Package: CDMConnector Check: tests New result: ERROR Running ‘testthat.R’ [268s/315s] 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/RtmpCTrtc9/filec41f160e510e0/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 [979ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [249ms] 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 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [823ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [253ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [224ms] 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 [469ms] 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 [217ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [250ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [243ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [250ms] ! 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 [348ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default_with_descendants v Generating cohort (1/1) - gibleed_default_with_descendants [297ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [419ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [283ms] ! 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 [201ms] 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 [224ms] i Generating cohort (2/5) - gibleed_default v Generating cohort (2/5) - gibleed_default [375ms] i Generating cohort (3/5) - gibleed_default_with_descendants v Generating cohort (3/5) - gibleed_default_with_descendants [468ms] i Generating cohort (4/5) - gibleed_all_end_10 v Generating cohort (4/5) - gibleed_all_end_10 [286ms] i Generating cohort (5/5) - gibleed_end_10 v Generating cohort (5/5) - gibleed_end_10 [235ms] 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 [208ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [175ms] i Generating 3 cohorts i Generating cohort (1/3) - another_gibleed_male v Generating cohort (1/3) - another_gibleed_male [615ms] i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [157ms] i Generating cohort (3/3) - another_deep_vein_thrombosis_01 v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [146ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [671ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [174ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [139ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [594ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [157ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [141ms] i `EUNOMIA_DATA_FOLDER` set to: '/home/hornik/tmp/scratch/RtmpCTrtc9'. 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/RtmpCTrtc9/GiBleed_5.3.zip ===============>--------------- 51% | ETA: 3s 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 [723ms] 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 , a list `attr(expected, 'cohort_codelist')` is absent [ FAIL 4 | WARN 11 | SKIP 21 | PASS 342 ] Error: Test failures Execution halted Package: CohortConstructor Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a00_introduction.Rmd’ using rmarkdown --- finished re-building ‘a00_introduction.Rmd’ --- re-building ‘a01_building_base_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a01_building_base_cohorts.Rmd’ --- re-building ‘a02_cohort_table_requirements.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB ** Processing: /home/hornik/tmp/CRAN_recheck/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-15-1.png 288x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3779 bytes Input file size = 4634 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3377 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 = 3377 Output IDAT size = 3377 bytes (402 bytes decrease) Output file size = 3455 bytes (1179 bytes = 25.44% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-16-1.png 288x288 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3614 bytes Input file size = 4460 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3284 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 = 3284 Output IDAT size = 3284 bytes (330 bytes decrease) Output file size = 3362 bytes (1098 bytes = 24.62% decrease) --- finished re-building ‘a02_cohort_table_requirements.Rmd’ --- re-building ‘a03_require_demographics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a03_require_demographics.Rmd’ --- re-building ‘a04_require_intersections.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a04_require_intersections.Rmd’ --- re-building ‘a05_update_cohort_start_end.Rmd’ using rmarkdown --- finished re-building ‘a05_update_cohort_start_end.Rmd’ --- re-building ‘a06_concatanate_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a06_concatanate_cohorts.Rmd’ --- re-building ‘a07_filter_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a07_filter_cohorts.Rmd’ --- re-building ‘a08_split_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB --- finished re-building ‘a08_split_cohorts.Rmd’ --- re-building ‘a09_combine_cohorts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 96-102 [unnamed-chunk-8] (a09_combine_cohorts.Rmd) Error: processing vignette 'a09_combine_cohorts.Rmd' failed with diagnostics: Failed to collect lazy table. Caused by error in `dbSendQuery()`: ! rapi_prepare: Failed to prepare query SELECT * FROM main.my_study_og_033_1739467406_attrition Error: Catalog Error: Table with name my_study_og_033_1739467406_attrition does not exist! Did you mean "my_study_medintersect_attrition"? LINE 2: FROM main.my_study_og_033_173946740... ^ --- failed re-building ‘a09_combine_cohorts.Rmd’ --- re-building ‘a10_match_cohorts.Rmd’ using rmarkdown --- finished re-building ‘a10_match_cohorts.Rmd’ --- re-building ‘a11_benchmark.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-5-1.png 960x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 133789 bytes Input file size = 134059 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 98903 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 = 98903 Output IDAT size = 98903 bytes (34886 bytes decrease) Output file size = 98981 bytes (35078 bytes = 26.17% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-7-1.png 960x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 76134 bytes Input file size = 76320 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59778 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 = 59778 Output IDAT size = 59778 bytes (16356 bytes decrease) Output file size = 59856 bytes (16464 bytes = 21.57% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-10-1.png 960x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42145 bytes Input file size = 42283 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36072 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 = 36072 Output IDAT size = 36072 bytes (6073 bytes decrease) Output file size = 36150 bytes (6133 bytes = 14.50% decrease) --- finished re-building ‘a11_benchmark.Rmd’ SUMMARY: processing the following file failed: ‘a09_combine_cohorts.Rmd’ Error: Vignette re-building failed. Execution halted