• using R Under development (unstable) (2025-12-05 r89107)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-9) 15.2.0     GNU Fortran (Debian 15.2.0-9) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘CDMConnector/DESCRIPTION’ ... OK
• this is package ‘CDMConnector’ version ‘2.2.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... WARNING Cannot process vignettes Packages suggested but not available for checking:   'SqlRender', 'CirceR', 'rJava', 'covr', 'knitr', 'rmarkdown',   'DatabaseConnector' VignetteBuilder package required for checking but not installed: ‘knitr’
• 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 ... 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/2s] 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/2s] 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] NOTE checkRd: (-1) tblGroup.Rd:21: height/width attributes should be in pixels
• 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 ... [189s/255s] ERROR   Running ‘testthat.R’ [189s/255s] 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://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip'   Content type 'application/zip' length 6754786 bytes (6.4 MB)   ==================================================   downloaded 6.4 MB         Download completed!   Creating CDM database /tmp/RtmpGjAiBA/file30ad6f4f9556ac/GiBleed_5.3.zip   Saving _problems/test-04-db-generateConceptCohortSet-584.R   ========================>------ 79% | ETA: 1s   ===========>------------------- 36% | ETA: 4s   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   Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',    target signature 'duckdb_connection#Id'.    "duckdb_connection#ANY" would also be valid   i `EUNOMIA_DATA_FOLDER` set to: '/tmp/RtmpGjAiBA'.   trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip'   Content type 'application/zip' length 6754786 bytes (6.4 MB)   ==================================================   downloaded 6.4 MB         Download completed!   Creating CDM database /tmp/RtmpGjAiBA/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   Saving _problems/test-db-cdmSubset-112.R   Saving _problems/test-omopgenerics-16.R   Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',    target signature 'duckdb_connection#Id'.    "duckdb_connection#ANY" would also be valid   [ FAIL 3 | WARN 0 | SKIP 33 | PASS 264 ]      ══ Skipped tests (33) ══════════════════════════════════════════════════════════   • On CRAN (7): 'test-04-db-generateConceptCohortSet.R:399:3',     'test-04-db-generateConceptCohortSet.R:417:3',     'test-04-db-generateConceptCohortSet.R:443:3', 'test-Eunomia.R:61:3',     'test-db-recordCohortAttrition.R:121:5',     'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3'   • 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:240:3',     'test-03-db-generateCohortSet.R:115:3',     'test-03-db-generateCohortSet.R:256:3', '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:597:3'   • {CirceR} is not installed (10): 'test-03-db-generateCohortSet.R:69:5',     'test-03-db-generateCohortSet.R:217:3',     'test-03-db-generateCohortSet.R:278:3',     'test-03-db-generateCohortSet.R:297:3',     'test-04-db-generateConceptCohortSet.R:387:5',     'test-13-db-custom_cohort_creation.R:35:5', 'test-17-db-generic-bind.R:22:5',     'test-18-db-newGeneratedCohortSet.R:126:3',     'test-18-db-newGeneratedCohortSet.R:181:3',     'test-write_prefix_cohort_generation_snowflake.R:3:3'   • {DatabaseConnector} is not installed (3): 'test-02-db-cdm.R:271:3',     'test-02-db-cdm.R:297:3', 'test-db-utils.R:258:5'   • {SqlRender} is not installed. (1): 'test-db-utils.R:194:7'   • {TreatmentPatterns} is not installed (1):     'test-03-db-generateCohortSet.R:134:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-04-db-generateConceptCohortSet.R:582:3'): attrition columns are correct ──   <rlib_error_package_not_found/rlang_error/error/condition>   Error in `generateCohortSet(cdm, cohortSet = cohort_set, name = "cohort2")`: The package "CirceR" is required.   Backtrace:       ▆    1. └─CDMConnector::generateCohortSet(...) at test-04-db-generateConceptCohortSet.R:582:3    2. └─rlang::check_installed("CirceR")   ── Error ('test-db-cdmSubset.R:112:5'): duckdb - sample database ───────────────   <rlib_error_package_not_found/rlang_error/error/condition>   Error in `generateCohortSet(cdm, cohortSet = cohortSet, name = "cohort")`: The package "CirceR" is required.   Backtrace:       ▆    1. └─CDMConnector (local) test_cdmSubset(con, cdmSchema, writeSchema) at test-db-cdmSubset.R:112:5    2. └─CDMConnector::generateCohortSet(cdm, cohortSet = cohortSet, name = "cohort") at test-db-cdmSubset.R:13:3    3. └─rlang::check_installed("CirceR")   ── Error ('test-omopgenerics.R:13:3'): omopgenerics::bind works for combining cohort tables ──   <rlib_error_package_not_found/rlang_error/error/condition>   Error in `CDMConnector::generateCohortSet(cdm, cohortSet, name = "cohort1", overwrite = TRUE)`: The package "CirceR" is required.   Backtrace:       ▆    1. └─CDMConnector::generateCohortSet(...) at test-omopgenerics.R:13:3    2. └─rlang::check_installed("CirceR")      [ FAIL 3 | WARN 0 | SKIP 33 | PASS 264 ]   Error:   ! Test failures.   Execution halted
• checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file?
• checking PDF version of manual ... [8s/12s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs