R Under development (unstable) (2024-05-29 r86642 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(multinma)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())

Attaching package: 'multinma'

The following objects are masked from 'package:stats':

    dgamma, pgamma, qgamma

> 
> test_check("multinma")

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'normal' NOW (CHAIN 4).

SAMPLING FOR MODEL 'binomial_1par' 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: 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 = 7
Chain 1:            adapt_window = 38
Chain 1:            term_buffer = 5
Chain 1: 
Chain 1: Iteration:  1 / 100 [  1%]  (Warmup)
Chain 1: Iteration: 10 / 100 [ 10%]  (Warmup)
Chain 1: Iteration: 20 / 100 [ 20%]  (Warmup)
Chain 1: Iteration: 30 / 100 [ 30%]  (Warmup)
Chain 1: Iteration: 40 / 100 [ 40%]  (Warmup)
Chain 1: Iteration: 50 / 100 [ 50%]  (Warmup)
Chain 1: Iteration: 51 / 100 [ 51%]  (Sampling)
Chain 1: Iteration: 60 / 100 [ 60%]  (Sampling)
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Chain 1: Iteration: 80 / 100 [ 80%]  (Sampling)
Chain 1: Iteration: 90 / 100 [ 90%]  (Sampling)
Chain 1: Iteration: 100 / 100 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.032 seconds (Warm-up)
Chain 1:                0.037 seconds (Sampling)
Chain 1:                0.069 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'binomial_1par' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 2.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: WARNING: There aren't enough warmup iterations to fit the
Chain 2:          three stages of adaptation as currently configured.
Chain 2:          Reducing each adaptation stage to 15%/75%/10% of
Chain 2:          the given number of warmup iterations:
Chain 2:            init_buffer = 7
Chain 2:            adapt_window = 38
Chain 2:            term_buffer = 5
Chain 2: 
Chain 2: Iteration:  1 / 100 [  1%]  (Warmup)
Chain 2: Iteration: 10 / 100 [ 10%]  (Warmup)
Chain 2: Iteration: 20 / 100 [ 20%]  (Warmup)
Chain 2: Iteration: 30 / 100 [ 30%]  (Warmup)
Chain 2: Iteration: 40 / 100 [ 40%]  (Warmup)
Chain 2: Iteration: 50 / 100 [ 50%]  (Warmup)
Chain 2: Iteration: 51 / 100 [ 51%]  (Sampling)
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Chain 2: Iteration: 80 / 100 [ 80%]  (Sampling)
Chain 2: Iteration: 90 / 100 [ 90%]  (Sampling)
Chain 2: Iteration: 100 / 100 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 0.045 seconds (Warm-up)
Chain 2:                0.038 seconds (Sampling)
Chain 2:                0.083 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL 'binomial_1par' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 2.6e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: WARNING: There aren't enough warmup iterations to fit the
Chain 3:          three stages of adaptation as currently configured.
Chain 3:          Reducing each adaptation stage to 15%/75%/10% of
Chain 3:          the given number of warmup iterations:
Chain 3:            init_buffer = 7
Chain 3:            adapt_window = 38
Chain 3:            term_buffer = 5
Chain 3: 
Chain 3: Iteration:  1 / 100 [  1%]  (Warmup)
Chain 3: Iteration: 10 / 100 [ 10%]  (Warmup)
Chain 3: Iteration: 20 / 100 [ 20%]  (Warmup)
Chain 3: Iteration: 30 / 100 [ 30%]  (Warmup)
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Chain 3: Iteration: 50 / 100 [ 50%]  (Warmup)
Chain 3: Iteration: 51 / 100 [ 51%]  (Sampling)
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Chain 3: Iteration: 70 / 100 [ 70%]  (Sampling)
Chain 3: Iteration: 80 / 100 [ 80%]  (Sampling)
Chain 3: Iteration: 90 / 100 [ 90%]  (Sampling)
Chain 3: Iteration: 100 / 100 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 0.032 seconds (Warm-up)
Chain 3:                0.035 seconds (Sampling)
Chain 3:                0.067 seconds (Total)
Chain 3: 

SAMPLING FOR MODEL 'binomial_1par' NOW (CHAIN 4).
Chain 4: 
Chain 4: Gradient evaluation took 2.2e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4: 
Chain 4: 
Chain 4: WARNING: There aren't enough warmup iterations to fit the
Chain 4:          three stages of adaptation as currently configured.
Chain 4:          Reducing each adaptation stage to 15%/75%/10% of
Chain 4:          the given number of warmup iterations:
Chain 4:            init_buffer = 7
Chain 4:            adapt_window = 38
Chain 4:            term_buffer = 5
Chain 4: 
Chain 4: Iteration:  1 / 100 [  1%]  (Warmup)
Chain 4: Iteration: 10 / 100 [ 10%]  (Warmup)
Chain 4: Iteration: 20 / 100 [ 20%]  (Warmup)
Chain 4: Iteration: 30 / 100 [ 30%]  (Warmup)
Chain 4: Iteration: 40 / 100 [ 40%]  (Warmup)
Chain 4: Iteration: 50 / 100 [ 50%]  (Warmup)
Chain 4: Iteration: 51 / 100 [ 51%]  (Sampling)
Chain 4: Iteration: 60 / 100 [ 60%]  (Sampling)
Chain 4: Iteration: 70 / 100 [ 70%]  (Sampling)
Chain 4: Iteration: 80 / 100 [ 80%]  (Sampling)
Chain 4: Iteration: 90 / 100 [ 90%]  (Sampling)
Chain 4: Iteration: 100 / 100 [100%]  (Sampling)
Chain 4: 
Chain 4:  Elapsed Time: 0.04 seconds (Warm-up)
Chain 4:                0.045 seconds (Sampling)
Chain 4:                0.085 seconds (Total)
Chain 4: 

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).

SAMPLING FOR MODEL 'binomial_1par' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 3.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.36 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 / 10 [ 10%]  (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%]  (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%]  (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%]  (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%]  (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%]  (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%]  (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%]  (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%]  (Sampling)
Chain 1: Iteration: 10 / 10 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.001 seconds (Warm-up)
Chain 1:                0.003 seconds (Sampling)
Chain 1:                0.004 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'binomial_1par' 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 / 10 [ 10%]  (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%]  (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%]  (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%]  (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%]  (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%]  (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%]  (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%]  (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%]  (Sampling)
Chain 2: Iteration: 10 / 10 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 0.001 seconds (Warm-up)
Chain 2:                0.001 seconds (Sampling)
Chain 2:                0.002 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL 'binomial_1par' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 4e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: WARNING: No variance estimation is
Chain 3:          performed for num_warmup < 20
Chain 3: 
Chain 3: Iteration: 1 / 10 [ 10%]  (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%]  (Warmup)
Chain 3: Iteration: 3 / 10 [ 30%]  (Warmup)
Chain 3: Iteration: 4 / 10 [ 40%]  (Warmup)
Chain 3: Iteration: 5 / 10 [ 50%]  (Warmup)
Chain 3: Iteration: 6 / 10 [ 60%]  (Sampling)
Chain 3: Iteration: 7 / 10 [ 70%]  (Sampling)
Chain 3: Iteration: 8 / 10 [ 80%]  (Sampling)
Chain 3: Iteration: 9 / 10 [ 90%]  (Sampling)
Chain 3: Iteration: 10 / 10 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 0 seconds (Warm-up)
Chain 3:                0 seconds (Sampling)
Chain 3:                0 seconds (Total)
Chain 3: 

SAMPLING FOR MODEL 'binomial_1par' NOW (CHAIN 4).
Chain 4: 
Chain 4: Gradient evaluation took 2.2e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4: 
Chain 4: 
Chain 4: WARNING: No variance estimation is
Chain 4:          performed for num_warmup < 20
Chain 4: 
Chain 4: Iteration: 1 / 10 [ 10%]  (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%]  (Warmup)
Chain 4: Iteration: 3 / 10 [ 30%]  (Warmup)
Chain 4: Iteration: 4 / 10 [ 40%]  (Warmup)
Chain 4: Iteration: 5 / 10 [ 50%]  (Warmup)
Chain 4: Iteration: 6 / 10 [ 60%]  (Sampling)
Chain 4: Iteration: 7 / 10 [ 70%]  (Sampling)
Chain 4: Iteration: 8 / 10 [ 80%]  (Sampling)
Chain 4: Iteration: 9 / 10 [ 90%]  (Sampling)
Chain 4: Iteration: 10 / 10 [100%]  (Sampling)
Chain 4: 
Chain 4:  Elapsed Time: 0.001 seconds (Warm-up)
Chain 4:                0 seconds (Sampling)
Chain 4:                0.001 seconds (Total)
Chain 4: 

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 1).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 2).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 3).

TESTING GRADIENT FOR MODEL 'binomial_1par' NOW (CHAIN 4).
[ FAIL 0 | WARN 0 | SKIP 20 | PASS 1059 ]

══ Skipped tests (20) ══════════════════════════════════════════════════════════
• On CRAN (20): 'test-add_integration.R:541:3',
  'test-example_atrial_fibrillation.R:4:1', 'test-example_bcg_vaccine.R:4:1',
  'test-example_blocker.R:4:1', 'test-example_diabetes.R:4:1',
  'test-example_dietary_fat.R:4:1', 'test-example_hta_psoriasis.R:4:1',
  'test-example_parkinsons.R:4:1', 'test-example_plaque_psoriasis.R:4:1',
  'test-example_smoking.R:4:1', 'test-example_statins.R:4:1',
  'test-example_thrombolytics.R:4:1', 'test-example_transfusion.R:4:1',
  'test-marginal_effects.R:65:1', 'test-nma.R:299:3', 'test-nodesplit.R:264:3',
  'test-plot_nma_data.R:2:1', 'test-posterior_ranks.R:99:1',
  'test-predict.R:110:1', 'test-relative_effects.R:65:1'

[ FAIL 0 | WARN 0 | SKIP 20 | PASS 1059 ]
Deleting unused snapshots:
• plot_nma_data/atrial-fibrillation-network-star.svg
• plot_nma_data/atrial-fibrillation-network.svg
• plot_nma_data/bcg-vaccine-network.svg
• plot_nma_data/blocker-network.svg
• plot_nma_data/diabetes-network.svg
• plot_nma_data/dietary-fat-network.svg
• plot_nma_data/duplicated-agd-arms-network.svg
• plot_nma_data/duplicated-agd-contrasts-network.svg
• plot_nma_data/duplicated-ipd-arms-network.svg
• plot_nma_data/hta-psoriasis-network.svg
• plot_nma_data/ndmm-network.svg
• plot_nma_data/parkinsons-arm-network.svg
• plot_nma_data/parkinsons-contrast-network.svg
• plot_nma_data/parkinsons-mixed-network.svg
• plot_nma_data/plaque-psoriasis-network.svg
• plot_nma_data/smoking-network.svg
• plot_nma_data/statins-network.svg
• plot_nma_data/thrombolytics-dias-network.svg
• plot_nma_data/thrombolytics-network.svg
• plot_nma_data/transfusion-network.svg
> 
> proc.time()
   user  system elapsed 
 110.32    3.43  113.86