* using log directory ‘/srv/hornik/tmp/CRAN/DrugUtilisation.Rcheck’
* using R Under development (unstable) (2024-02-08 r85876)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘DrugUtilisation/DESCRIPTION’ ... OK
* this is package ‘DrugUtilisation’ version ‘0.5.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/6s] Note_to_CRAN_maintainers
Maintainer: ‘Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>’
* 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 serialization versions ... OK
* checking whether package ‘DrugUtilisation’ can be installed ... [4s/4s] 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 R 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 ... [6s/6s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [171s/115s] ERROR
  Running ‘testthat.R’ [170s/115s]
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(DrugUtilisation)
  > 
  > test_check("DrugUtilisation")
  Starting 2 test processes
  [ FAIL 4 | WARN 6 | SKIP 19 | PASS 46 ]
  
  ══ Skipped tests (19) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-benchmarkDUS.R:2:3', 'test-dailyDose.R:2:3',
    'test-generateDrugUtilisationCohortSet.R:48:3',
    'test-generateDrugUtilisationCohortSet.R:147:3',
    'test-generateDrugUtilisationCohortSet.R:203:3',
    'test-generateDrugUtilisationCohortSet.R:253:3',
    'test-generateDrugUtilisationCohortSet.R:349:3', 'test-indication.R:3:3',
    'test-indication.R:185:3', 'test-indication.R:339:3',
    'test-indication.R:464:3', 'test-drugUse.R:2:3', 'test-drugUse.R:40:3',
    'test-drugUse.R:254:3', 'test-drugUse.R:455:3', 'test-drugUse.R:597:3',
    'test-drugUse.R:847:3', 'test-drugUse.R:868:3', 'test-drugUse.R:914:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-indication.R:598:3'): summariseIndication ──────────────────────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(PatientProfiles::summariseResult(table = cohort, 
      group = list("cohort_name"), includeOverallGroup = FALSE, 
      includeOverallStrata = TRUE, strata = strata, variables = indicationVariables, 
      functions = c("count", "percentage")) %>% PatientProfiles::addCdmName(cdm = cdm), 
      variable_level = dplyr::if_else(substr(.data$variable_name, 
          1, 15) == "indication_gap_", lapply(strsplit(.data$variable_name, 
          "_"), function(x) {
          if (length(x) > 3) {
              x <- paste0(x[-c(1:3)], collapse = "_")
              x <- paste0(toupper(substr(x, 1, 1)), substr(x, 2, 
                  nchar(x)))
          }
          else {
              x <- as.character(NA)
          }
          return(x)
      }) %>% unlist(), as.character(NA)), variable_name = dplyr::if_else(substr(.data$variable_name, 
          1, 15) == "indication_gap_", lapply(strsplit(.data$variable_name, 
          "_"), function(x) {
          x <- paste0(x[1:min(3, length(x))], collapse = "_")
          x <- indicationColumnName(x)
      }) %>% unlist(), .data$variable_name), result_type = "summarised_indication", 
      package_name = "DrugUtilisation", package_version = as.character(utils::packageVersion("Drugutilisation")))`: i In argument: `package_version = as.character(utils::packageVersion("Drugutilisation"))`.
  Caused by error in `utils::packageVersion()`:
  ! there is no package called 'Drugutilisation'
  Backtrace:
       ▆
    1. ├─DrugUtilisation::summariseIndication(res) at test-indication.R:598:3
    2. │ ├─omopgenerics::suppress(...)
    3. │ ├─omopgenerics::newSummarisedResult(...)
    4. │ │ └─omopgenerics:::assertClass(x, "data.frame")
    5. │ │   ├─base::paste0(...)
    6. │ │   └─base::paste0(base::class(x), collapse = ", ")
    7. │ ├─dplyr::mutate(...)
    8. │ └─dplyr:::mutate.data.frame(...)
    9. │   └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
   10. │     ├─base::withCallingHandlers(...)
   11. │     └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
   12. │       └─mask$eval_all_mutate(quo)
   13. │         └─dplyr (local) eval()
   14. ├─utils::packageVersion("Drugutilisation")
   15. │ └─base::stop(packageNotFoundError(pkg, lib.loc, sys.call()))
   16. └─dplyr (local) `<fn>`(`<pckgNtFE>`)
   17.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  ── Error ('test-drugUse.R:984:5'): check all estimates ─────────────────────────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(., cdm_name = dplyr::coalesce(omopgenerics::cdmName(cdm), 
      as.character(NA)), result_type = "summarised_drug_use", package_name = "DrugUtilisation", 
      package_version = as.character(utils::packageVersion("Drugutilisation")))`: i In argument: `package_version = as.character(utils::packageVersion("Drugutilisation"))`.
  Caused by error in `utils::packageVersion()`:
  ! there is no package called 'Drugutilisation'
  Backtrace:
       ▆
    1. ├─... %>% dplyr::filter(.data$group_name == "cohort_name") at test-drugUse.R:984:5
    2. ├─dplyr::filter(., .data$group_name == "cohort_name")
    3. ├─DrugUtilisation::summariseDrugUse(cdm[["dose_table"]], drugUseEstimates = all_estimates[k])
    4. │ ├─omopgenerics::suppress(...)
    5. │ ├─omopgenerics::newSummarisedResult(...)
    6. │ │ └─omopgenerics:::assertClass(x, "data.frame")
    7. │ │   ├─base::paste0(...)
    8. │ │   └─base::paste0(base::class(x), collapse = ", ")
    9. │ └─... %>% ...
   10. ├─dplyr::mutate(...)
   11. ├─dplyr:::mutate.data.frame(...)
   12. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
   13. │   ├─base::withCallingHandlers(...)
   14. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
   15. │     └─mask$eval_all_mutate(quo)
   16. │       └─dplyr (local) eval()
   17. ├─utils::packageVersion("Drugutilisation")
   18. │ └─base::stop(packageNotFoundError(pkg, lib.loc, sys.call()))
   19. └─dplyr (local) `<fn>`(`<pckgNtFE>`)
   20.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  ── Failure ('test-drugUse.R:1022:3'): check all variables ──────────────────────
  Expected `.` to run without any errors.
  i Actually got a <dplyr:::mutate_error> with text:
    i In argument: `package_version = as.character(utils::packageVersion("Drugutilisation"))`.
    Caused by error in `utils::packageVersion()`:
    ! there is no package called 'Drugutilisation'
  Backtrace:
      ▆
   1. ├─... %>% expect_no_error() at test-drugUse.R:1022:3
   2. └─testthat::expect_no_error(.)
  ── Failure ('test-drugUse.R:1026:3'): check all variables ──────────────────────
  all(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 4 | WARN 6 | SKIP 19 | PASS 46 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [228s/198s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘addDrugUse.Rmd’ using rmarkdown

Quitting from lines 351-359 [unnamed-chunk-21] (addDrugUse.Rmd)
Error: processing vignette 'addDrugUse.Rmd' failed with diagnostics:
ℹ In argument: `package_version =
  as.character(utils::packageVersion("Drugutilisation"))`.
Caused by error in `utils::packageVersion()`:
! there is no package called 'Drugutilisation'
--- failed re-building ‘addDrugUse.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
--- re-building ‘addIndications-example.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.

Quitting from lines 120-131 [unnamed-chunk-6] (addIndications-example.Rmd)
Error: processing vignette 'addIndications-example.Rmd' failed with diagnostics:
ℹ In argument: `package_version =
  as.character(utils::packageVersion("Drugutilisation"))`.
Caused by error in `utils::packageVersion()`:
! there is no package called 'Drugutilisation'
--- failed re-building ‘addIndications-example.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
--- re-building ‘introCreateCohort.Rmd’ using rmarkdown
--- finished re-building ‘introCreateCohort.Rmd’

--- re-building ‘routePatternDose.Rmd’ using rmarkdown
--- finished re-building ‘routePatternDose.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
Warning: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
SUMMARY: processing the following files failed:
  ‘addDrugUse.Rmd’ ‘addIndications-example.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs