Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(topr)
  > 
  > test_check("topr")
  [ FAIL 6 | WARN 0 | SKIP 4 | PASS 5 ]
  
  == Skipped tests ===============================================================
  * empty test (4)
  
  == Failed tests ================================================================
  -- Failure ('test-locuszoom.R:2'): locuszoom works -----------------------------
  Expected `locuszoom(R2_CD_UKBB, gene = "IL23R")` to run without any errors.
  i Actually got a <rlang_error>:
    Error in `dplyr::rename_with()`:
    ! `.fn` must return a vector of length 0, not 1.
  -- Failure ('test-manhattan.R:2'): basic manhattan works -----------------------
  `manhattan(CD_UKBB)` threw an unexpected error.
  Message: `.fn` must return a vector of length 0, not 1.
  Class:   rlang_error/error/condition
  Backtrace:
       x
    1. +-testthat::expect_error(manhattan(CD_UKBB), NA) at test-manhattan.R:2:2
    2. | \-testthat:::expect_condition_matching(...)
    3. |   \-testthat:::quasi_capture(...)
    4. |     +-testthat (local) .capture(...)
    5. |     | \-base::withCallingHandlers(...)
    6. |     \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. +-topr::manhattan(CD_UKBB)
    8. | \-topr:::dat_check(df, verbose = verbose)
    9. |   +-... %>% dat_chr_check()
   10. |   \-topr:::dat_column_check_and_set(dat, verbose = verbose, locuszoomplot = locuszoomplot)
   11. |     \-... %>% ...
   12. +-topr:::dat_chr_check(.)
   13. +-dplyr::rename_with(., ~"ALT", matches(c("^alt$"), ignore.case = TRUE))
   14. +-dplyr::rename_with(., ~"REF", matches(c("^ref$"), ignore.case = TRUE))
   15. +-dplyr::rename_with(., ~"BETA", matches(c("^beta$"), ignore.case = TRUE))
   16. +-dplyr::rename_with(...)
   17. +-dplyr::rename_with(...)
   18. +-dplyr::rename_with(...)
   19. +-dplyr::rename_with(...)
   20. \-dplyr:::rename_with.data.frame(., ~"ID", matches(c("^rsid$", "^rsname$", "^snp$"), ignore.case = TRUE))
   21.   \-cli::cli_abort("{.arg .fn} must return a vector of length {length(sel)}, not {length(new)}.")
   22.     \-rlang::abort(...)
  -- Failure ('test-manhattan.R:7'): adcvanced manhattan works -------------------
  Expected `manhattan(CD_UKBB)` to run without any errors.
  i Actually got a <rlang_error>:
    Error in `dplyr::rename_with()`:
    ! `.fn` must return a vector of length 0, not 1.
  -- Failure ('test-regionplot.R:2'): basic regionplot works ---------------------
  `regionplot(CD_UKBB, gene = "IL23R")` threw an unexpected error.
  Message: `.fn` must return a vector of length 0, not 1.
  Class:   rlang_error/error/condition
  Backtrace:
       x
    1. +-testthat::expect_error(regionplot(CD_UKBB, gene = "IL23R"), NA) at test-regionplot.R:2:2
    2. | \-testthat:::expect_condition_matching(...)
    3. |   \-testthat:::quasi_capture(...)
    4. |     +-testthat (local) .capture(...)
    5. |     | \-base::withCallingHandlers(...)
    6. |     \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. +-topr::regionplot(CD_UKBB, gene = "IL23R")
    8. | +-... %>% ...
    9. | \-topr:::dat_check(df, verbose = verbose, locuszoomplot = locuszoomplot)
   10. |   +-... %>% dat_chr_check()
   11. |   \-topr:::dat_column_check_and_set(dat, verbose = verbose, locuszoomplot = locuszoomplot)
   12. |     \-... %>% ...
   13. +-topr:::set_size_shape_alpha(., size, shape, alpha, locuszoomplot = locuszoomplot)
   14. | \-topr:::set_size(df, size, locuszoomplot = locuszoomplot)
   15. +-topr:::set_log10p(., ntop)
   16. +-topr:::dat_chr_check(.)
   17. +-dplyr::rename_with(., ~"ALT", matches(c("^alt$"), ignore.case = TRUE))
   18. +-dplyr::rename_with(., ~"REF", matches(c("^ref$"), ignore.case = TRUE))
   19. +-dplyr::rename_with(., ~"BETA", matches(c("^beta$"), ignore.case = TRUE))
   20. +-dplyr::rename_with(...)
   21. +-dplyr::rename_with(...)
   22. +-dplyr::rename_with(...)
   23. +-dplyr::rename_with(...)
   24. \-dplyr:::rename_with.data.frame(., ~"ID", matches(c("^rsid$", "^rsname$", "^snp$"), ignore.case = TRUE))
   25.   \-cli::cli_abort("{.arg .fn} must return a vector of length {length(sel)}, not {length(new)}.")
   26.     \-rlang::abort(...)
  -- Failure ('test-regionplot.R:6'): advanecd regionplot works ------------------
  Expected `regionplot(CD_UKBB, gene = "IL23R")` to run without any errors.
  i Actually got a <rlang_error>:
    Error in `dplyr::rename_with()`:
    ! `.fn` must return a vector of length 0, not 1.
  -- Error ('test-utils.R:2'): get_lead_snps works -------------------------------
  Error in `dplyr::rename_with(., ~"ID", matches(c("^rsid$", "^rsname$", 
      "^snp$"), ignore.case = TRUE))`: `.fn` must return a vector of length 0, not 1.
  Backtrace:
       x
    1. +-topr::get_lead_snps(CD_UKBB) at test-utils.R:2:2
    2. | \-topr:::dat_check(dat, verbose = verbose)
    3. |   +-... %>% dat_chr_check()
    4. |   \-topr:::dat_column_check_and_set(dat, verbose = verbose, locuszoomplot = locuszoomplot)
    5. |     \-... %>% ...
    6. +-topr:::dat_chr_check(.)
    7. +-dplyr::rename_with(., ~"ALT", matches(c("^alt$"), ignore.case = TRUE))
    8. +-dplyr::rename_with(., ~"REF", matches(c("^ref$"), ignore.case = TRUE))
    9. +-dplyr::rename_with(., ~"BETA", matches(c("^beta$"), ignore.case = TRUE))
   10. +-dplyr::rename_with(...)
   11. +-dplyr::rename_with(...)
   12. +-dplyr::rename_with(...)
   13. +-dplyr::rename_with(...)
   14. \-dplyr:::rename_with.data.frame(., ~"ID", matches(c("^rsid$", "^rsname$", "^snp$"), ignore.case = TRUE))
   15.   \-cli::cli_abort("{.arg .fn} must return a vector of length {length(sel)}, not {length(new)}.")
   16.     \-rlang::abort(...)
  
  [ FAIL 6 | WARN 0 | SKIP 4 | PASS 5 ]
  Error: Test failures
  Execution halted