Running 'testthat.R' [242s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(epitopR)
  > 
  > test_check("epitopR")
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 0 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-core_mut.R:10:3): test core_mut  ────────────────────────────────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `mutate(., antigen = str_remove(gsub(".*/", "", id), paste0("_", 
      nm_method, ".txt")))`: Problem while computing `antigen = str_remove(gsub(".*/", "", id), paste0("_", nm_method, ".txt"))`.
  Caused by error in `as.character()`:
  ! cannot coerce type 'closure' to vector of type 'character'
  Backtrace:
       ▆
    1. ├─epitopR::mhcII_hu(...) at test-core_mut.R:10:2
    2. │ └─epitopR:::comb_pred_tbl(...)
    3. │   └─... %>% ...
    4. ├─dplyr::filter(...)
    5. ├─dplyr::mutate(...)
    6. ├─dplyr::mutate(...)
    7. ├─dplyr::filter(., ic50 != "-")
    8. ├─dplyr::select(., -c(id, seq_num))
    9. ├─dplyr::mutate(...)
   10. ├─dplyr:::mutate.data.frame(., antigen = str_remove(gsub(".*/", "", id), paste0("_", nm_method, ".txt")))
   11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
   12. │   ├─base::withCallingHandlers(...)
   13. │   └─mask$eval_all_mutate(quo)
   14. ├─stringr::str_remove(...)
   15. │ └─stringr::str_replace(string, pattern, "")
   16. │   └─stringi::stri_replace_first_regex(...)
   17. ├─base::gsub(".*/", "", id)
   18. └─base::.handleSimpleError(...)
   19.   └─dplyr (local) h(simpleError(msg, call))
   20.     └─rlang::abort(...)
  ── Error (test-mhcII_hu.R:2:3): test mhcII_hu prediction works ─────────────────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `mutate(., antigen = str_remove(gsub(".*/", "", id), paste0("_", 
      nm_method, ".txt")))`: Problem while computing `antigen = str_remove(gsub(".*/", "", id), paste0("_", nm_method, ".txt"))`.
  Caused by error in `as.character()`:
  ! cannot coerce type 'closure' to vector of type 'character'
  Backtrace:
       ▆
    1. ├─epitopR::mhcII_hu(...) at test-mhcII_hu.R:2:2
    2. │ └─epitopR:::comb_pred_tbl(...)
    3. │   └─... %>% ...
    4. ├─dplyr::filter(...)
    5. ├─dplyr::mutate(...)
    6. ├─dplyr::mutate(...)
    7. ├─dplyr::filter(., ic50 != "-")
    8. ├─dplyr::select(., -c(id, seq_num))
    9. ├─dplyr::mutate(...)
   10. ├─dplyr:::mutate.data.frame(., antigen = str_remove(gsub(".*/", "", id), paste0("_", nm_method, ".txt")))
   11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
   12. │   ├─base::withCallingHandlers(...)
   13. │   └─mask$eval_all_mutate(quo)
   14. ├─stringr::str_remove(...)
   15. │ └─stringr::str_replace(string, pattern, "")
   16. │   └─stringi::stri_replace_first_regex(...)
   17. ├─base::gsub(".*/", "", id)
   18. └─base::.handleSimpleError(...)
   19.   └─dplyr (local) h(simpleError(msg, call))
   20.     └─rlang::abort(...)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 0 ]
  Error: Test failures
  Execution halted