Running ‘testthat.R’ [14s/38s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(PopPsiSeqR)
  > 
  > test_check("PopPsiSeqR")
  Saving _problems/test-io-6.R
  Saving _problems/test-io-8.R
  Saving _problems/test-io-17.R
  Saving _problems/test-io-22.R
  Saving _problems/test-io-32.R
  Saving _problems/test-io-33.R
  Saving _problems/test-io-35.R
  Saving _problems/test-plot-26.R
  Saving _problems/test-plot-27.R
  [ FAIL 9 | WARN 3 | SKIP 1 | PASS 3 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • {rtracklayer} is not installed. (1): 'test-frqshft.R:8:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-io.R:6:3'): merged allele frequencies can be loaded ──────────
  Expected `frequencies.bg <- import.freqtbl(merged_frequencies.filename)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rtracklayer'
  ── Error ('test-io.R:8:3'): merged allele frequencies can be loaded ────────────
  Error in `eval(code, test_env)`: object 'frequencies.bg' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-io.R:8:3
   2. │ └─testthat::quasi_label(enquo(expected), expected.label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─utils::head(frequencies.bg, n = 1)
  ── Failure ('test-io.R:17:3'): shifted frequencies can be saved ────────────────
  Expected `PopPsiSeqR::export.freqshft(shift2save, shift_frequencies.filename)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rtracklayer'
  ── Failure ('test-io.R:22:3'): shifted frequencies can be saved ────────────────
  Expected `correct_hashes` to contain all values in `tools::md5sum(shift_frequencies.filename)[[1]]`.
  Actual: "e37492c5b6b3396449ec70e2ae27862a", "8f3feb89facba1da64e34533b8a0b618"
  Expected: NA
  Missing: NA
  ── Failure ('test-io.R:32:3'): windowed shifts can be loaded ───────────────────
  Expected `windowed_shifts.bg <- import.smvshift(windowed_shifts.filename)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'rtracklayer'
  ── Failure ('test-io.R:33:3'): windowed shifts can be loaded ───────────────────
  Expected `windowed_shifts.bg <- windowed_shifts.bg %>% as.data.frame()` not to throw any errors.
  Actually got a <simpleError> with message:
    object 'windowed_shifts.bg' not found
  ── Error ('test-io.R:35:3'): windowed shifts can be loaded ─────────────────────
  Error in `eval(code, test_env)`: object 'windowed_shifts.bg' not found
  ── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
  Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'ggbio'
  ── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
  Error in `eval(code, test_env)`: object 'mock.plot' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─ggplot2::is.ggplot(mock.plot@ggplot)
   5.   └─ggplot2::is_ggplot(x)
   6.     └─S7::S7_inherits(x, class_ggplot)
  
  [ FAIL 9 | WARN 3 | SKIP 1 | PASS 3 ]
  Error:
  ! Test failures.
  Execution halted