R Under development (unstable) (2024-09-01 r87083 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\RtmpEpTX7z/GiBleed_5.3.zip to: D:\temp\RtmpEpTX7z/GiBleed_5.3.sqlite
Connecting using SQLite driver
Executing SQL took 0.0268 secs
Cohorts created in table main.cohort
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.426 secs
Constructing features on server
Fetching data from server
Fetching data took 0.237 secs
# CovariateData object

Cohorts of interest IDs: 1, 2

Inherits from Andromeda:
# Andromeda object
# Physical location:  D:\temp\RtmpEpTX7z\file7dbc2e2d7ad4.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 0.169 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.215 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.198 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.235 secs
Constructing features on server
Fetching data from server
Fetching data took 0.187 secs
Aggregating covariates took 0.741 secs
Constructing features on server
Fetching data from server
Fetching data took 0.205 secs
Constructing features on server
Fetching data from server
Fetching data took 0.181 secs
Constructing features on server
Fetching data from server
Fetching data took 0.181 secs
Constructing features on server
Fetching data from server
Fetching data took 0.196 secs
Constructing features on server
Fetching data from server
Fetching data took 0.173 secs
Constructing features on server
Fetching data from server
Fetching data took 0.237 secs
Constructing features on server
Fetching data from server
Fetching data took 0.274 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.397 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.312 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.177 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.243 secs
Tidying covariates took 0.233 secs
Removing 1 redundant covariates
Removing 1 infrequent covariates
Normalizing covariates
Tidying covariates took 1.29 secs
Sending temp tables to server
Constructing features on server
Fetching data from server
Fetching data took 0.201 secs
Removing 0 redundant covariate ID - time ID combinations
Removing 0 infrequent covariates
Normalizing covariates
Tidying covariates took 1.53 secs
[ FAIL 4 | WARN 5 | SKIP 84 | PASS 120 ]

══ Skipped tests (84) ══════════════════════════════════════════════════════════
• On CRAN (28): 'test-Aggregation.R:6:3', 'test-CompareCohorts.R:42:3',
  'test-CovariateData.R:55:3', 'test-CovariateData.R:99:3',
  'test-CovariateData.R:160:3', 'test-CovariateData.R:174:3',
  'test-GetCohortBasedCovariates.R:489:3',
  'test-GetCohortBasedCovariates.R:500:3',
  'test-GetCohortBasedCovariates.R:511:3',
  'test-GetCohortBasedCovariates.R:522:3',
  'test-GetCohortBasedCovariates.R:533:3',
  'test-GetCohortBasedCovariates.R:544:3',
  'test-GetCohortBasedCovariates.R:555:3',
  'test-GetCohortBasedCovariates.R:566:3', 'test-GetCovariates.R:63:3',
  'test-GetCovariates.R:87:3', 'test-GetCovariates.R:100:3',
  'test-GetCovariates.R:113:3', 'test-GetCovariates.R:136:3',
  'test-GetCovariates.R:179:3',
  'test-GetCovariatesFromCohortAttributes.R:30:3',
  'test-GetCovariatesFromCohortAttributes.R:51:3',
  'test-GetCovariatesFromCohortAttributes.R:79:3',
  'test-GetCovariatesTemporalSequence.R:81:3',
  'test-GetDefaultCovariates.R:6:3', 'test-HelperFunctions.R:31:3',
  'test-Table1.R:85:3', 'test-Table1.R:146:3'
• dbms == "oracle" is not TRUE (14): 'test-GetCohortBasedCovariates.R:796:3',
  'test-GetCohortBasedCovariates.R:808:3',
  'test-GetCohortBasedCovariates.R:820:3',
  'test-GetCohortBasedCovariates.R:832:3',
  'test-GetCohortBasedCovariates.R:844:3',
  'test-GetCohortBasedCovariates.R:856:3',
  'test-GetCohortBasedCovariates.R:868:3',
  'test-GetCohortBasedCovariates.R:880:3',
  'test-GetCohortBasedCovariates.R:892:3', 'test-query-no-fail.R:162:3',
  'test-query-no-fail.R:343:3', 'test-query-no-fail.R:449:3',
  'test-query-no-fail.R:556:3', 'test-spot-checks.R:204:3'
• dbms == "postgresql" is not TRUE (14):
  'test-GetCohortBasedCovariates.R:578:3',
  'test-GetCohortBasedCovariates.R:590:3',
  'test-GetCohortBasedCovariates.R:602:3',
  'test-GetCohortBasedCovariates.R:614:3',
  'test-GetCohortBasedCovariates.R:626:3',
  'test-GetCohortBasedCovariates.R:638:3',
  'test-GetCohortBasedCovariates.R:650:3',
  'test-GetCohortBasedCovariates.R:662:3',
  'test-GetCohortBasedCovariates.R:674:3', 'test-query-no-fail.R:146:3',
  'test-query-no-fail.R:327:3', 'test-query-no-fail.R:433:3',
  'test-query-no-fail.R:540:3', 'test-spot-checks.R:190:3'
• dbms == "redshift" is not TRUE (14): 'test-GetCohortBasedCovariates.R:905:3',
  'test-GetCohortBasedCovariates.R:917:3',
  'test-GetCohortBasedCovariates.R:929:3',
  'test-GetCohortBasedCovariates.R:941:3',
  'test-GetCohortBasedCovariates.R:953:3',
  'test-GetCohortBasedCovariates.R:965:3',
  'test-GetCohortBasedCovariates.R:977:3',
  'test-GetCohortBasedCovariates.R:989:3',
  'test-GetCohortBasedCovariates.R:1001:3', 'test-query-no-fail.R:170:3',
  'test-query-no-fail.R:351:3', 'test-query-no-fail.R:457:3',
  'test-query-no-fail.R:564:3', 'test-spot-checks.R:211:3'
• dbms == "sql server" is not TRUE (14):
  'test-GetCohortBasedCovariates.R:687:3',
  'test-GetCohortBasedCovariates.R:699:3',
  'test-GetCohortBasedCovariates.R:711:3',
  'test-GetCohortBasedCovariates.R:723:3',
  'test-GetCohortBasedCovariates.R:735:3',
  'test-GetCohortBasedCovariates.R:747:3',
  'test-GetCohortBasedCovariates.R:759:3',
  'test-GetCohortBasedCovariates.R:771:3',
  'test-GetCohortBasedCovariates.R:783:3', 'test-query-no-fail.R:154:3',
  'test-query-no-fail.R:335:3', 'test-query-no-fail.R:441:3',
  'test-query-no-fail.R:548:3', 'test-spot-checks.R:197:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Table1.R:39:3'): createTable1 works with categorical covariates ──
names(table1)[2] not equal to "% (n = 638)".
1/1 mismatches
x[1]: "% (n = 1,844)"
y[1]: "% (n = 638)"
── Failure ('test-Table1.R:44:3'): createTable1 works with categorical covariates ──
names(table1) not equal to c("Characteristic", "% (n = 638)").
1/2 mismatches
x[2]: "% (n = 1,844)"
y[2]: "% (n = 638)"
── Failure ('test-Table1.R:59:3'): createTable1 works with categorical covariates ──
names(table1) not equal to c(...).
4/8 mismatches
x[2]: "% (n = 1,844)"
y[2]: "% (n = 638)"

x[3]: "% (n = 850)"
y[3]: "% (n = 252)"

x[6]: "% (n = 1,844)"
y[6]: "% (n = 638)"

x[7]: "% (n = 850)"
y[7]: "% (n = 252)"
── Failure ('test-Table1.R:67:3'): createTable1 works with categorical covariates ──
names(table1) not equal to c("Characteristic", "% (n = 638)", "% (n = 252)", "Std.Diff").
2/4 mismatches
x[2]: "% (n = 1,844)"
y[2]: "% (n = 638)"

x[3]: "% (n = 850)"
y[3]: "% (n = 252)"

[ FAIL 4 | WARN 5 | SKIP 84 | PASS 120 ]
Error: Test failures
Executing SQL took 0.00981 secs
Execution halted