* using log directory ‘/srv/hornik/tmp/CRAN/CDMConnector.Rcheck’
* using R Under development (unstable) (2024-03-24 r86185)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘CDMConnector/DESCRIPTION’ ... OK
* this is package ‘CDMConnector’ version ‘1.3.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/9s] NOTE
Maintainer: ‘Adam Black <black@ohdsi.org>’

Suggests or Enhances not in mainstream repositories:
  CirceR, Capr
Availability using Additional_repositories specification:
  CirceR   yes   https://OHDSI.github.io/drat
  Capr     yes   https://OHDSI.github.io/drat
* 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 ‘CDMConnector’ can be installed ... [4s/4s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [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 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [68s/67s] ERROR
  Running ‘testthat.R’ [68s/66s]
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/Rtmpsp7pfb/working_dir/Rtmpd7EIHu/file18f1d019b64a52/GiBleed_5.3.zip
  [ FAIL 6 | WARN 0 | SKIP 19 | PASS 225 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • Capr cannot be loaded (1): 'test-db-generateCohortSet.R:77:3'
  • CirceR cannot be loaded (9): 'test-db-custom_cohort_creation.R:42:5',
    'test-db-generateCohortSet.R:64:5', 'test-db-generateCohortSet.R:210:3',
    'test-db-generateConceptCohortSet.R:303:5', 'test-db-generic-bind.R:22:5',
    'test-db-newGeneratedCohortSet.R:126:3',
    'test-db-newGeneratedCohortSet.R:179:3',
    'test-db-recordCohortAttrition.R:133:3',
    'test-write_prefix_cohort_generation_snowflake.R:3:3'
  • TreatmentPatterns cannot be loaded (1): 'test-db-generateCohortSet.R:127:3'
  • arrow cannot be loaded (1): 'test-local_cdm.R:3:3'
  • 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:323:5'): missing domains produce warning ──
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-db-generateConceptCohortSet.R:322:3
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─CDMConnector::generateConceptCohortSet(...) at test-db-generateConceptCohortSet.R:323:5
    8.   └─base::Ops.numeric_version(...)
    9.     └─base::as.numeric_version(e2)
   10.       └─base::numeric_version(x)
   11.         └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  ── Failure ('test-db-generateConceptCohortSet.R:343:5'): Regimen domain does not cause error ──
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    invalid non-character version specification 'x' (type: double)
  ── Failure ('test-db-generateConceptCohortSet.R:349:3'): Regimen domain does not cause error ──
  cdm$cohort is not an S3 object
  ── Failure ('test-db-generateConceptCohortSet.R:367:2'): Eunomia ───────────────
  Expected `... <- NULL` to run without any errors.
  i Actually got a <simpleError> with text:
    invalid non-character version specification 'x' (type: double)
  ── Error ('test-db-recordCohortAttrition.R:127:5'): duckdb - recordCohortAttrition ──
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. └─CDMConnector (local) test_record_cohort_attrition(con, cdm_schema, write_schema) at test-db-recordCohortAttrition.R:127:5
   2.   └─CDMConnector::generateConceptCohortSet(...) at test-db-recordCohortAttrition.R:9:3
   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()$valid_numeric_version)
  ── Error ('test-memory-issue.R:14:3'): memory leak does not happen ─────────────
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. └─CDMConnector::generateConceptCohortSet(...) at test-memory-issue.R:14:3
   2.   └─base::Ops.numeric_version(...)
   3.     └─base::as.numeric_version(e2)
   4.       └─base::numeric_version(x)
   5.         └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 6 | WARN 0 | SKIP 19 | PASS 225 ]
  Error: Test failures
  In addition: There were 11 warnings (use warnings() to see them)
  Execution halted
  Warning message:
  Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this. 
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [19s/19s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘a01_getting-started.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
--- finished re-building ‘a01_getting-started.Rmd’

--- re-building ‘a02_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

--- finished re-building ‘a02_cohorts.Rmd’

--- re-building ‘a03_dbplyr.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

--- finished re-building ‘a03_dbplyr.Rmd’

Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
--- re-building ‘a04_DBI_connection_examples.Rmd’ using rmarkdown
--- finished re-building ‘a04_DBI_connection_examples.Rmd’

--- re-building ‘a05_cdm_reference_backends.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

--- finished re-building ‘a05_cdm_reference_backends.Rmd’

--- re-building ‘a06_using_cdm_attributes.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.

Quitting from lines 86-96 [unnamed-chunk-9] (a06_using_cdm_attributes.Rmd)
Error: processing vignette 'a06_using_cdm_attributes.Rmd' failed with diagnostics:
invalid non-character version specification 'x' (type: double)
--- failed re-building ‘a06_using_cdm_attributes.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
SUMMARY: processing the following file failed:
  ‘a06_using_cdm_attributes.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [8s/8s] 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: 2 ERRORs, 1 NOTE