Package: CDMConnector Check: tests New result: ERROR Running ‘testthat.R’ [279s/328s] 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 /home/hornik/tmp/scratch/RtmpXq7Ner/file377f182c668203/GiBleed_5.3.zip i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [840ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [182ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [255ms] i Generating 3 cohorts i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [750ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [154ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [277ms] 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 [504ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [426ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [277ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [233ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [263ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [260ms] 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 [705ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default v Generating cohort (1/1) - gibleed_default [304ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default_with_descendants v Generating cohort (1/1) - gibleed_default_with_descendants [216ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [294ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [265ms] i Generating 1 cohort i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [213ms] i Generating 5 cohorts i Generating cohort (1/5) - gibleed_all v Generating cohort (1/5) - gibleed_all [272ms] i Generating cohort (2/5) - gibleed_default v Generating cohort (2/5) - gibleed_default [231ms] i Generating cohort (3/5) - gibleed_default_with_descendants v Generating cohort (3/5) - gibleed_default_with_descendants [232ms] i Generating cohort (4/5) - gibleed_all_end_10 v Generating cohort (4/5) - gibleed_all_end_10 [270ms] i Generating cohort (5/5) - gibleed_end_10 v Generating cohort (5/5) - gibleed_end_10 [234ms] 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 [149ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [137ms] i Generating 3 cohorts i Generating cohort (1/3) - another_gibleed_male v Generating cohort (1/3) - another_gibleed_male [602ms] i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [143ms] i Generating cohort (3/3) - another_deep_vein_thrombosis_01 v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [149ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [681ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [180ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [171ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [755ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [168ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [143ms] i `EUNOMIA_DATA_FOLDER` set to: '/home/hornik/tmp/scratch/RtmpXq7Ner'. 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 /home/hornik/tmp/scratch/RtmpXq7Ner/GiBleed_5.3.zip ==================>------------ 61% | ETA: 1s 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 [290ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_male v Generating cohort (1/1) - gibleed_male [600ms] 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 0 | SKIP 20 | PASS 363 ] ══ 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 ════════════════════════════════════════════════════════════════ ── Failure ('test-03-db-generateCohortSet.R:306:3'): cohort era collapse is recorded in attrition ── `actualCohortCount` (`actual`) not equal to `expectedCohortCount` (`expected`). `class(actual)`: "tbl_df" "tbl" "data.frame" `class(expected)`: "cohort_table" "tbl_df" "tbl" "data.frame" [ FAIL 1 | WARN 0 | SKIP 20 | PASS 363 ] Error: Test failures Execution halted Package: PhenotypeR Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a01_DatabaseDiagnostics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB --- finished re-building ‘a01_DatabaseDiagnostics.Rmd’ --- re-building ‘a02_CodelistDiagnostics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from a02_CodelistDiagnostics.Rmd:78-83 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a02_CodelistDiagnostics.Rmd' failed with diagnostics: Names must be unique. ✖ These names are duplicated: * "codelist_type" at locations 4 and 5. --- failed re-building ‘a02_CodelistDiagnostics.Rmd’ --- re-building ‘a03_CohortDiagnostics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB ** Processing: /home/hornik/tmp/CRAN_recheck/PhenotypeR.Rcheck/vign_test/PhenotypeR/vignettes/a03_CohortDiagnostics_files/figure-html/unnamed-chunk-5-1.png 672x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 26097 bytes Input file size = 26211 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20271 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20271 Output IDAT size = 20271 bytes (5826 bytes decrease) Output file size = 20349 bytes (5862 bytes = 22.36% decrease) --- finished re-building ‘a03_CohortDiagnostics.Rmd’ --- re-building ‘a04_MatchedDiagnostics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB --- finished re-building ‘a04_MatchedDiagnostics.Rmd’ --- re-building ‘a05_PopulationDiagnostics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB --- finished re-building ‘a05_PopulationDiagnostics.Rmd’ SUMMARY: processing the following file failed: ‘a02_CodelistDiagnostics.Rmd’ Error: Vignette re-building failed. Execution halted