• using R Under development (unstable) (2023-03-22 r84023)
• using platform: x86_64-pc-linux-gnu (64-bit)
• R was compiled by
      Debian clang version 15.0.6
      GNU Fortran (Debian 12.2.0-14) 12.2.0
• running under: Debian GNU/Linux bookworm/sid
• using session charset: UTF-8
• checking for file ‘epitopR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘epitopR’ version ‘0.1.2’
• package encoding: UTF-8
• 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 whether package ‘epitopR’ can be installed ... 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 ... [8s/9s] OK
• checking whether the package can be loaded with stated dependencies ... [7s/8s] OK
• checking whether the package can be unloaded cleanly ... [6s/7s] OK
• checking whether the namespace can be loaded with stated dependencies ... [6s/7s] OK
• checking whether the namespace can be unloaded cleanly ... [7s/8s] OK
• checking loading without being on the library search path ... [7s/8s] 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 ... [34s/40s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [8s/10s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [234s/274s] ERROR
    Running ‘testthat.R’ [233s/273s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(epitopR)
    >
    > test_check("epitopR")
    [ FAIL 1 | WARN 30 | SKIP 2 | PASS 0 ]
    
    ══ Skipped tests ═══════════════════════════════════════════════════════════════
    • empty test (2)
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-mhcII_hu.R:2:3'): test mhcII_hu prediction works ───────────────
    <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
    Error in `select(., -c(id, seq_num))`: Can't subset columns that don't exist.
    x Column `id` doesn't exist.
    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:::select.data.frame(., -c(id, seq_num))
     10. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
     11. │ └─tidyselect:::eval_select_impl(...)
     12. │ ├─tidyselect:::with_subscript_errors(...)
     13. │ │ └─rlang::try_fetch(...)
     14. │ │ └─base::withCallingHandlers(...)
     15. │ └─tidyselect:::vars_select_eval(...)
     16. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
     17. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
     18. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
     19. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
     20. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
     21. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
     22. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
     23. │ └─tidyselect:::as_indices_sel_impl(...)
     24. │ └─tidyselect:::as_indices_impl(...)
     25. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
     26. │ └─vctrs::vec_as_location(...)
     27. └─vctrs (local) `<fn>`()
     28. └─vctrs:::stop_subscript_oob(...)
     29. └─vctrs:::stop_subscript(...)
     30. └─rlang::abort(...)
    
    [ FAIL 1 | WARN 30 | SKIP 2 | PASS 0 ]
    Error: Test failures
    Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [19s/52s] OK
• checking PDF version of manual ... [5s/8s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR