* using log directory ‘/srv/hornik/tmp/CRAN_pretest/FeatureExtraction.Rcheck’
* using R Under development (unstable) (2024-09-01 r87083)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* 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 ... [5s/5s] 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FeatureExtraction’ can be installed ... [5s/5s] 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] 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 ... [7s/7s] OK
* checking Rd files ... [0s/0s] 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 ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [180s/172s] ERROR
  Running ‘testBigQuery.R’ [0s/0s]
  Running ‘testOracle.R’ [0s/0s]
  Running ‘testPostgres.R’ [0s/0s]
  Running ‘testRedshift.R’ [0s/0s]
  Running ‘testSnowflake.R’ [0s/0s]
  Running ‘testSpark.R’ [0s/0s]
  Running ‘testSqlServer.R’ [0s/0s]
  Running ‘testSqlite.R’ [178s/170s]
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: /tmp/RtmpkfqeDh/working_dir/RtmptSQG0x/GiBleed_5.3.zip to: /tmp/RtmpkfqeDh/working_dir/RtmptSQG0x/GiBleed_5.3.sqlite
  Connecting using SQLite driver
  Executing SQL took 0.015 secs
  Cohorts created in table main.cohort
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 0.23 secs
  Constructing features on server
  Fetching data from server
  Fetching data took 0.119 secs
  # CovariateData object
  
  Cohorts of interest IDs: 1, 2
  
  Inherits from Andromeda:
  # Andromeda object
  # Physical location:  /tmp/RtmpkfqeDh/working_dir/RtmptSQG0x/file38a37d42ffb410.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 0.0992 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 0.0998 secs
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 0.124 secs
  Constructing features on server
  Fetching data from server
  Fetching data took 0.0924 secs
  Aggregating covariates took 0.398 secs
  Constructing features on server
  Fetching data from server
  Fetching data took 0.0877 secs
  Constructing features on server
  Fetching data from server
  Fetching data took 0.0813 secs
  Constructing features on server
  Fetching data from server
  Fetching data took 0.0874 secs
  Constructing features on server
  Fetching data from server
  Fetching data took 0.0873 secs
  Constructing features on server
  Fetching data from server
  Fetching data took 0.0903 secs
  Constructing features on server
  Fetching data from server
  Fetching data took 0.109 secs
  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 0.15 secs
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 0.157 secs
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 0.0824 secs
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 0.105 secs
  Tidying covariates took 0.122 secs
  Removing 1 redundant covariates
  Removing 1 infrequent covariates
  Normalizing covariates
  Tidying covariates took 0.686 secs
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 0.105 secs
  Removing 0 redundant covariate ID - time ID combinations
  Removing 0 infrequent covariates
  Normalizing covariates
  Tidying covariates took 0.817 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 0.00378 secs
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [27s/26s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE