* using log directory 'd:/RCompile/CRANincoming/R-devel/FeatureExtraction.Rcheck'
* using R Under development (unstable) (2024-09-01 r87083 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'FeatureExtraction/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FeatureExtraction' version '3.7.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [11s] Note_to_CRAN_maintainers
Maintainer: 'Ger Inberg <g.inberg@erasmusmc.nl>'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'FeatureExtraction' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  'target' 'tmp'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [357s] ERROR
  Running 'testBigQuery.R'
  Running 'testOracle.R'
  Running 'testPostgres.R'
  Running 'testRedshift.R'
  Running 'testSnowflake.R'
  Running 'testSpark.R'
  Running 'testSqlServer.R'
  Running 'testSqlite.R' [352s]
Running the tests in 'tests/testSqlite.R' failed.
Complete output:
  > 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [94s] OK
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE