• using R Under development (unstable) (2026-02-03 r89373)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.8     flang version 21.1.8
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-02-03 12:34:13Z
• using option ‘--no-stop-on-test-error’
• checking for file ‘DrugExposureDiagnostics/DESCRIPTION’ ... OK
• this is package ‘DrugExposureDiagnostics’ version ‘1.1.5’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘pryr’
• 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 ‘DrugExposureDiagnostics’ can be installed ... [15s/38s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... 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 ... [14s/36s] 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 ... [12m/16m] ERROR   Running ‘testthat.R’ [12m/16m] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(DrugExposureDiagnostics)   >   > test_check("DrugExposureDiagnostics")      Attaching package: 'plotly'      The following object is masked from 'package:ggplot2':          last_plot      The following object is masked from 'package:stats':          filter      The following object is masked from 'package:graphics':          layout         Attaching package: 'dplyr'      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      population after earliestStartDate smaller than sample, sampling ignored   i The following estimates will be calculated:   * 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 2026-02-03 12:40:40.217778   v Summary finished, at 2026-02-03 12:40:42.318233   population after earliestStartDate smaller than sample, sampling ignored   population after earliestStartDate smaller than sample, sampling ignored   i The following estimates will be calculated:   * 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 2026-02-03 12:42:35.772393   ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 12...   ==============================> 4/4 group-strata combinations @ 2026-02-03 12...   v Summary finished, at 2026-02-03 12:42:39.883098   population after earliestStartDate smaller than sample, sampling ignored   Saving _problems/test-SummariseChecks-213.R   i The following estimates will be calculated:   * 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 2026-02-03 12:43:38.913646   ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 12...   ==============================> 4/4 group-strata combinations @ 2026-02-03 12...   v Summary finished, at 2026-02-03 12:43:41.32061   i The following estimates will be calculated:   * 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 2026-02-03 12:43:49.715222   ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 12...   ==============================> 4/4 group-strata combinations @ 2026-02-03 12...   v Summary finished, at 2026-02-03 12:43:52.385411   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 3 seconds   Time taken: 0 minutes and 3 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 4 seconds   Progress: check ExposureDuration   Time taken: 0 minutes and 0 seconds   Progress: check drugQuantity   Time taken: 0 minutes and 0 seconds   Finished   i The following estimates will be calculated:   * 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 2026-02-03 12:46:13.210137   ===============>--------------- 2/4 group-strata combinations @ 2026-02-03 12...   ==============================> 4/4 group-strata combinations @ 2026-02-03 12...   v Summary finished, at 2026-02-03 12:46:15.91536   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 calculated:   * 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 2026-02-03 12:49:13.89034   v Summary finished, at 2026-02-03 12:49:15.686697   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   Saving _problems/test-executeChecks-373.R   i The following estimates will be calculated:   * 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 2026-02-03 12:52:31.182264   v Summary finished, at 2026-02-03 12:52:32.96847   Time taken: 0 minutes and 0 seconds   testMessage   [ FAIL 2 | WARN 122 | SKIP 5 | PASS 483 ]      ══ Skipped tests (5) ═══════════════════════════════════════════════════════════   • Skipping (1): 'test-shiny.R:2:3'   • Sys.getenv("TESTDB_USER2222") == "" is TRUE (1):     'test-SyntheaSqlServer.R:5:3'   • does not work with latest omopgenerics (3): 'test-runBenchmark.R:2:3',     'test-runBenchmark.R:36:3', 'test-runBenchmark.R:47:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-SummariseChecks.R:213:3'): summariseChecks partial inputs with combination of not empty and empty ingredient: summary of missing and quantity and dose ──   <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>   Error in `bind_rows(...)`: Can't combine `..1$dose_form` <character> and `..2$dose_form` <integer>.   Backtrace:        ▆     1. ├─DrugExposureDiagnostics::executeChecks(...) at test-SummariseChecks.R:213:3     2. │ ├─base::do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList)))     3. │ └─base (local) `<fn>`(f = `<fn>`, `<named list>`, `<named list>`)     4. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)     5. │ └─base (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])     6. │ └─dplyr (local) rbind(deparse.level, ...)     7. │ └─dplyr::bind_rows(...)     8. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())     9. │ └─vctrs (local) `<fn>`()    10. │ └─vctrs (local) vec_ptype2.rowwise_df.rowwise_df(...)    11. │ └─vctrs:::rww_ptype2(x, y, ...)    12. │ ├─dplyr::rowwise(df_ptype2(x, y, ...))    13. │ └─vctrs::df_ptype2(x, y, ...)    14. └─vctrs (local) `<fn>`()    15. └─vctrs::vec_default_ptype2(...)    16. ├─base::withRestarts(...)    17. │ └─base (local) withOneRestart(expr, restarts[[1L]])    18. │ └─base (local) doWithOneRestart(return(expr), restart)    19. └─vctrs::stop_incompatible_type(...)    20. └─vctrs:::stop_incompatible(...)    21. └─vctrs:::stop_vctrs(...)    22. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)   ── Error ('test-executeChecks.R:370:3'): results from multiple ingredients should be joined also if there is one in between that doesn't exist ──   <vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>   Error in `bind_rows(...)`: Can't combine `..1$dose_form` <character> and `..2$dose_form` <integer>.   Backtrace:        ▆     1. ├─DrugExposureDiagnostics (local) executeChecksMock(...) at test-executeChecks.R:370:3     2. │ └─DrugExposureDiagnostics::executeChecks(...) at test-executeChecks.R:14:3     3. │ ├─base::do.call(Map, c(f = rbind, Filter(Negate(is.null), resultList)))     4. │ └─base (local) `<fn>`(f = `<fn>`, `<named list>`, `<named list>`, `<named list>`)     5. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)     6. │ └─base (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]])     7. │ └─dplyr (local) rbind(deparse.level, ...)     8. │ └─dplyr::bind_rows(...)     9. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env())    10. │ └─vctrs (local) `<fn>`()    11. │ └─vctrs (local) vec_ptype2.rowwise_df.rowwise_df(...)    12. │ └─vctrs:::rww_ptype2(x, y, ...)    13. │ ├─dplyr::rowwise(df_ptype2(x, y, ...))    14. │ └─vctrs::df_ptype2(x, y, ...)    15. └─vctrs (local) `<fn>`()    16. └─vctrs::vec_default_ptype2(...)    17. ├─base::withRestarts(...)    18. │ └─base (local) withOneRestart(expr, restarts[[1L]])    19. │ └─base (local) doWithOneRestart(return(expr), restart)    20. └─vctrs::stop_incompatible_type(...)    21. └─vctrs:::stop_incompatible(...)    22. └─vctrs:::stop_vctrs(...)    23. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)      [ FAIL 2 | WARN 122 | SKIP 5 | PASS 483 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [295s/415s] OK
• checking PDF version of manual ... [8s/11s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR