* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/CDMConnector.Rcheck’
* using R Under development (unstable) (2024-04-24 r86484)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘CDMConnector/DESCRIPTION’ ... OK
* this is package ‘CDMConnector’ version ‘1.3.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Capr’
* 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 ‘CDMConnector’ can be installed ... [15s/19s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/CDMConnector-00install.html' for details.
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 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 ... [23s/29s] 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 R/sysdata.rda ... 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 ... [280s/336s] ERROR
  Running ‘testthat.R’ [280s/335s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(CDMConnector)
  > 
  > test_check("CDMConnector")
  trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
  Content type 'application/zip' length 6754786 bytes (6.4 MB)
  ==================================================
  downloaded 6.4 MB
  
  
  Download completed!
  Creating CDM database /tmp/RtmpqUCxeg/working_dir/RtmpVnJ0ga/file1893bb167a740c/GiBleed_5.3.zip
  ===================>-----------   64% | ETA:  1s
  i Generating 5 cohorts
  i Generating cohort (1/5) - gibleed_all)
  v Generating cohort (1/5) - gibleed_all) [1s]
  
  i Generating cohort (2/5) - gibleed_all_end_10)
  v Generating cohort (2/5) - gibleed_all_end_10) [632ms]
  
  i Generating cohort (3/5) - gibleed_default)
  v Generating cohort (3/5) - gibleed_default) [426ms]
  
  i Generating cohort (4/5) - gibleed_default_with_descendants)
  v Generating cohort (4/5) - gibleed_default_with_descendants) [315ms]
  
  i Generating cohort (5/5) - gibleed_end_10)
  v Generating cohort (5/5) - gibleed_end_10) [337ms]
  
  i Generating 3 cohorts
  i Generating cohort (1/3) - gibleed_male)
  v Generating cohort (1/3) - gibleed_male) [796ms]
  
  i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [286ms]
  
  i Generating cohort (3/3) - deep_vein_thrombosis_01)
  v Generating cohort (3/3) - deep_vein_thrombosis_01) [335ms]
  
  i Generating 3 cohorts
  i Generating 3 cohorts
  i Generating cohort (1/3) - gibleed_male)
  v Generating cohort (1/3) - gibleed_male) [655ms]
  
  i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [237ms]
  
  i Generating cohort (3/3) - deep_vein_thrombosis_01)
  v Generating cohort (3/3) - deep_vein_thrombosis_01) [249ms]
  
  i Generating 3 cohorts
  i Generating 2 cohorts
  i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [390ms]
  
  i Generating cohort (2/2) - deep_vein_thrombosis_01)
  v Generating cohort (2/2) - deep_vein_thrombosis_01) [521ms]
  
  i Generating 2 cohorts
  i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [319ms]
  
  i Generating cohort (2/2) - deep_vein_thrombosis_01)
  v Generating cohort (2/2) - deep_vein_thrombosis_01) [305ms]
  
  i Generating 2 cohorts
  i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [239ms]
  
  i Generating cohort (2/2) - deep_vein_thrombosis_01)
  v Generating cohort (2/2) - deep_vein_thrombosis_01) [234ms]
  
  i Generating 2 cohorts
  i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [229ms]
  
  i Generating cohort (2/2) - deep_vein_thrombosis_01)
  v Generating cohort (2/2) - deep_vein_thrombosis_01) [359ms]
  
  i Generating 3 cohorts
  i Generating cohort (1/3) - another_gibleed_male)
  v Generating cohort (1/3) - another_gibleed_male) [723ms]
  
  i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01) [409ms]
  
  i Generating cohort (3/3) - another_deep_vein_thrombosis_01)
  v Generating cohort (3/3) - another_deep_vein_thrombosis_01) [384ms]
  
  i Generating 3 cohorts
  i Generating cohort (1/3) - gibleed_male)
  v Generating cohort (1/3) - gibleed_male) [672ms]
  
  i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [309ms]
  
  i Generating cohort (3/3) - deep_vein_thrombosis_01)
  v Generating cohort (3/3) - deep_vein_thrombosis_01) [275ms]
  
  i Generating 3 cohorts
  i Generating cohort (1/3) - gibleed_male)
  v Generating cohort (1/3) - gibleed_male) [641ms]
  
  i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [278ms]
  
  i Generating cohort (3/3) - deep_vein_thrombosis_01)
  v Generating cohort (3/3) - deep_vein_thrombosis_01) [219ms]
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 260 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • Capr cannot be loaded (1): 'test-db-generateCohortSet.R:77:3'
  • On CRAN (9): 'test-db-generateCohortSet.R:128:3',
    'test-db-generateConceptCohortSet.R:315:3',
    'test-db-generateConceptCohortSet.R:332:3',
    'test-db-generateConceptCohortSet.R:357:3',
    'test-db-recordCohortAttrition.R:121:5',
    'test-db-recordCohortAttrition.R:134:3', 'test-local_cdm.R:5:3',
    'test-memory-issue.R:6:3',
    'test-write_prefix_cohort_generation_snowflake.R:4:3'
  • eunomia_is_available("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
  • failing test (1): 'test-db-dateadd.R:126:3'
  • manual test (5): 'test-Eunomia.R:2:3', 'test-db-copy_cdm_to.R:62:3',
    'test-db-generateCohortSet.R:108:3', 'test-db-generateCohortSet.R:243:3',
    'test-db-write_schema_with_database.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-db-generateConceptCohortSet.R:308:5'): duckdb - generateConceptCohortSet ──
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-db-generateConceptCohortSet.R:308:5
   2.   └─CDMConnector::generateConceptCohortSet(...) at test-db-generateConceptCohortSet.R:18:3
   3.     └─base::Ops.numeric_version(...)
   4.       └─base::as.numeric_version(e2)
   5.         └─base::numeric_version(x)
   6.           └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 260 ]
  Error: Test failures
  In addition: Warning message:
  Connection is garbage-collected, use dbDisconnect() to avoid this. 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [80s/109s] OK
* checking PDF version of manual ... [20s/27s] OK
* checking HTML version of manual ... 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