• using R Under development (unstable) (2025-02-20 r87772)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-16) 14.2.0     GNU Fortran (Debian 14.2.0-16) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘CDMConnector/DESCRIPTION’ ... OK
• this is package ‘CDMConnector’ version ‘1.7.0’
• 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 ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘benchmarkCDMConnector.R’ ‘cdm.R’ ‘cdmSubset.R’ ‘copy_cdm_to.R’     ‘dbSource.R’ ‘generateCohortSet.R’ ‘generateConceptCohortSet.R’
• 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 ... [10s/11s] 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 ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [298s/370s] ERROR   Running ‘testthat.R’ [298s/369s] 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/Rtmpc67J3J/file3575102b5dedb3/GiBleed_5.3.zip   Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',    target signature 'duckdb_connection#Id'.    "duckdb_connection#ANY" would also be valid   Support for 'prefix' in writeSchema is deprecated and will be removed in a future release. Please use the `writePrefix` argument in `cdmFromCon()` instead.   This message is displayed once per session.   ! cdm name not specified and could not be inferred from the cdm source table   ! cdm name not specified and could not be inferred from the cdm source table   ! cdm name not specified and could not be inferred from the cdm source table   ! cdm name not specified and could not be inferred from the cdm source table   i Generating 3 cohorts   i Generating cohort (1/3) - gibleed_male   v Generating cohort (1/3) - gibleed_male [1.4s]      i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01   v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [435ms]      i Generating cohort (3/3) - deep_vein_thrombosis_01   v Generating cohort (3/3) - deep_vein_thrombosis_01 [268ms]      i Generating 3 cohorts   i Generating 3 cohorts   i Generating cohort (1/3) - gibleed_male   v Generating cohort (1/3) - gibleed_male [772ms]      i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01   v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [216ms]      i Generating cohort (3/3) - deep_vein_thrombosis_01   v Generating cohort (3/3) - deep_vein_thrombosis_01 [265ms]      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 [347ms]      i Generating cohort (2/2) - deep_vein_thrombosis_01   v Generating cohort (2/2) - deep_vein_thrombosis_01 [419ms]      i Generating 2 cohorts   i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01   v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [329ms]      i Generating cohort (2/2) - deep_vein_thrombosis_01   v Generating cohort (2/2) - deep_vein_thrombosis_01 [257ms]      i Generating 2 cohorts   i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01   v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [297ms]      i Generating cohort (2/2) - deep_vein_thrombosis_01   v Generating cohort (2/2) - deep_vein_thrombosis_01 [282ms]      ! cdm name not specified and could not be inferred from the cdm source table   i Generating 2 cohorts   i Generating 2 cohorts   i Generating 2 cohorts   i Generating 1 cohort   i Generating cohort (1/1) - gibleed_default   v Generating cohort (1/1) - gibleed_default [454ms]      i Generating 1 cohort   i Generating cohort (1/1) - gibleed_default_with_descendants   v Generating cohort (1/1) - gibleed_default_with_descendants [472ms]      i Generating 1 cohort   i Generating cohort (1/1) - gibleed_all   v Generating cohort (1/1) - gibleed_all [519ms]      i Generating 1 cohort   i Generating cohort (1/1) - gibleed_all   v Generating cohort (1/1) - gibleed_all [378ms]      ! cdm name not specified and could not be inferred from the cdm source table   i Generating 1 cohort   i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01   v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [252ms]         Attaching package: 'clock'      The following object is masked from 'package:CDMConnector':          as_date      ! cdm name not specified and could not be inferred from the cdm source table   i Generating 5 cohorts   i Generating cohort (1/5) - gibleed_all   v Generating cohort (1/5) - gibleed_all [626ms]      i Generating cohort (2/5) - gibleed_default   v Generating cohort (2/5) - gibleed_default [434ms]      i Generating cohort (3/5) - gibleed_default_with_descendants   v Generating cohort (3/5) - gibleed_default_with_descendants [601ms]      i Generating cohort (4/5) - gibleed_all_end_10   v Generating cohort (4/5) - gibleed_all_end_10 [545ms]      i Generating cohort (5/5) - gibleed_end_10   v Generating cohort (5/5) - gibleed_end_10 [583ms]      Getting distinct count of concept relationship table   Getting count of different relationship IDs in concept relationship table   Getting join of concept and concept class computed to a temp table   Getting concept table collected into memory   Getting join of person and observation period collected into memory   Getting summary of observation period start and end dates by gender concept id   i Generating 2 cohorts   i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01   v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [513ms]      i Generating cohort (2/2) - deep_vein_thrombosis_01   v Generating cohort (2/2) - deep_vein_thrombosis_01 [258ms]      i Generating 3 cohorts   i Generating cohort (1/3) - another_gibleed_male   v Generating cohort (1/3) - another_gibleed_male [781ms]      i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01   v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [266ms]      i Generating cohort (3/3) - another_deep_vein_thrombosis_01   v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [252ms]      i Generating 3 cohorts   i Generating cohort (1/3) - gibleed_male   v Generating cohort (1/3) - gibleed_male [754ms]      i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01   v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [292ms]      i Generating cohort (3/3) - deep_vein_thrombosis_01   v Generating cohort (3/3) - deep_vein_thrombosis_01 [257ms]      i Generating 3 cohorts   i Generating cohort (1/3) - gibleed_male   v Generating cohort (1/3) - gibleed_male [601ms]      i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01   v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [221ms]      i Generating cohort (3/3) - deep_vein_thrombosis_01   v Generating cohort (3/3) - deep_vein_thrombosis_01 [241ms]      i `EUNOMIA_DATA_FOLDER` set to: '/tmp/Rtmpc67J3J'.   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/Rtmpc67J3J/GiBleed_5.3.zip   Getting distinct count of concept relationship table   Getting count of different relationship IDs in concept relationship table   Getting join of concept and concept class computed to a temp table   Getting concept table collected into memory   Getting join of person and observation period collected into memory   Getting summary of observation period start and end dates by gender concept id   ! cdm name not specified and could not be inferred from the cdm source table   ! cdm name not specified and could not be inferred from the cdm source table   ! cdm name not specified and could not be inferred from the cdm source table   i Generating 1 cohort   i Generating cohort (1/1) - gibleed_male   v Generating cohort (1/1) - gibleed_male [565ms]      Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',    target signature 'duckdb_connection#Id'.    "duckdb_connection#ANY" would also be valid   ! cdm name not specified and could not be inferred from the cdm source table   ! cdm name not specified and could not be inferred from the cdm source table   [ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]      ══ Skipped tests (21) ══════════════════════════════════════════════════════════   • On CRAN (8): 'test-04-db-generateConceptCohortSet.R:381:3',     'test-04-db-generateConceptCohortSet.R:399:3',     'test-04-db-generateConceptCohortSet.R:425:3', 'test-Eunomia.R:61:3',     'test-db-recordCohortAttrition.R:121:5',     'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3',     'test-write_prefix_cohort_generation_snowflake.R:4:3'   • arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3'   • eunomiaIsAvailable("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'   • failing test (2): 'test-07-db-dateadd.R:126:3', 'test-db-in_schema.R:34:5'   • manual test (7): 'test-02-db-cdm.R:234:3',     '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-in_schema.R:46:3',     'test-db-write_schema_with_database.R:5:3'   • {Capr} is not installed (1): 'test-04-db-generateConceptCohortSet.R:578:3'   • {TreatmentPatterns} is not installed (1):     'test-03-db-generateCohortSet.R:130:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──   `actual` (`actual`) not equal to `expected` (`expected`).        `attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1   `attr(attr(expected, 'cohort_codelist'), 'row.names')`:        `attr(actual, 'cohort_codelist')$cohort_definition_id`: 1   `attr(expected, 'cohort_codelist')$cohort_definition_id`:      `attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"   `attr(expected, 'cohort_codelist')$codelist_name`:        `attr(actual, 'cohort_codelist')$concept_id`: 192671   `attr(expected, 'cohort_codelist')$concept_id`:      `attr(actual, 'cohort_codelist')$type`: "index event"   `attr(expected, 'cohort_codelist')$type`:   Backtrace:       ▆    1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5    2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:58:3   ── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──   `actual` (`actual`) not equal to `expected` (`expected`).        `attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1   `attr(attr(expected, 'cohort_codelist'), 'row.names')`:        `attr(actual, 'cohort_codelist')$cohort_definition_id`: 1   `attr(expected, 'cohort_codelist')$cohort_definition_id`:      `attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"   `attr(expected, 'cohort_codelist')$codelist_name`:        `attr(actual, 'cohort_codelist')$concept_id`: 192671   `attr(expected, 'cohort_codelist')$concept_id`:      `attr(actual, 'cohort_codelist')$type`: "index event"   `attr(expected, 'cohort_codelist')$type`:   Backtrace:       ▆    1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5    2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:230:3   ── Failure ('test-04-db-generateConceptCohortSet.R:374:5'): duckdb - generateConceptCohortSet ──   `actual` (`actual`) not equal to `expected` (`expected`).        `attr(attr(actual, 'cohort_codelist'), 'row.names')`: 1   `attr(attr(expected, 'cohort_codelist'), 'row.names')`:        `attr(actual, 'cohort_codelist')$cohort_definition_id`: 1   `attr(expected, 'cohort_codelist')$cohort_definition_id`:      `attr(actual, 'cohort_codelist')$codelist_name`: "gibleed"   `attr(expected, 'cohort_codelist')$codelist_name`:        `attr(actual, 'cohort_codelist')$concept_id`: 192671   `attr(expected, 'cohort_codelist')$concept_id`:      `attr(actual, 'cohort_codelist')$type`: "index event"   `attr(expected, 'cohort_codelist')$type`:   Backtrace:       ▆    1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:374:5    2. └─testthat::expect_equal(actual, expected) at test-04-db-generateConceptCohortSet.R:272:3   ── Failure ('test-04-db-generateConceptCohortSet.R:547:3'): invalid cdm records are ignored in generateConceptCohortSet ──   `actual` (`actual`) not equal to `expected` (`expected`).      `attr(actual, 'cohort_codelist')` is an S3 object of class <tbl_df/tbl/data.frame>, a list   `attr(expected, 'cohort_codelist')` is absent      [ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [45s/61s] OK
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE