* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/CDMConnector.Rcheck’
* using R Under development (unstable) (2024-08-23 r87043)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.5.0’
* package encoding: UTF-8
* 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 ... [15s/22s] OK
* 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 ... [24s/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 ...
  Running ‘testthat.R’
 [9s/10s] ERROR
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!
  [1] "CI tests not run on snowflake - duckdb package is not installed"
  [ FAIL 4 | WARN 4 | SKIP 38 | PASS 25 ]
  
  ══ Skipped tests (38) ══════════════════════════════════════════════════════════
  • "duckdb" %in% dbToTest is not TRUE (1):
    'test-04-db-generateConceptCohortSet.R:553:3'
  • Capr cannot be loaded (1): 'test-04-db-generateConceptCohortSet.R:579:3'
  • CirceR cannot be loaded (3): 'test-03-db-generateCohortSet.R:215:3',
    'test-18-db-newGeneratedCohortSet.R:126:3',
    'test-write_prefix_cohort_generation_snowflake.R:3:3'
  • On CRAN (5): 'test-04-db-generateConceptCohortSet.R:381:3',
    'test-04-db-generateConceptCohortSet.R:399:3',
    'test-04-db-generateConceptCohortSet.R:425:3',
    'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3'
  • TreatmentPatterns cannot be loaded (1):
    'test-03-db-generateCohortSet.R:130:3'
  • arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3'
  • duckdb cannot be loaded (19): 'test-02-db-cdm.R:56:3',
    'test-02-db-cdm.R:81:3', 'test-02-db-cdm.R:184:3',
    'test-03-db-generateCohortSet.R:179:3', 'test-06-db-compute.R:99:3',
    'test-09-db-copy_cdm_to.R:40:3', 'test-11-cdm_tranformations.R:2:3',
    'test-15-db-benchmarkCDMConnector.R:19:5',
    'test-18-db-newGeneratedCohortSet.R:103:3',
    'test-18-db-newGeneratedCohortSet.R:178:3', 'test-Eunomia.R:41:3',
    'test-db-benchmarkCDMConnector.R:19:5', 'test-db-utils.R:86:3',
    'test-db-utils.R:112:3', 'test-deprecations.R:2:3', 'test-pool.R:2:3',
    'test-validate.R:2:3', 'test-validate.R:17:3', 'test-validate.R:77:3'
  • failing test (1): 'test-07-db-dateadd.R:126:3'
  • manual test (6): 'test-02-db-cdm.R:230:3',
    'test-03-db-generateCohortSet.R:111:3',
    'test-03-db-generateCohortSet.R:248:3', 'test-09-db-copy_cdm_to.R:62:3',
    'test-Eunomia.R:2:3', 'test-db-write_schema_with_database.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-02-db-cdm.R:221:3'): write_schema argument specification and cdm_disconnect works ──
  Error in `(function (cond) 
  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", 
      call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", 
  "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
  Backtrace:
      ▆
   1. ├─DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-02-db-cdm.R:221:3
   2. ├─base::loadNamespace(x)
   3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   5. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   6. │ └─base::stop(cond)
   7. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-04-db-generateConceptCohortSet.R:523:3'): invalid cdm records are ignored in generateConceptCohortSet ──
  Error in `(function (cond) 
  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", 
      call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", 
  "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
  Backtrace:
      ▆
   1. ├─DBI::dbConnect(duckdb::duckdb()) at test-04-db-generateConceptCohortSet.R:523:3
   2. ├─base::loadNamespace(x)
   3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   5. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   6. │ └─base::stop(cond)
   7. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-cohort-reconnect.R:5:3'): cohort codelist attributes are preserved ──
  Error in `(function (cond) 
  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", 
      call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", 
  "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
  Backtrace:
      ▆
   1. ├─DBI::dbConnect(duckdb::duckdb(eunomia_dir())) at test-cohort-reconnect.R:5:3
   2. ├─base::loadNamespace(x)
   3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   5. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   6. │ └─base::stop(cond)
   7. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-local_cdm.R:41:3'): softValidation is passed correctly ─────────
  Error in `(function (cond) 
  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", 
      call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", 
  "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
  Backtrace:
      ▆
   1. ├─DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-local_cdm.R:41:3
   2. ├─base::loadNamespace(x)
   3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   5. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   6. │ └─base::stop(cond)
   7. └─base (local) `<fn>`(`<pckgNtFE>`)
  
  [ FAIL 4 | WARN 4 | SKIP 38 | PASS 25 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [16s/26s] 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
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/CDMConnector.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:02.95, 120.72 + 13.48