Last updated on 2025-09-18 09:50:35 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| hmde | 8 | 2 | 3 |
Current CRAN status: ERROR: 8, NOTE: 2, OK: 3
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(hmde)
>
> test_check("hmde")
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001399 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 13.99 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.242 seconds (Warm-up)
Chain 1: 0.261 seconds (Sampling)
Chain 1: 0.503 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.001163 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 11.63 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 3.93 seconds (Warm-up)
Chain 2: 2.157 seconds (Sampling)
Chain 2: 6.087 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.16 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.419 seconds (Warm-up)
Chain 1: 0.755 seconds (Sampling)
Chain 1: 1.174 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0.001 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.003 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'vb_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.57 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.894 seconds (Warm-up)
Chain 1: 0.962 seconds (Sampling)
Chain 1: 1.856 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000162 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.62 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.022 seconds (Warm-up)
Chain 1: 0.022 seconds (Sampling)
Chain 1: 0.044 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.006 seconds (Warm-up)
Chain 2: 0.02 seconds (Sampling)
Chain 2: 0.026 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.61 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.054 seconds (Warm-up)
Chain 1: 0.043 seconds (Sampling)
Chain 1: 0.097 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.056 seconds (Warm-up)
Chain 1: 0.073 seconds (Sampling)
Chain 1: 0.129 seconds (Total)
Chain 1:
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hmde_plot_de_pieces.R:17:3'): Execution and output: plot_de_pieces function ──
`plot` does not have names.
── Failure ('test-hmde_plot_de_pieces.R:21:3'): Execution and output: plot_de_pieces function ──
`plot` has type 'object', not 'list'.
── Failure ('test-hmde_plot_obs_est_inds.R:5:3'): Execution and output: plot_obs_est_inds function ──
`plot` does not have names.
── Failure ('test-hmde_plot_obs_est_inds.R:9:3'): Execution and output: plot_obs_est_inds function ──
`plot` has type 'object', not 'list'.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(hmde)
>
> test_check("hmde")
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001019 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 10.19 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.205 seconds (Warm-up)
Chain 1: 0.028 seconds (Sampling)
Chain 1: 0.233 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.001021 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 10.21 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.379 seconds (Warm-up)
Chain 2: 0.594 seconds (Sampling)
Chain 2: 0.973 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.161 seconds (Warm-up)
Chain 1: 0.469 seconds (Sampling)
Chain 1: 0.63 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.006 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 8e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.007 seconds (Sampling)
Chain 2: 0.014 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'vb_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.404 seconds (Warm-up)
Chain 1: 1.249 seconds (Sampling)
Chain 1: 1.653 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.026 seconds (Sampling)
Chain 1: 0.028 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.006 seconds (Warm-up)
Chain 2: 0.148 seconds (Sampling)
Chain 2: 0.154 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.042 seconds (Warm-up)
Chain 1: 0.056 seconds (Sampling)
Chain 1: 0.098 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.056 seconds (Warm-up)
Chain 1: 0.039 seconds (Sampling)
Chain 1: 0.095 seconds (Total)
Chain 1:
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hmde_plot_de_pieces.R:17:3'): Execution and output: plot_de_pieces function ──
`plot` does not have names.
── Failure ('test-hmde_plot_de_pieces.R:21:3'): Execution and output: plot_de_pieces function ──
`plot` has type 'object', not 'list'.
── Failure ('test-hmde_plot_obs_est_inds.R:5:3'): Execution and output: plot_obs_est_inds function ──
`plot` does not have names.
── Failure ('test-hmde_plot_obs_est_inds.R:9:3'): Execution and output: plot_obs_est_inds function ──
`plot` has type 'object', not 'list'.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [29s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(hmde)
>
> test_check("hmde")
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.51 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.002169 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 21.69 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.379 seconds (Warm-up)
Chain 1: 0.157 seconds (Sampling)
Chain 1: 0.536 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.005116 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 51.16 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 4.282 seconds (Warm-up)
Chain 2: 0.134 seconds (Sampling)
Chain 2: 4.416 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.171 seconds (Warm-up)
Chain 1: 2.782 seconds (Sampling)
Chain 1: 3.953 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.54 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.007 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.033 seconds (Sampling)
Chain 2: 0.04 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'vb_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.703 seconds (Warm-up)
Chain 1: 4.733 seconds (Sampling)
Chain 1: 6.436 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.88 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.025 seconds (Warm-up)
Chain 1: 0.03 seconds (Sampling)
Chain 1: 0.055 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 6.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.63 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.016 seconds (Warm-up)
Chain 2: 0.273 seconds (Sampling)
Chain 2: 0.289 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000101 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.01 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.306 seconds (Warm-up)
Chain 1: 0.416 seconds (Sampling)
Chain 1: 0.722 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.68 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.07 seconds (Warm-up)
Chain 1: 0.55 seconds (Sampling)
Chain 1: 0.62 seconds (Total)
Chain 1:
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hmde_plot_de_pieces.R:17:3'): Execution and output: plot_de_pieces function ──
`plot` does not have names.
── Failure ('test-hmde_plot_de_pieces.R:21:3'): Execution and output: plot_de_pieces function ──
`plot` has type 'object', not 'list'.
── Failure ('test-hmde_plot_obs_est_inds.R:5:3'): Execution and output: plot_obs_est_inds function ──
`plot` does not have names.
── Failure ('test-hmde_plot_obs_est_inds.R:9:3'): Execution and output: plot_obs_est_inds function ──
`plot` has type 'object', not 'list'.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.1
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [19s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(hmde)
>
> test_check("hmde")
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0.001 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001431 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 14.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.56 seconds (Warm-up)
Chain 1: 0.204 seconds (Sampling)
Chain 1: 0.764 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.001247 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 12.47 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 2.051 seconds (Warm-up)
Chain 2: 0.359 seconds (Sampling)
Chain 2: 2.41 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.39 seconds (Warm-up)
Chain 1: 0.701 seconds (Sampling)
Chain 1: 1.091 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.006 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.007 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.009 seconds (Sampling)
Chain 2: 0.011 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'vb_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.236 seconds (Warm-up)
Chain 1: 1.532 seconds (Sampling)
Chain 1: 2.768 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.67 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.047 seconds (Warm-up)
Chain 1: 0.034 seconds (Sampling)
Chain 1: 0.081 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.021 seconds (Sampling)
Chain 2: 0.024 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.51 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.083 seconds (Warm-up)
Chain 1: 0.072 seconds (Sampling)
Chain 1: 0.155 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.45 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.166 seconds (Warm-up)
Chain 1: 0.142 seconds (Sampling)
Chain 1: 0.308 seconds (Total)
Chain 1:
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hmde_plot_de_pieces.R:17:3'): Execution and output: plot_de_pieces function ──
`plot` does not have names.
── Failure ('test-hmde_plot_de_pieces.R:21:3'): Execution and output: plot_de_pieces function ──
`plot` has type 'object', not 'list'.
── Failure ('test-hmde_plot_obs_est_inds.R:5:3'): Execution and output: plot_obs_est_inds function ──
`plot` does not have names.
── Failure ('test-hmde_plot_obs_est_inds.R:9:3'): Execution and output: plot_obs_est_inds function ──
`plot` has type 'object', not 'list'.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(hmde)
>
> test_check("hmde")
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001522 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 15.22 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.579 seconds (Warm-up)
Chain 1: 1.63 seconds (Sampling)
Chain 1: 3.209 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.00132 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 13.2 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.047 seconds (Warm-up)
Chain 2: 2.255 seconds (Sampling)
Chain 2: 2.302 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.27 seconds (Warm-up)
Chain 1: 0.255 seconds (Sampling)
Chain 1: 0.525 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0.001 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.003 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'vb_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.112 seconds (Warm-up)
Chain 1: 1.251 seconds (Sampling)
Chain 1: 2.363 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.71 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.029 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.043 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.027 seconds (Sampling)
Chain 2: 0.028 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.44 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.022 seconds (Warm-up)
Chain 1: 0.098 seconds (Sampling)
Chain 1: 0.12 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.082 seconds (Warm-up)
Chain 1: 0.102 seconds (Sampling)
Chain 1: 0.184 seconds (Total)
Chain 1:
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hmde_plot_de_pieces.R:17:3'): Execution and output: plot_de_pieces function ──
`plot` does not have names.
── Failure ('test-hmde_plot_de_pieces.R:21:3'): Execution and output: plot_de_pieces function ──
`plot` has type 'object', not 'list'.
── Failure ('test-hmde_plot_obs_est_inds.R:5:3'): Execution and output: plot_obs_est_inds function ──
`plot` does not have names.
── Failure ('test-hmde_plot_obs_est_inds.R:9:3'): Execution and output: plot_obs_est_inds function ──
`plot` has type 'object', not 'list'.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running 'testthat.R' [22s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(hmde)
>
> test_check("hmde")
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000191 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.91 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.002389 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 23.89 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.089 seconds (Warm-up)
Chain 1: 0.047 seconds (Sampling)
Chain 1: 1.136 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.002424 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 24.24 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 3.808 seconds (Warm-up)
Chain 2: 1.697 seconds (Sampling)
Chain 2: 5.505 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.402 seconds (Warm-up)
Chain 1: 0.897 seconds (Sampling)
Chain 1: 1.299 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.007 seconds (Sampling)
Chain 1: 0.011 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 9e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'vb_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.334 seconds (Warm-up)
Chain 1: 1.821 seconds (Sampling)
Chain 1: 3.155 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.74 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.01 seconds (Warm-up)
Chain 1: 0.008 seconds (Sampling)
Chain 1: 0.018 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.01 seconds (Sampling)
Chain 2: 0.013 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.045 seconds (Warm-up)
Chain 1: 0.152 seconds (Sampling)
Chain 1: 0.197 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.53 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.097 seconds (Warm-up)
Chain 1: 0.059 seconds (Sampling)
Chain 1: 0.156 seconds (Total)
Chain 1:
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hmde_plot_de_pieces.R:17:3'): Execution and output: plot_de_pieces function ──
`plot` does not have names.
── Failure ('test-hmde_plot_de_pieces.R:21:3'): Execution and output: plot_de_pieces function ──
`plot` has type 'object', not 'list'.
── Failure ('test-hmde_plot_obs_est_inds.R:5:3'): Execution and output: plot_obs_est_inds function ──
`plot` does not have names.
── Failure ('test-hmde_plot_obs_est_inds.R:9:3'): Execution and output: plot_obs_est_inds function ──
`plot` has type 'object', not 'list'.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.2.1
Check: installed package size
Result: NOTE
installed size is 113.0Mb
sub-directories of 1Mb or more:
article 3.0Mb
doc 1.1Mb
libs 108.3Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.2.1
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(hmde)
>
> test_check("hmde")
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.54 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0.001 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.004185 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 41.85 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.127 seconds (Warm-up)
Chain 1: 0.251 seconds (Sampling)
Chain 1: 0.378 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.00388 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 38.8 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 1.677 seconds (Warm-up)
Chain 2: 2.535 seconds (Sampling)
Chain 2: 4.212 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.643 seconds (Warm-up)
Chain 1: 1.533 seconds (Sampling)
Chain 1: 2.176 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.55 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.009 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: 0.022 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.01 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.013 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'vb_single_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.55 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 1.428 seconds (Warm-up)
Chain 1: 2.075 seconds (Sampling)
Chain 1: 3.503 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000119 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.19 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 1: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 1: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 1: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 1: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 1: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 1: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 1: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 1: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 1: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 1: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 1: Iteration: 20 / 20 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.019 seconds (Warm-up)
Chain 1: 0.027 seconds (Sampling)
Chain 1: 0.046 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.6 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 20 [ 5%] (Warmup)
Chain 2: Iteration: 2 / 20 [ 10%] (Warmup)
Chain 2: Iteration: 4 / 20 [ 20%] (Warmup)
Chain 2: Iteration: 6 / 20 [ 30%] (Warmup)
Chain 2: Iteration: 8 / 20 [ 40%] (Warmup)
Chain 2: Iteration: 10 / 20 [ 50%] (Warmup)
Chain 2: Iteration: 11 / 20 [ 55%] (Sampling)
Chain 2: Iteration: 12 / 20 [ 60%] (Sampling)
Chain 2: Iteration: 14 / 20 [ 70%] (Sampling)
Chain 2: Iteration: 16 / 20 [ 80%] (Sampling)
Chain 2: Iteration: 18 / 20 [ 90%] (Sampling)
Chain 2: Iteration: 20 / 20 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.011 seconds (Warm-up)
Chain 2: 0.018 seconds (Sampling)
Chain 2: 0.029 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.96 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.076 seconds (Warm-up)
Chain 1: 0.063 seconds (Sampling)
Chain 1: 0.139 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.91 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 3
Chain 1: adapt_window = 20
Chain 1: term_buffer = 2
Chain 1:
Chain 1: Iteration: 1 / 50 [ 2%] (Warmup)
Chain 1: Iteration: 5 / 50 [ 10%] (Warmup)
Chain 1: Iteration: 10 / 50 [ 20%] (Warmup)
Chain 1: Iteration: 15 / 50 [ 30%] (Warmup)
Chain 1: Iteration: 20 / 50 [ 40%] (Warmup)
Chain 1: Iteration: 25 / 50 [ 50%] (Warmup)
Chain 1: Iteration: 26 / 50 [ 52%] (Sampling)
Chain 1: Iteration: 30 / 50 [ 60%] (Sampling)
Chain 1: Iteration: 35 / 50 [ 70%] (Sampling)
Chain 1: Iteration: 40 / 50 [ 80%] (Sampling)
Chain 1: Iteration: 45 / 50 [ 90%] (Sampling)
Chain 1: Iteration: 50 / 50 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.157 seconds (Warm-up)
Chain 1: 0.073 seconds (Sampling)
Chain 1: 0.23 seconds (Total)
Chain 1:
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-hmde_plot_de_pieces.R:17:3'): Execution and output: plot_de_pieces function ──
`plot` does not have names.
── Failure ('test-hmde_plot_de_pieces.R:21:3'): Execution and output: plot_de_pieces function ──
`plot` has type 'object', not 'list'.
── Failure ('test-hmde_plot_obs_est_inds.R:5:3'): Execution and output: plot_obs_est_inds function ──
`plot` does not have names.
── Failure ('test-hmde_plot_obs_est_inds.R:9:3'): Execution and output: plot_obs_est_inds function ──
`plot` has type 'object', not 'list'.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64