Last updated on 2023-03-21 07:54:18 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | ERROR | ||||
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 2.73 | 51.81 | 54.54 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 89.48 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 99.26 | ERROR | |||
| r-patched-linux-x86_64 | 1.1.1 | 3.07 | 66.87 | 69.94 | ERROR | |
| r-release-linux-x86_64 | 1.1.1 | 3.50 | 67.22 | 70.72 | ERROR | |
| r-release-macos-arm64 | 1.1.1 | 37.00 | NOTE | |||
| r-release-macos-x86_64 | 1.1.1 | 72.00 | NOTE | |||
| r-release-windows-x86_64 | 1.1.1 | 23.00 | 108.00 | 131.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.1.1 | 44.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.1.1 | 62.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 1.1.1 | 7.00 | 101.00 | 108.00 | ERROR |
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/27s]
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:73:3'): 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:50:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:50:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:89:3'): remove_unknown_alleles correctly removes Ns when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:138:3'): make_binary_matrix performs as expected when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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:202:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:202:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:258:3'): parse_snpeff gives error when given invalid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘getting_started_with_prewas.Rmd’ using rmarkdown
Quitting from lines 136-141 (getting_started_with_prewas.Rmd)
Error: processing vignette ‘getting_started_with_prewas.Rmd’ failed with diagnostics:
Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
--- failed re-building ‘getting_started_with_prewas.Rmd’
SUMMARY: processing the following file failed:
‘getting_started_with_prewas.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/27s]
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:73:3'): 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:50:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:50:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:89:3'): remove_unknown_alleles correctly removes Ns when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:138:3'): make_binary_matrix performs as expected when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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:202:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:202:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:258:3'): parse_snpeff gives error when given invalid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.1
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘stats’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/37s]
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:73:3'): 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:50:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:50:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:89:3'): remove_unknown_alleles correctly removes Ns when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:138:3'): make_binary_matrix performs as expected when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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:202:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:202:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:258:3'): parse_snpeff gives error when given invalid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_prewas.Rmd’ using rmarkdown
Quitting from lines 136-141 (getting_started_with_prewas.Rmd)
Error: processing vignette 'getting_started_with_prewas.Rmd' failed with diagnostics:
Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
--- failed re-building ‘getting_started_with_prewas.Rmd’
SUMMARY: processing the following file failed:
‘getting_started_with_prewas.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/91s]
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:73:3'): 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:50:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:50:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:89:3'): remove_unknown_alleles correctly removes Ns when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:138:3'): make_binary_matrix performs as expected when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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:202:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:202:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:258:3'): parse_snpeff gives error when given invalid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/25s]
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:73:3'): 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:50:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:50:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:89:3'): remove_unknown_alleles correctly removes Ns when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:138:3'): make_binary_matrix performs as expected when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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:202:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:202:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:258:3'): parse_snpeff gives error when given invalid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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
Flavor: r-patched-linux-x86_64
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/26s]
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:73:3'): 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:50:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:50:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:89:3'): remove_unknown_alleles correctly removes Ns when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:138:3'): make_binary_matrix performs as expected when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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:202:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:202:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:258:3'): parse_snpeff gives error when given invalid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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
Flavor: r-release-linux-x86_64
Version: 1.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [20s]
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:73:3'): 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:50:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:50:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:89:3'): remove_unknown_alleles correctly removes Ns when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:138:3'): make_binary_matrix performs as expected when given valid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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:202:3'): 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$variant_only_dna_mat) at test-reference_alleles.R:202:2
2. └─future::plan(future::multiprocess)
3. └─future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. └─future (local) warn_about_multiprocess(newStack)
5. └─future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. └─base (local) dfcn(msg = msg, package = .packageName)
── Error ('test-reference_alleles.R:258:3'): parse_snpeff gives error when given invalid input ──
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
▆
1. └─prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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
Flavor: r-release-windows-x86_64
Version: 1.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [26s]
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:73:3'): 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:
x
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:50:3'): 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:
x
1. \-prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat$variant_only_dna_mat) at test-reference_alleles.R:50:2
2. \-future::plan(future::multiprocess)
3. \-future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. \-future (local) warn_about_multiprocess(newStack)
5. \-future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. \-base (local) dfcn(msg = msg, package = .packageName)
-- Error ('test-reference_alleles.R:89:3'): remove_unknown_alleles correctly removes Ns when given valid input --
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
x
1. \-prewas:::get_ancestral_alleles(temp_tree, temp_dna_mat) at test-reference_alleles.R:89:2
2. \-future::plan(future::multiprocess)
3. \-future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. \-future (local) warn_about_multiprocess(newStack)
5. \-future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. \-base (local) dfcn(msg = msg, package = .packageName)
-- Error ('test-reference_alleles.R:138:3'): make_binary_matrix performs as expected when given valid input --
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
x
1. \-prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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:202:3'): 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:
x
1. \-prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$variant_only_dna_mat) at test-reference_alleles.R:202:2
2. \-future::plan(future::multiprocess)
3. \-future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4. \-future (local) warn_about_multiprocess(newStack)
5. \-future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
6. \-base (local) dfcn(msg = msg, package = .packageName)
-- Error ('test-reference_alleles.R:258:3'): parse_snpeff gives error when given invalid input --
<defunctError/error/condition>
Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
Backtrace:
x
1. \-prewas:::get_ancestral_alleles(tree = temp_tree, mat = temp_dna_list$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
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.1.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'getting_started_with_prewas.Rmd' using rmarkdown
Quitting from lines 136-141 (getting_started_with_prewas.Rmd)
Error: processing vignette 'getting_started_with_prewas.Rmd' failed with diagnostics:
Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
--- failed re-building 'getting_started_with_prewas.Rmd'
SUMMARY: processing the following file failed:
'getting_started_with_prewas.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64