* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/CDMConnector.Rcheck’ * using R Under development (unstable) (2024-11-11 r87319) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-1) 14.2.0 GNU Fortran (Debian 14.2.0-1) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CDMConnector/DESCRIPTION’ ... OK * this is package ‘CDMConnector’ version ‘1.6.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [7s/8s] NOTE Maintainer: ‘Adam Black ’ Found the following (possibly) invalid URLs: URL: https://darwin-eu-dev.github.io/PatientProfiles/ From: inst/doc/a02_cohorts.html Status: 404 Message: Not Found * 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 ... [5s/5s] 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 ... [9s/9s] OK * 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 ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 ... [3s/3s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [3s/3s] ERROR Running ‘testthat.R’ [3s/3s] 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! [1] "CI tests not run on snowflake - duckdb package is not installed" i `EUNOMIA_DATA_FOLDER` set to: '/home/hornik/tmp/scratch/RtmpdgBJOC/working_dir/RtmpafMR35'. 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! [ FAIL 7 | WARN 0 | SKIP 39 | PASS 29 ] ══ Skipped tests (39) ══════════════════════════════════════════════════════════ • "duckdb" %in% dbToTest is not TRUE (1): 'test-04-db-generateConceptCohortSet.R:551:3' • Capr cannot be loaded (1): 'test-04-db-generateConceptCohortSet.R:577:3' • CirceR cannot be loaded (4): 'test-03-db-generateCohortSet.R:215:3', 'test-03-db-generateCohortSet.R:260:3', 'test-18-db-newGeneratedCohortSet.R:126:3', 'test-write_prefix_cohort_generation_snowflake.R:3:3' • On CRAN (6): 'test-04-db-generateConceptCohortSet.R:381:3', 'test-04-db-generateConceptCohortSet.R:399:3', 'test-04-db-generateConceptCohortSet.R:425:3', 'test-Eunomia.R:59:3', 'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3' • TreatmentPatterns cannot be loaded (1): 'test-03-db-generateCohortSet.R:130:3' • arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3' • duckdb cannot be loaded (18): 'test-02-db-cdm.R:56:3', 'test-02-db-cdm.R:185:3', 'test-03-db-generateCohortSet.R:179:3', 'test-06-db-compute.R:92:3', 'test-09-db-copy_cdm_to.R:40:3', 'test-11-cdm_tranformations.R:2:3', 'test-15-db-benchmarkCDMConnector.R:19:5', 'test-18-db-newGeneratedCohortSet.R:103:3', 'test-18-db-newGeneratedCohortSet.R:180:3', 'test-Eunomia.R:41:3', 'test-db-benchmarkCDMConnector.R:19:5', 'test-db-utils.R:85:3', 'test-db-utils.R:111:3', 'test-deprecations.R:2:3', 'test-pool.R:2:3', 'test-validate.R:2:3', 'test-validate.R:17:3', 'test-validate.R:77:3' • failing test (1): 'test-07-db-dateadd.R:126:3' • manual test (6): '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-write_schema_with_database.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-02-db-cdm.R:225:3'): write_schema argument specification and cdm_disconnect works ── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-02-db-cdm.R:225:3 2. ├─base::loadNamespace(x) 3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 5. │ │ └─base (local) doWithOneRestart(return(expr), restart) 6. │ └─base::stop(cond) 7. └─base (local) ``(``) ── Error ('test-04-db-generateConceptCohortSet.R:522:3'): invalid cdm records are ignored in generateConceptCohortSet ── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb()) at test-04-db-generateConceptCohortSet.R:522:3 2. ├─base::loadNamespace(x) 3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 5. │ │ └─base (local) doWithOneRestart(return(expr), restart) 6. │ └─base::stop(cond) 7. └─base (local) ``(``) ── Failure ('test-Eunomia.R:81:5'): requireEunomia ───────────────────────────── Expected `con <- duckdb::dbConnect(duckdb::duckdb(), eunomiaDir())` to run without any errors. i Actually got a with text: there is no package called 'duckdb' Backtrace: ▆ 1. ├─withr::with_envvar(...) at test-Eunomia.R:77:3 2. │ └─base::force(code) 3. └─testthat::expect_no_error(...) at test-Eunomia.R:81:5 ── Error ('test-Eunomia.R:82:5'): requireEunomia ─────────────────────────────── Error in `loadNamespace(x)`: there is no package called 'duckdb' Backtrace: ▆ 1. ├─withr::with_envvar(...) at test-Eunomia.R:77:3 2. │ └─base::force(code) 3. └─base::loadNamespace(x) at test-Eunomia.R:82:5 4. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 5. └─base (local) withOneRestart(expr, restarts[[1L]]) 6. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-cohort-reconnect.R:5:3'): cohort codelist attributes are preserved ── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(eunomia_dir())) at test-cohort-reconnect.R:5:3 2. ├─base::loadNamespace(x) 3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 5. │ │ └─base (local) doWithOneRestart(return(expr), restart) 6. │ └─base::stop(cond) 7. └─base (local) ``(``) ── Error ('test-local_cdm.R:41:3'): softValidation is passed correctly ───────── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) at test-local_cdm.R:41:3 2. ├─base::loadNamespace(x) 3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 5. │ │ └─base (local) doWithOneRestart(return(expr), restart) 6. │ └─base::stop(cond) 7. └─base (local) ``(``) ── Error ('test-write_prefix.r:2:3'): write_prefix works with cdm_from_con ───── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir())) at test-write_prefix.r:2:3 2. ├─base::loadNamespace(x) 3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 5. │ │ └─base (local) doWithOneRestart(return(expr), restart) 6. │ └─base::stop(cond) 7. └─base (local) ``(``) [ FAIL 7 | WARN 0 | SKIP 39 | PASS 29 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [7s/6s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE