* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CDMConnector.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CDMConnector/DESCRIPTION’ ... OK * this is package ‘CDMConnector’ version ‘2.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/8s] OK * 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] NOTE insertCdmTo.db_cdm: no visible binding for global variable ‘cohort’ Undefined global functions or variables: cohort * 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 ... WARNING Undocumented code objects: ‘dropTable.db_cdm’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'cdmDisconnect.db_cdm.Rd' ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... [186s/164s] ERROR Running ‘testthat.R’ [186s/164s] 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/Rtmp8Lab2c/working_dir/Rtmp5N4Bnj/file20774c130c229f/GiBleed_5.3.zip i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [408ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [114ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [115ms] i Generating 3 cohorts i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [323ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [112ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [114ms] 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 [116ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [117ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [116ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [126ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [113ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [116ms] i Generating 2 cohorts i Generating 2 cohorts i Generating 2 cohorts i Generating 1 cohort i Generating cohort (1/1) - viral_sinusitus v Generating cohort (1/1) - viral_sinusitus [300ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default v Generating cohort (1/1) - gibleed_default [153ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default_with_descendants v Generating cohort (1/1) - gibleed_default_with_descendants [148ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [150ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [156ms] i Generating 1 cohort i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [129ms] i Generating 5 cohorts i Generating cohort (1/5) - gibleed_all v Generating cohort (1/5) - gibleed_all [161ms] i Generating cohort (2/5) - gibleed_default v Generating cohort (2/5) - gibleed_default [155ms] i Generating cohort (3/5) - gibleed_default_with_descendants v Generating cohort (3/5) - gibleed_default_with_descendants [147ms] i Generating cohort (4/5) - gibleed_all_end_10 v Generating cohort (4/5) - gibleed_all_end_10 [148ms] i Generating cohort (5/5) - gibleed_end_10 v Generating cohort (5/5) - gibleed_end_10 [167ms] 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 Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [117ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [119ms] i Generating 3 cohorts i Generating cohort (1/3) - another_gibleed_male v Generating cohort (1/3) - another_gibleed_male [267ms] i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [114ms] i Generating cohort (3/3) - another_deep_vein_thrombosis_01 v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [119ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [282ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [111ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [108ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [276ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [107ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [114ms] i `EUNOMIA_DATA_FOLDER` set to: '/tmp/Rtmp8Lab2c/working_dir/Rtmp5N4Bnj'. 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/Rtmp8Lab2c/working_dir/Rtmp5N4Bnj/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 i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [145ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_male v Generating cohort (1/1) - gibleed_male [291ms] Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable', target signature 'duckdb_connection#Id'. "duckdb_connection#ANY" would also be valid [ FAIL 1 | WARN 1 | SKIP 20 | PASS 364 ] ══ Skipped tests (20) ══════════════════════════════════════════════════════════ • On CRAN (8): 'test-04-db-generateConceptCohortSet.R:384:3', 'test-04-db-generateConceptCohortSet.R:402:3', 'test-04-db-generateConceptCohortSet.R:428:3', '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' • 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:233:3', 'test-03-db-generateCohortSet.R:109:3', 'test-03-db-generateCohortSet.R:244:3', '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:582:3' • {TreatmentPatterns} is not installed (1): 'test-03-db-generateCohortSet.R:128:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-07-db-dateadd.R:263:5'): duckdb - date functions ─────────────── Error in `abs(df$dif_days)`: non-numeric argument to mathematical function Backtrace: ▆ 1. └─CDMConnector (local) test_clock_functions(con, write_schema) at test-07-db-dateadd.R:263:5 [ FAIL 1 | WARN 1 | SKIP 20 | PASS 364 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [22s/23s] OK * checking PDF version of manual ... [6s/6s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 1 NOTE