Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(UKB.COVID19)
  > 
  > test_check("UKB.COVID19")
  [1] "965 participants got tested until 2021-04-05."
  [1] "218 participants got positive test results until 2021-04-05."
  [1] "There are 21 deaths with COVID-19. 20 of them primary death cause is COVID-19."
  [1] "50 patients admitted to hospital were diagnosed as COVID-19 until 2021-04-05."
  [1] "32 patients' primary diagnosis is COVID-19."
  [1] "1 patients in hospitalization with COVID-19 diagnosis but show negative in the result file. Modified their test results."
  [1] "There are 219 COVID-19 patients identified. 32 individuals are admitted to hospital. 3 had been in ICU. 1 had been in advanced ICU."
  [1] "965 participants got tested until 2021-04-05."
  [1] "218 participants got positive test results until 2021-04-05."
  [1] "There are 21 deaths with COVID-19. 20 of them primary death cause is COVID-19."
  [1] "50 patients admitted to hospital were diagnosed as COVID-19 until 2021-04-05."
  [1] "32 patients' primary diagnosis is COVID-19."
  [1] "1 patients in hospitalization with COVID-19 diagnosis but show negative in the result file. Modified their test results."
  [1] "There are 219 COVID-19 patients identified. 32 individuals are admitted to hospital. 3 had been in ICU. 1 had been in advanced ICU."
  [1] "965 participants got tested until 2021-04-05."
  [1] "218 participants got positive test results until 2021-04-05."
  [1] "There are 21 deaths with COVID-19. 20 of them primary death cause is COVID-19."
  [1] "50 patients admitted to hospital were diagnosed as COVID-19 until 2021-04-05."
  [1] "32 patients' primary diagnosis is COVID-19."
  [1] "1 patients in hospitalization with COVID-19 diagnosis but show negative in the result file. Modified their test results."
  [1] "There are 219 COVID-19 patients identified. 32 individuals are admitted to hospital. 3 had been in ICU. 1 had been in advanced ICU."
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_asso_test.R:9:3'): Covariate association test ──────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─UKB.COVID19::makePhenotypes(...) at test_asso_test.R:9:2
    2.   ├─dplyr::full_join(pheno, ids, by = "ID")
    3.   └─dplyr:::full_join.data.frame(pheno, ids, by = "ID")
    4.     └─dplyr:::join_mutate(...)
    5.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    6.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.             ├─base::withCallingHandlers(...)
   10.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test_comorbidity_asso.R:9:3'): Comorbildity association test ────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─UKB.COVID19::makePhenotypes(...) at test_comorbidity_asso.R:9:2
    2.   ├─dplyr::full_join(pheno, ids, by = "ID")
    3.   └─dplyr:::full_join.data.frame(pheno, ids, by = "ID")
    4.     └─dplyr:::join_mutate(...)
    5.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    6.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.             ├─base::withCallingHandlers(...)
   10.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test_makePhenotypes.R:4:3'): Generate phenotypes ────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─UKB.COVID19::makePhenotypes(...) at test_makePhenotypes.R:4:2
    2.   ├─dplyr::full_join(pheno, ids, by = "ID")
    3.   └─dplyr:::full_join.data.frame(pheno, ids, by = "ID")
    4.     └─dplyr:::join_mutate(...)
    5.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    6.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.             ├─base::withCallingHandlers(...)
   10.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted