removing 1 redundant covariates
Removing 1 infrequent covariates
Normalizing covariates
Tidying covariates took 0.811 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.112 secs
Removing 0 redundant covariate ID - time ID combinations
Removing 0 infrequent covariates
Normalizing covariates
Tidying covariates took 0.973 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 0.00428 secs
> 
> proc.time()
   user  system elapsed 
 259.57    6.39  251.57