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

Last updated on 2024-04-18 01:03:39 CEST.

Package ERROR NOTE
CDMConnector 1 13

Package CDMConnector

Current CRAN status: ERROR: 1, NOTE: 13

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

Version: 1.3.1
Check: for unstated dependencies in ‘tests’
Result: WARN Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES' Flavor: r-prerel-windows-x86_64

Version: 1.3.1
Check: tests
Result: ERROR Running 'testthat.R' [27s] 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' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Downloading GiBleed trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' [ FAIL 25 | WARN 25 | SKIP 31 | PASS 25 ] ══ Skipped tests (31) ══════════════════════════════════════════════════════════ • CirceR cannot be loaded (7): 'test-db-generateCohortSet.R:64:5', 'test-db-generateCohortSet.R:210:3', 'test-db-generateConceptCohortSet.R:303:5', 'test-db-generic-bind.R:22:5', 'test-db-newGeneratedCohortSet.R:126:3', 'test-db-newGeneratedCohortSet.R:179:3', 'test-write_prefix_cohort_generation_snowflake.R:3:3' • On CRAN (6): '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-memory-issue.R:6:3' • TreatmentPatterns cannot be loaded (1): 'test-db-generateCohortSet.R:127:3' • arrow cannot be loaded (1): 'test-local_cdm.R:3:3' • eunomia_is_available("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3' • eunomia_is_available() is not TRUE (9): 'test-db-cdm.R:58:3', 'test-db-cdm.R:81:3', 'test-db-cdm.R:182:3', 'test-db-generateCohortSet.R:76:3', 'test-db-utils.R:87:3', 'test-db-utils.R:113:3', 'test-validate.R:3:3', 'test-validate.R:18:3', 'test-validate.R:78:3' • 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-cdm_tranformations.R:6:3'): cdm_sample works ─────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(eunomia_dir())) at test-cdm_tranformations.R:6:3 2. ├─duckdb::duckdb(eunomia_dir()) 3. │ └─duckdb:::path_normalize(dbdir) 4. ├─CDMConnector::eunomia_dir() 5. │ └─CDMConnector::eunomiaDir(...) 6. │ └─CDMConnector::downloadEunomiaData(...) 7. │ ├─withr::with_options(...) 8. │ │ └─base::force(code) 9. │ └─utils::download.file(...) 10. └─base::.handleSimpleError(...) 11. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-DBI.R:75:5'): duckdb - dbi ────────────────────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-DBI.R:75:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-casing.R:30:5'): duckdb - lowercase columns ───────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-casing.R:30:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-cdm.R:47:5'): duckdb - cdm_from_con ───────────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-cdm.R:47:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-cohortTransformations.R:378:5'): duckdb - cohort_collapse ─── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-cohortTransformations.R:378:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-cohort_ddl.R:54:5'): duckdb - createCohortTables ──────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-cohort_ddl.R:54:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-compute.R:82:5'): duckdb - compute_query ──────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-compute.R:82:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-compute.R:98:3'): message does not duplicate when prefix is used ── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(eunomia_dir())) at test-db-compute.R:98:3 2. ├─duckdb::duckdb(eunomia_dir()) 3. │ └─duckdb:::path_normalize(dbdir) 4. ├─CDMConnector::eunomia_dir() 5. │ └─CDMConnector::eunomiaDir(...) 6. │ └─CDMConnector::downloadEunomiaData(...) 7. │ ├─withr::with_options(...) 8. │ │ └─base::force(code) 9. │ └─utils::download.file(...) 10. └─base::.handleSimpleError(...) 11. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-copy_cdm_to.R:30:5'): duckdb - copy_cdm_to ────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-copy_cdm_to.R:30:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-copy_cdm_to.R:41:3'): duckdb - copy_cdm_to without prefix ─── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(eunomia_dir())) at test-db-copy_cdm_to.R:41:3 2. ├─duckdb::duckdb(eunomia_dir()) 3. │ └─duckdb:::path_normalize(dbdir) 4. ├─CDMConnector::eunomia_dir() 5. │ └─CDMConnector::eunomiaDir(...) 6. │ └─CDMConnector::downloadEunomiaData(...) 7. │ ├─withr::with_options(...) 8. │ │ └─base::force(code) 9. │ └─utils::download.file(...) 10. └─base::.handleSimpleError(...) 11. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-custom_cohort_creation.R:38:5'): duckdb - test_custom_derived_cohort ── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-custom_cohort_creation.R:38:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-dateadd.R:110:5'): duckdb - date functions ────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-dateadd.R:110:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-dbSource.R:21:5'): duckdb - db source insert from source table ── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-dbSource.R:21:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-example-analysis.R:201:5'): duckdb - checking common usage ── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-example-analysis.R:201:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-generateCohortSet.R:176:3'): newGeneratedCohortSet works with prefix ── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(eunomia_dir())) at test-db-generateCohortSet.R:176:3 2. ├─duckdb::duckdb(eunomia_dir()) 3. │ └─duckdb:::path_normalize(dbdir) 4. ├─CDMConnector::eunomia_dir() 5. │ └─CDMConnector::eunomiaDir(...) 6. │ └─CDMConnector::downloadEunomiaData(...) 7. │ ├─withr::with_options(...) 8. │ │ └─base::force(code) 9. │ └─utils::download.file(...) 10. └─base::.handleSimpleError(...) 11. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-newGeneratedCohortSet.R:91:5'): duckdb - recordCohortAttrition ── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-newGeneratedCohortSet.R:91:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-newGeneratedCohortSet.R:104:3'): error in newGeneratedCohortSet if cohort_ref has not been computed ── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at test-db-newGeneratedCohortSet.R:104:3 2. ├─duckdb::duckdb(dbdir = eunomia_dir()) 3. │ └─duckdb:::path_normalize(dbdir) 4. ├─CDMConnector::eunomia_dir() 5. │ └─CDMConnector::eunomiaDir(...) 6. │ └─CDMConnector::downloadEunomiaData(...) 7. │ ├─withr::with_options(...) 8. │ │ └─base::force(code) 9. │ └─utils::download.file(...) 10. └─base::.handleSimpleError(...) 11. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-sample.R:42:5'): duckdb - sample database ─────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-sample.R:42:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-summariseQuantile.R:63:5'): duckdb - summariseQuantile ────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-summariseQuantile.R:63:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-temp-tables.R:50:5'): duckdb - temp_tables ────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-temp-tables.R:50:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-utils.R:66:5'): duckdb - inSchema ─────────────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-utils.R:66:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-db-verify_write_schema.R:20:5'): duckdb - verify_write_access ── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-db-verify_write_schema.R:20:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ── Error ('test-deprecations.R:3:3'): computeQuery gives warning ─────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(eunomia_dir())) at test-deprecations.R:3:3 2. ├─duckdb::duckdb(eunomia_dir()) 3. │ └─duckdb:::path_normalize(dbdir) 4. ├─CDMConnector::eunomia_dir() 5. │ └─CDMConnector::eunomiaDir(...) 6. │ └─CDMConnector::downloadEunomiaData(...) 7. │ ├─withr::with_options(...) 8. │ │ └─base::force(code) 9. │ └─utils::download.file(...) 10. └─base::.handleSimpleError(...) 11. └─base (local) h(simpleError(msg, call)) ── Error ('test-pool.R:4:3'): pool connections work ──────────────────────────── Error in `utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.zip"), destfile = file.path(pathToData, zipName), mode = "wb", method = "auto", quiet = FALSE, extra = list(progressfunction = function(downloaded, total) { progress <- min(1, downloaded/total) cli::cli_progress_update(id = pb, set = progress) }))`: cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─duckdb::duckdb(eunomia_dir()) at test-pool.R:4:3 2. │ └─duckdb:::path_normalize(dbdir) 3. └─CDMConnector::eunomia_dir() 4. └─CDMConnector::eunomiaDir(...) 5. └─CDMConnector::downloadEunomiaData(...) 6. ├─withr::with_options(...) 7. │ └─base::force(code) 8. └─utils::download.file(...) ── Error ('test-zzz-DBI.R:50:5'): duckdb - dbi ───────────────────────────────── Error in `h(simpleError(msg, call))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' Backtrace: ▆ 1. ├─CDMConnector:::get_connection(dbtype) at test-zzz-DBI.R:50:5 2. │ ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 3. │ ├─duckdb::duckdb(dbdir = eunomia_dir()) at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 4. │ │ └─duckdb:::path_normalize(dbdir) 5. │ └─CDMConnector::eunomia_dir() at D:\RCompile\CRANpkg\local\4.4\CDMConnector.Rcheck\tests\testthat\setup.R:35:5 6. │ └─CDMConnector::eunomiaDir(...) 7. │ └─CDMConnector::downloadEunomiaData(...) 8. │ ├─withr::with_options(...) 9. │ │ └─base::force(code) 10. │ └─utils::download.file(...) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) [ FAIL 25 | WARN 25 | SKIP 31 | PASS 25 ] Error: Test failures In addition: Warning message: In utils::download.file(url = glue::glue("https://example-data.ohdsi.dev/{datasetName}.zip"), : URL 'https://example-data.ohdsi.dev/GiBleed.zip': status was 'Couldn't resolve host name' Execution halted Flavor: r-prerel-windows-x86_64

Version: 1.3.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'a01_getting-started.Rmd' using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Quitting from lines at lines 11-21 [setup] (a01_getting-started.Rmd) Error: processing vignette 'a01_getting-started.Rmd' failed with diagnostics: cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' --- failed re-building 'a01_getting-started.Rmd' --- re-building 'a02_cohorts.Rmd' using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Quitting from lines at lines 11-25 [unnamed-chunk-1] (a02_cohorts.Rmd) Error: processing vignette 'a02_cohorts.Rmd' failed with diagnostics: cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' --- failed re-building 'a02_cohorts.Rmd' --- re-building 'a03_dbplyr.Rmd' using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Quitting from lines at lines 11-21 [unnamed-chunk-1] (a03_dbplyr.Rmd) Error: processing vignette 'a03_dbplyr.Rmd' failed with diagnostics: cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' --- failed re-building 'a03_dbplyr.Rmd' --- re-building 'a04_DBI_connection_examples.Rmd' using rmarkdown --- finished re-building 'a04_DBI_connection_examples.Rmd' --- re-building 'a05_cdm_reference_backends.Rmd' using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Quitting from lines at lines 11-22 [unnamed-chunk-1] (a05_cdm_reference_backends.Rmd) Error: processing vignette 'a05_cdm_reference_backends.Rmd' failed with diagnostics: cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' --- failed re-building 'a05_cdm_reference_backends.Rmd' --- re-building 'a06_using_cdm_attributes.Rmd' using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Quitting from lines at lines 20-29 [unnamed-chunk-2] (a06_using_cdm_attributes.Rmd) Error: processing vignette 'a06_using_cdm_attributes.Rmd' failed with diagnostics: cannot open URL 'https://example-data.ohdsi.dev/GiBleed.zip' --- failed re-building 'a06_using_cdm_attributes.Rmd' SUMMARY: processing the following files failed: 'a01_getting-started.Rmd' 'a02_cohorts.Rmd' 'a03_dbplyr.Rmd' 'a05_cdm_reference_backends.Rmd' 'a06_using_cdm_attributes.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-prerel-windows-x86_64