CRAN Package Check Results for Maintainer ‘Adam Black <black at ohdsi.org>’

Last updated on 2024-04-25 20:48:55 CEST.

Package	ERROR	NOTE
CDMConnector	1	12

Package CDMConnector

Current CRAN status: ERROR: 1, NOTE: 12

Additional issues

M1mac

Version: 1.3.1
Check: package dependencies
Result: NOTE Package which this enhances but not available for checking: ‘Capr’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 1.3.1
Check: tests
Result: ERROR Running ‘testthat.R’ [280s/335s] 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/RtmpqUCxeg/working_dir/RtmpVnJ0ga/file1893bb167a740c/GiBleed_5.3.zip ===================>----------- 64% | ETA: 1s i Generating 5 cohorts i Generating cohort (1/5) - gibleed_all) v Generating cohort (1/5) - gibleed_all) [1s] i Generating cohort (2/5) - gibleed_all_end_10) v Generating cohort (2/5) - gibleed_all_end_10) [632ms] i Generating cohort (3/5) - gibleed_default) v Generating cohort (3/5) - gibleed_default) [426ms] i Generating cohort (4/5) - gibleed_default_with_descendants) v Generating cohort (4/5) - gibleed_default_with_descendants) [315ms] i Generating cohort (5/5) - gibleed_end_10) v Generating cohort (5/5) - gibleed_end_10) [337ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male) v Generating cohort (1/3) - gibleed_male) [796ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [286ms] i Generating cohort (3/3) - deep_vein_thrombosis_01) v Generating cohort (3/3) - deep_vein_thrombosis_01) [335ms] i Generating 3 cohorts i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male) v Generating cohort (1/3) - gibleed_male) [655ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [237ms] i Generating cohort (3/3) - deep_vein_thrombosis_01) v Generating cohort (3/3) - deep_vein_thrombosis_01) [249ms] 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) [390ms] i Generating cohort (2/2) - deep_vein_thrombosis_01) v Generating cohort (2/2) - deep_vein_thrombosis_01) [521ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [319ms] i Generating cohort (2/2) - deep_vein_thrombosis_01) v Generating cohort (2/2) - deep_vein_thrombosis_01) [305ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [239ms] i Generating cohort (2/2) - deep_vein_thrombosis_01) v Generating cohort (2/2) - deep_vein_thrombosis_01) [234ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [229ms] i Generating cohort (2/2) - deep_vein_thrombosis_01) v Generating cohort (2/2) - deep_vein_thrombosis_01) [359ms] i Generating 3 cohorts i Generating cohort (1/3) - another_gibleed_male) v Generating cohort (1/3) - another_gibleed_male) [723ms] i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01) v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01) [409ms] i Generating cohort (3/3) - another_deep_vein_thrombosis_01) v Generating cohort (3/3) - another_deep_vein_thrombosis_01) [384ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male) v Generating cohort (1/3) - gibleed_male) [672ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [309ms] i Generating cohort (3/3) - deep_vein_thrombosis_01) v Generating cohort (3/3) - deep_vein_thrombosis_01) [275ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male) v Generating cohort (1/3) - gibleed_male) [641ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [278ms] i Generating cohort (3/3) - deep_vein_thrombosis_01) v Generating cohort (3/3) - deep_vein_thrombosis_01) [219ms] [ FAIL 1 | WARN 0 | SKIP 17 | PASS 260 ] ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • Capr cannot be loaded (1): 'test-db-generateCohortSet.R:77:3' • On CRAN (9): 'test-db-generateCohortSet.R:128:3', 'test-db-generateConceptCohortSet.R:315:3', 'test-db-generateConceptCohortSet.R:332:3', 'test-db-generateConceptCohortSet.R:357:3', 'test-db-recordCohortAttrition.R:121:5', 'test-db-recordCohortAttrition.R:134:3', 'test-local_cdm.R:5:3', 'test-memory-issue.R:6:3', 'test-write_prefix_cohort_generation_snowflake.R:4:3' • eunomia_is_available("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3' • failing test (1): 'test-db-dateadd.R:126:3' • manual test (5): 'test-Eunomia.R:2:3', 'test-db-copy_cdm_to.R:62:3', 'test-db-generateCohortSet.R:108:3', 'test-db-generateCohortSet.R:243:3', 'test-db-write_schema_with_database.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-db-generateConceptCohortSet.R:308:5'): duckdb - generateConceptCohortSet ── Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double) Backtrace: ▆ 1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-db-generateConceptCohortSet.R:308:5 2. └─CDMConnector::generateConceptCohortSet(...) at test-db-generateConceptCohortSet.R:18:3 3. └─base::Ops.numeric_version(...) 4. └─base::as.numeric_version(e2) 5. └─base::numeric_version(x) 6. └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) [ FAIL 1 | WARN 0 | SKIP 17 | PASS 260 ] Error: Test failures In addition: Warning message: Connection is garbage-collected, use dbDisconnect() to avoid this. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.3.1
Check: package dependencies
Result: NOTE Packages which this enhances but not available for checking: 'CirceR', 'Capr' Flavors: r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64