Running ‘testthat.R’ [27s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("prewas")
  Loading required package: prewas
  [1] "Start building tree"
  optimize edge weights:  -2422.38 --> -2416.99 
  optimize base frequencies:  -2416.99 --> -2415.352 
  optimize rate matrix:  -2415.352 --> -2413.974 
  optimize edge weights:  -2413.974 --> -2413.97 
  optimize topology:  -2413.97 --> -2413.97  NNI moves:  0 
  optimize topology:  -2661.917 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  1 , best pscore so far: -2413.97042504321"
  optimize topology:  -2538.254 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  2 , best pscore so far: -2413.97042504321"
  optimize topology:  -2494.638 --> -2413.97  NNI moves:  3 
  [1] "Ratchet iteration  3 , best pscore so far: -2413.97042504321"
  optimize topology:  -2594.497 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  4 , best pscore so far: -2413.97042504321"
  optimize topology:  -2567.5 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  5 , best pscore so far: -2413.97042504321"
  optimize topology:  -2662.81 --> -2413.97  NNI moves:  8 
  [1] "Ratchet iteration  6 , best pscore so far: -2413.97042504321"
  optimize topology:  -2572.781 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  7 , best pscore so far: -2413.97042504321"
  optimize topology:  -2553.716 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  8 , best pscore so far: -2413.97042504321"
  optimize topology:  -2673.058 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  9 , best pscore so far: -2413.97042504321"
  optimize topology:  -2625.107 --> -2413.97  NNI moves:  6 
  [1] "Ratchet iteration  10 , best pscore so far: -2413.97042504321"
  optimize topology:  -2581.016 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  11 , best pscore so far: -2413.97042504321"
  optimize topology:  -2657.016 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  12 , best pscore so far: -2413.97042504321"
  optimize topology:  -2591.68 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  13 , best pscore so far: -2413.97042504321"
  optimize topology:  -2506.7 --> -2413.97  NNI moves:  4 
  [1] "Ratchet iteration  14 , best pscore so far: -2413.97042504321"
  optimize topology:  -2534.947 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  15 , best pscore so far: -2413.97042504321"
  optimize topology:  -2456.814 --> -2413.97  NNI moves:  2 
  [1] "Ratchet iteration  16 , best pscore so far: -2413.97042504321"
  optimize topology:  -2524.705 --> -2413.97  NNI moves:  4 
  [1] "Ratchet iteration  17 , best pscore so far: -2413.97042504321"
  optimize topology:  -2551.812 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  18 , best pscore so far: -2413.97042504321"
  optimize topology:  -2604.265 --> -2413.97  NNI moves:  6 
  [1] "Ratchet iteration  19 , best pscore so far: -2413.97042504321"
  optimize topology:  -2577.085 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  20 , best pscore so far: -2413.97042504321"
  optimize topology:  -2760.734 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  21 , best pscore so far: -2413.97042504321"
  optimize topology:  -2563.341 --> -2413.97  NNI moves:  4 
  [1] "Ratchet iteration  22 , best pscore so far: -2413.97042504321"
  optimize topology:  -2710.596 --> -2413.97  NNI moves:  6 
  [1] "Ratchet iteration  23 , best pscore so far: -2413.97042504321"
  optimize topology:  -2580.238 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  24 , best pscore so far: -2413.97042504321"
  optimize topology:  -2527.646 --> -2413.97  NNI moves:  4 
  [1] "Ratchet iteration  25 , best pscore so far: -2413.97042504321"
  optimize topology:  -2532.136 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  26 , best pscore so far: -2413.97042504321"
  optimize topology:  -2688.996 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  27 , best pscore so far: -2413.97042504321"
  optimize topology:  -2483.879 --> -2413.97  NNI moves:  3 
  [1] "Ratchet iteration  28 , best pscore so far: -2413.97042504321"
  optimize topology:  -2700.534 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  29 , best pscore so far: -2413.97042504321"
  optimize topology:  -2610.073 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  30 , best pscore so far: -2413.97042504321"
  optimize topology:  -2534.905 --> -2413.97  NNI moves:  4 
  [1] "Ratchet iteration  31 , best pscore so far: -2413.97042504321"
  optimize topology:  -2672.915 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  32 , best pscore so far: -2413.97042504321"
  optimize topology:  -2608.751 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  33 , best pscore so far: -2413.97042504321"
  optimize topology:  -2764.32 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  34 , best pscore so far: -2413.97042504321"
  optimize topology:  -2545.965 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  35 , best pscore so far: -2413.97042504321"
  optimize topology:  -2544.794 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  36 , best pscore so far: -2413.97042504321"
  optimize topology:  -2591.631 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  37 , best pscore so far: -2413.97042504321"
  optimize topology:  -2523.633 --> -2413.97  NNI moves:  4 
  [1] "Ratchet iteration  38 , best pscore so far: -2413.97042504321"
  optimize topology:  -2566.529 --> -2413.97  NNI moves:  4 
  [1] "Ratchet iteration  39 , best pscore so far: -2413.97042504321"
  optimize topology:  -2650.749 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  40 , best pscore so far: -2413.97042504321"
  optimize topology:  -2601.235 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  41 , best pscore so far: -2413.97042504321"
  optimize topology:  -2659.268 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  42 , best pscore so far: -2413.97042504321"
  optimize topology:  -2593.453 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  43 , best pscore so far: -2413.97042504321"
  optimize topology:  -2743.319 --> -2413.97  NNI moves:  8 
  [1] "Ratchet iteration  44 , best pscore so far: -2413.97042504321"
  optimize topology:  -2581.982 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  45 , best pscore so far: -2413.97042504321"
  optimize topology:  -2620.784 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  46 , best pscore so far: -2413.97042504321"
  optimize topology:  -2495.05 --> -2413.97  NNI moves:  3 
  [1] "Ratchet iteration  47 , best pscore so far: -2413.97042504321"
  optimize topology:  -2699.065 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  48 , best pscore so far: -2413.97042504321"
  optimize topology:  -2653.956 --> -2413.97  NNI moves:  7 
  [1] "Ratchet iteration  49 , best pscore so far: -2413.97042504321"
  optimize topology:  -2611.661 --> -2413.97  NNI moves:  5 
  [1] "Ratchet iteration  50 , best pscore so far: -2413.97042504321"
  optimize base frequencies:  -2413.97 --> -2413.741 
  optimize rate matrix:  -2413.741 --> -2413.699 
  optimize edge weights:  -2413.699 --> -2413.699 
  optimize topology:  -2413.699 --> -2413.699  NNI moves:  0 
  optimize base frequencies:  -2413.699 --> -2413.692 
  optimize rate matrix:  -2413.692 --> -2413.691 
  optimize edge weights:  -2413.691 --> -2413.691 
  optimize base frequencies:  -2413.691 --> -2413.691 
  optimize rate matrix:  -2413.691 --> -2413.691 
  optimize edge weights:  -2413.691 --> -2413.691 
  optimize base frequencies:  -2413.691 --> -2413.691 
  optimize rate matrix:  -2413.691 --> -2413.691 
  optimize edge weights:  -2413.691 --> -2413.691 
  optimize base frequencies:  -2413.691 --> -2413.691 
  optimize rate matrix:  -2413.691 --> -2413.691 
  optimize edge weights:  -2413.691 --> -2413.691 
  [1] "Finished building tree"
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 312 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-prewas.R:73'): prewas() gives a warning when given an outgroup not found in the tree ──
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-prewas.R:73:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─prewas::prewas(dna = prewas::vcf, tree = prewas::tree, outgroup = "foo")
    7.   └─prewas:::get_ancestral_alleles(tree, allele_mat_only_var)
    8.     └─future::plan(future::multiprocess)
    9.       └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   10.         └─future (local) warn_about_multiprocess(newStack)
   11.           └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   12.             └─base (local) dfcn(msg = msg, package = .packageName)
  ── Error ('test-reference_alleles.R:50'): get_ancestral_alleles behaves as expected when given valid inputs ──
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
      ▆
   1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat$variant_only_dna_mat) at test-reference_alleles.R:50:2
   2.   └─future::plan(future::multiprocess)
   3.     └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   4.       └─future (local) warn_about_multiprocess(newStack)
   5.         └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   6.           └─base (local) dfcn(msg = msg, package = .packageName)
  ── Error ('test-reference_alleles.R:89'): remove_unknown_alleles correctly removes Ns when given valid input ──
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
      ▆
   1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
   2.   └─future::plan(future::multiprocess)
   3.     └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   4.       └─future (local) warn_about_multiprocess(newStack)
   5.         └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   6.           └─base (local) dfcn(msg = msg, package = .packageName)
  ── Error ('test-reference_alleles.R:138'): make_binary_matrix performs as expected when given valid input ──
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
      ▆
   1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$variant_only_dna_mat) at test-reference_alleles.R:138:2
   2.   └─future::plan(future::multiprocess)
   3.     └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   4.       └─future (local) warn_about_multiprocess(newStack)
   5.         └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   6.           └─base (local) dfcn(msg = msg, package = .packageName)
  ── Error ('test-reference_alleles.R:202'): parse_snpeff performs as expected when given valid input ──
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
      ▆
   1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$variant_only_dna_mat) at test-reference_alleles.R:202:2
   2.   └─future::plan(future::multiprocess)
   3.     └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   4.       └─future (local) warn_about_multiprocess(newStack)
   5.         └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   6.           └─base (local) dfcn(msg = msg, package = .packageName)
  ── Error ('test-reference_alleles.R:258'): parse_snpeff gives error when given invalid input ──
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
      ▆
   1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$variant_only_dna_mat) at test-reference_alleles.R:258:2
   2.   └─future::plan(future::multiprocess)
   3.     └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   4.       └─future (local) warn_about_multiprocess(newStack)
   5.         └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   6.           └─base (local) dfcn(msg = msg, package = .packageName)
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 312 ]
  Error: Test failures
  Execution halted