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\Rtmpe4X9aX/GiBleed_5.3.zip to: D:\temp\Rtmpe4X9aX/GiBleed_5.3.sqlite
Connecting using SQLite driver
Executing SQL took 0.0189 secs
Cohorts created in table main.cohort
Constructing features on server
Fetching data from server
Fetching data took 0.238 secs
Aggregating covariates took 0.522 secs
Aggregating covariates took 0.345 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.123 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 0.101 secs
Constructing features on server
Fetching data from server
Fetching data took 0.111 secs
Constructing features on server
Fetching data from server
Fetching data took 0.127 secs
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 0.167 secs
# CovariateData object

Cohorts of interest IDs: 1, 2

Inherits from Andromeda:
# Andromeda object
# Physical location:  D:\temp\Rtmpe4X9aX\fileaf5029a143c3.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 0.121 secs
Constructing length of observation covariates
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.0881 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0943 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 0.12 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0821 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0869 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 0.11 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0802 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.0857 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 0.148 secs
Constructing features on server
Fetching data from server
Fetching data took 0.132 secs
Constructing length of observation covariates
Constructing features on server
Fetching data from server
Fetching data took 0.0915 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0864 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0854 secs
Constructing covariates from cohort attributes table
Loading took 0.0505 secs
Constructing covariates from cohort attributes table
Loading took 0.0763 secs
Constructing covariates from cohort attributes table
Loading took 0.0589 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.14 secs
Sending temp tables to server
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 0.092 secs
Aggregating covariates took 0.444 secs
Constructing features on server
Fetching data from server
Fetching data took 0.11 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0965 secs
Constructing features on server
Fetching data from server
Fetching data took 0.0938 secs
Constructing features on server
Fetching data from server
Fetching data took 0.106 secs
Constructing features on server
Fetching data from server
Fetching data took 0.165 secs
Constructing features on server
Fetching data from server
Fetching data took 0.166 secs
Constructing features on server
Fetching data from server
Fetching data took 0.096 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 0.0835 secs
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 0.122 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.174 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 0.161 secs
Tidying covariates took 0.158 secs
Removing 1 redundant covariates
Removing 1 infrequent covariates
Normalizing covariates
Tidying covariates took 0.873 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.113 secs
Removing 0 redundant covariate ID - time ID combinations
Removing 0 infrequent covariates
Normalizing covariates
Tidying covariates took 1.05 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 0.00581 secs
> 
> proc.time()
   user  system elapsed 
 260.60    6.01  253.40