* using log directory 'd:/RCompile/CRANincoming/R-devel/DrugExposureDiagnostics.Rcheck' * using R Under development (unstable) (2024-11-21 r87360 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'DrugExposureDiagnostics/DESCRIPTION' ... OK * this is package 'DrugExposureDiagnostics' version '1.0.10' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [13s] OK * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'DrugExposureDiagnostics' can be installed ... OK * checking installed package size ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... OK * checking Rd files ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [295s] ERROR Running 'testthat.R' [294s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(DrugExposureDiagnostics) > > test_check("DrugExposureDiagnostics") Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable', target signature 'duckdb_connection#Id'. "duckdb_connection#ANY" would also be valid population after earliestStartDate smaller than sample, sampling ignored `sample_size` casted to character. `sample_size` eliminated from settings as all elements are NA. population after earliestStartDate smaller than sample, sampling ignored i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2024-11-22 08:57:03.830092 v Summary finished, at 2024-11-22 08:57:04.572548 `sample_size` casted to character. `sample_size` eliminated from settings as all elements are NA. population after earliestStartDate smaller than sample, sampling ignored `sample_size` casted to character. `sample_size` eliminated from settings as all elements are NA. i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2024-11-22 08:57:23.253895 v Summary finished, at 2024-11-22 08:57:23.818209 `sample_size` casted to character. `sample_size` eliminated from settings as all elements are NA. i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2024-11-22 08:57:26.635294 v Summary finished, at 2024-11-22 08:57:27.145779 `sample_size` casted to character. `sample_size` eliminated from settings as all elements are NA. Progress: getting descendant concepts of ingredient (1125315) used in database Progress: getting descendant concepts of ingredient Progress: adding drug strength info Progress: limiting to concepts in the db Progress: adding concept names Overall time taken: 0 minutes and 1 seconds Time taken: 0 minutes and 1 seconds Progress: getting drug strength for ingredient Time taken: 0 minutes and 0 seconds Progress: getting drug records for ingredient Time taken: 0 minutes and 0 seconds Progress: get concepts used Time taken: 0 minutes and 0 seconds Progress: sampling drug records population after earliestStartDate smaller than sample, sampling ignored Time taken: 0 minutes and 0 seconds Progress: check drugsMissing Time taken: 0 minutes and 2 seconds Progress: check ExposureDuration Time taken: 0 minutes and 0 seconds Progress: check drugQuantity Time taken: 0 minutes and 0 seconds Finished population after earliestStartDate smaller than sample, sampling ignored i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2024-11-22 08:58:09.531237 v Summary finished, at 2024-11-22 08:58:10.424768 `sample_size` casted to character. `sample_size` eliminated from settings as all elements are NA. population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2024-11-22 08:59:07.133349 v Summary finished, at 2024-11-22 08:59:07.650012 `sample_size` casted to character. `sample_size` eliminated from settings as all elements are NA. population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored i The following estimates will be computed: * daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2024-11-22 09:00:28.627607 v Summary finished, at 2024-11-22 09:00:29.192284 `sample_size` casted to character. `sample_size` eliminated from settings as all elements are NA. population after earliestStartDate smaller than sample, sampling ignored `result_type`, `package_name`, and `package_version` moved to settings. population after earliestStartDate smaller than sample, sampling ignored population after earliestStartDate smaller than sample, sampling ignored `result_type`, `package_name`, and `package_version` moved to settings. Time taken: 0 minutes and 0 seconds testMessage [ FAIL 2 | WARN 119 | SKIP 2 | PASS 479 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-shiny.R:2:3' • Sys.getenv("TESTDB_USER") == "" is TRUE (1): 'test-SyntheaSqlServer.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-runBenchmark.R:28:3'): runBenchmarkExecuteSingleIngredient output contents, and format ── `expectedSettings` (`actual`) not equal to omopgenerics::settings(res) (`expected`). `actual` is length 4 `expected` is length 8 names(actual) | names(expected) [2] "result_type" | "result_type" [2] [3] "package_name" | "package_name" [3] [4] "package_version" | "package_version" [4] - "group" [5] - "strata" [6] - "additional" [7] - "min_cell_count" [8] `actual$group` is absent `expected$group` is a character vector ('') `actual$strata` is absent `expected$strata` is a character vector ('') `actual$additional` is absent `expected$additional` is a character vector ('') `actual$min_cell_count` is absent `expected$min_cell_count` is a character vector ('0') ── Error ('test-runBenchmark.R:45:3'): runBenchmarkExecuteSingleIngredient duplicate ingredients ── Error in `omopgenerics::newSummarisedResult(.)`: Each `result_id` must be unique and contain a unique set of settings. Backtrace: ▆ 1. ├─DrugExposureDiagnostics::runBenchmarkExecuteSingleIngredient(...) at test-runBenchmark.R:45:3 2. │ └─... %>% omopgenerics::newSummarisedResult() 3. └─omopgenerics::newSummarisedResult(.) 4. └─omopgenerics:::validateSummarisedResult(x) 5. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call) 6. └─cli::cli_abort(...) 7. └─rlang::abort(...) [ FAIL 2 | WARN 119 | SKIP 2 | PASS 479 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [113s] OK * checking PDF version of manual ... [22s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR