Last updated on 2019-01-15 00:46:40 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.7 | 12.45 | 648.25 | 660.70 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.4.0 | 10.62 | 456.11 | 466.73 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.4.0 | 839.72 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.4.0 | 716.08 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 0.3.7 | 28.00 | 305.00 | 333.00 | OK | --no-vignettes |
| r-patched-linux-x86_64 | 0.3.7 | 11.09 | 561.85 | 572.94 | ERROR | |
| r-patched-solaris-x86 | 0.3.7 | 1058.80 | WARN | |||
| r-release-linux-x86_64 | 0.3.7 | 11.29 | 550.42 | 561.71 | ERROR | |
| r-release-windows-ix86+x86_64 | 0.3.7 | 30.00 | 354.00 | 384.00 | OK | --no-vignettes |
| r-release-osx-x86_64 | 0.3.7 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 0.3.6 | 23.00 | 461.00 | 484.00 | ERROR | --no-vignettes |
| r-oldrel-osx-x86_64 | 0.3.7 | ERROR |
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [106s/117s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(psycho)
>
> test_check("psycho")
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.93 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)
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Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
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Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
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Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 3.83179 seconds (Warm-up)
Chain 1: 3.14683 seconds (Sampling)
Chain 1: 6.97862 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000111 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.11 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)
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Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
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Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
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Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 2.37714 seconds (Warm-up)
Chain 1: 2.12671 seconds (Sampling)
Chain 1: 4.50385 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' 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: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
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Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
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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: 0.116585 seconds (Warm-up)
Chain 1: 0.111156 seconds (Sampling)
Chain 1: 0.227741 seconds (Total)
Chain 1:
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 6.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.64 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -403.800 1.000 1.000
Chain 1: 200 -199.756 1.011 1.021
Chain 1: 300 -195.131 0.682 1.000
Chain 1: 400 -195.234 0.511 1.000
Chain 1: 500 -194.906 0.409 0.024
Chain 1: 600 -195.149 0.341 0.024
Chain 1: 700 -195.587 0.293 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 5.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.58 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -93424.409 1.000 1.000
Chain 1: 200 -590.743 79.074 157.147
Chain 1: 300 -522.796 52.759 1.000
Chain 1: 400 -197.216 39.982 1.651
Chain 1: 500 -200.744 31.989 1.000
Chain 1: 600 -197.522 26.660 1.000
Chain 1: 700 -200.282 22.854 0.130
Chain 1: 800 -197.453 19.999 0.130
Chain 1: 900 -195.347 17.778 0.018
Chain 1: 1000 -196.061 16.000 0.018
Chain 1: 1100 -198.630 15.902 0.016 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1200 -195.774 0.188 0.015
Chain 1: 1300 -196.035 0.176 0.014
Chain 1: 1400 -195.408 0.011 0.014
Chain 1: 1500 -196.486 0.010 0.013 MEAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
── 1. Failure: If it works. (@test-analyze.stanreg.R#89) ──────────────────────
round(values$effects$Sepal.Width$median, 2) not equal to -0.12.
1/1 mismatches
[1] -0.33 - -0.12 == -0.21
The Crawford-Howell (1998) t-test suggests no dissociation between test X and test Y (t(5) = 2.10, p = 0.09<b0>). The patient's score on test X is not significantly altered compared to its score on test Y.
SAMPLING FOR MODEL 'continuous' 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: Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 1: Iteration: 200 / 2000 [ 10%] (Warmup)
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Chain 1: Iteration: 1000 / 2000 [ 50%] (Warmup)
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Chain 1: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.721728 seconds (Warm-up)
Chain 1: 0.775505 seconds (Sampling)
Chain 1: 1.49723 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000115 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.15 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 2: Iteration: 200 / 2000 [ 10%] (Warmup)
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Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.73919 seconds (Warm-up)
Chain 2: 0.97019 seconds (Sampling)
Chain 2: 1.70938 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000115 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.15 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 2000 [ 0%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.739604 seconds (Warm-up)
Chain 3: 0.767031 seconds (Sampling)
Chain 3: 1.50664 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000105 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.05 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 2000 [ 0%] (Warmup)
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Chain 4: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.72208 seconds (Warm-up)
Chain 4: 0.776135 seconds (Sampling)
Chain 4: 1.49822 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.64 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 1: Iteration: 200 / 2000 [ 10%] (Warmup)
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Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.248337 seconds (Warm-up)
Chain 1: 0.113588 seconds (Sampling)
Chain 1: 0.361925 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' 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: Iteration: 1 / 2000 [ 0%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.226971 seconds (Warm-up)
Chain 2: 0.128185 seconds (Sampling)
Chain 2: 0.355156 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 2.9e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 2000 [ 0%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.306314 seconds (Warm-up)
Chain 3: 0.286067 seconds (Sampling)
Chain 3: 0.592381 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3.2e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
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Chain 4:
Chain 4: Elapsed Time: 0.247253 seconds (Warm-up)
Chain 4: 0.11441 seconds (Sampling)
Chain 4: 0.361663 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'bernoulli' 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: Iteration: 1 / 2000 [ 0%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.162656 seconds (Warm-up)
Chain 1: 0.168118 seconds (Sampling)
Chain 1: 0.330774 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 2000 [ 0%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.160894 seconds (Warm-up)
Chain 2: 0.188466 seconds (Sampling)
Chain 2: 0.34936 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.7e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.47 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
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Chain 3:
Chain 3: Elapsed Time: 0.15212 seconds (Warm-up)
Chain 3: 0.153252 seconds (Sampling)
Chain 3: 0.305372 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.3 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
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Chain 4:
Chain 4: Elapsed Time: 0.136887 seconds (Warm-up)
Chain 4: 0.151089 seconds (Sampling)
Chain 4: 0.287976 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'continuous' 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:
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Chain 1:
Chain 1: Elapsed Time: 0.124964 seconds (Warm-up)
Chain 1: 0.119263 seconds (Sampling)
Chain 1: 0.244227 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' 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:
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Chain 2:
Chain 2: Elapsed Time: 0.127014 seconds (Warm-up)
Chain 2: 0.114641 seconds (Sampling)
Chain 2: 0.241655 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'continuous' 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!
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Chain 4:
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Chain 4:
SAMPLING FOR MODEL 'continuous' 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.
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Chain 2:
Chain 2: Gradient evaluation took 4.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
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Chain 3:
Chain 3: Gradient evaluation took 4.1e-05 seconds
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Chain 4:
Chain 4: Gradient evaluation took 6.5e-05 seconds
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Chain 1:
Chain 1: Gradient evaluation took 0.000199 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.99 seconds.
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Chain 2:
Chain 2: Gradient evaluation took 0.000197 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.97 seconds.
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Chain 3:
Chain 3: Gradient evaluation took 0.00021 seconds
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Chain 4:
Chain 4: Gradient evaluation took 0.000165 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.65 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.64 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:
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Chain 2:
Chain 2: Gradient evaluation took 3.5e-05 seconds
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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:
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Chain 3:
Chain 3: Gradient evaluation took 7.2e-05 seconds
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Chain 3:
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Chain 3: three stages of adaptation as currently configured.
Chain 3: Reducing each adaptation stage to 15%/75%/10% of
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Chain 4:
Chain 4: Gradient evaluation took 4.6e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
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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
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SAMPLING FOR MODEL 'continuous' 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:
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Chain 2:
Chain 2: Gradient evaluation took 7.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.71 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:
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 5.2e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.52 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:
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Chain 4:
Chain 4: Gradient evaluation took 7.9e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.79 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
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Chain 4:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.64 seconds.
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Chain 2:
Chain 2: Gradient evaluation took 3.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 3.9e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
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Chain 3:
Chain 3: Elapsed Time: 0.211517 seconds (Warm-up)
Chain 3: 0.214205 seconds (Sampling)
Chain 3: 0.425722 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 4.2e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
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Chain 4:
Chain 4: Elapsed Time: 0.205136 seconds (Warm-up)
Chain 4: 0.189858 seconds (Sampling)
Chain 4: 0.394994 seconds (Total)
Chain 4:
.0%
.33%
.67%
.100%
1
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 6.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.65 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
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Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -403.800 1.000 1.000
Chain 1: 200 -199.756 1.011 1.021
Chain 1: 300 -195.131 0.682 1.000
Chain 1: 400 -195.234 0.511 1.000
Chain 1: 500 -194.906 0.409 0.024
Chain 1: 600 -195.149 0.341 0.024
Chain 1: 700 -195.587 0.293 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
══ testthat results ═══════════════════════════════════════════════════════════
OK: 182 SKIPPED: 0 FAILED: 1
1. Failure: If it works. (@test-analyze.stanreg.R#89)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.4.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [103s/113s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(psycho)
>
> test_check("psycho")
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.65 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 3.18095 seconds (Warm-up)
Chain 1: 2.76684 seconds (Sampling)
Chain 1: 5.94779 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000149 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.49 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 2.17102 seconds (Warm-up)
Chain 1: 1.91002 seconds (Sampling)
Chain 1: 4.08103 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.59 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.116548 seconds (Warm-up)
Chain 1: 0.10781 seconds (Sampling)
Chain 1: 0.224358 seconds (Total)
Chain 1:
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 6.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.63 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -403.800 1.000 1.000
Chain 1: 200 -199.756 1.011 1.021
Chain 1: 300 -195.131 0.682 1.000
Chain 1: 400 -195.234 0.511 1.000
Chain 1: 500 -194.906 0.409 0.024
Chain 1: 600 -195.149 0.341 0.024
Chain 1: 700 -195.587 0.293 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 4.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.47 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -93424.409 1.000 1.000
Chain 1: 200 -590.743 79.074 157.147
Chain 1: 300 -522.796 52.759 1.000
Chain 1: 400 -197.216 39.982 1.651
Chain 1: 500 -200.744 31.989 1.000
Chain 1: 600 -197.522 26.660 1.000
Chain 1: 700 -200.282 22.854 0.130
Chain 1: 800 -197.453 19.999 0.130
Chain 1: 900 -195.347 17.778 0.018
Chain 1: 1000 -196.061 16.000 0.018
Chain 1: 1100 -198.630 15.902 0.016 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1200 -195.774 0.188 0.015
Chain 1: 1300 -196.035 0.176 0.014
Chain 1: 1400 -195.408 0.011 0.014
Chain 1: 1500 -196.486 0.010 0.013 MEAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
── 1. Failure: If it works. (@test-analyze.stanreg.R#89) ──────────────────────
round(values$effects$Sepal.Width$median, 2) not equal to -0.12.
1/1 mismatches
[1] -0.33 - -0.12 == -0.21
The Crawford-Howell (1998) t-test suggests no dissociation between test X and test Y (t(5) = 2.10, p = 0.09<b0>). The patient's score on test X is not significantly altered compared to its score on test Y.
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000246 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.46 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 0.734338 seconds (Warm-up)
Chain 1: 0.78279 seconds (Sampling)
Chain 1: 1.51713 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 9.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.98 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.755302 seconds (Warm-up)
Chain 2: 0.949606 seconds (Sampling)
Chain 2: 1.70491 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000112 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.12 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
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Chain 3:
Chain 3: Elapsed Time: 0.758733 seconds (Warm-up)
Chain 3: 0.792692 seconds (Sampling)
Chain 3: 1.55143 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 9.3e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.93 seconds.
Chain 4: Adjust your expectations accordingly!
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Chain 4:
Chain 4: Elapsed Time: 0.738124 seconds (Warm-up)
Chain 4: 0.803414 seconds (Sampling)
Chain 4: 1.54154 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'continuous' 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:
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Chain 1:
Chain 1: Elapsed Time: 0.222802 seconds (Warm-up)
Chain 1: 0.094557 seconds (Sampling)
Chain 1: 0.317359 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.197732 seconds (Warm-up)
Chain 2: 0.115586 seconds (Sampling)
Chain 2: 0.313318 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 2.2e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
Chain 3: Adjust your expectations accordingly!
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Chain 3:
Chain 3: Elapsed Time: 0.241412 seconds (Warm-up)
Chain 3: 0.225644 seconds (Sampling)
Chain 3: 0.467056 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 2.9e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 4: Adjust your expectations accordingly!
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Chain 4:
Chain 4: Elapsed Time: 0.193361 seconds (Warm-up)
Chain 4: 0.095674 seconds (Sampling)
Chain 4: 0.289035 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'bernoulli' 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:
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Chain 1:
Chain 1: Elapsed Time: 0.137842 seconds (Warm-up)
Chain 1: 0.145317 seconds (Sampling)
Chain 1: 0.283159 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
Chain 2: Adjust your expectations accordingly!
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Chain 2:
Chain 2: Elapsed Time: 0.134092 seconds (Warm-up)
Chain 2: 0.161936 seconds (Sampling)
Chain 2: 0.296028 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 5e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.5 seconds.
Chain 3: Adjust your expectations accordingly!
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Chain 3: 0.250312 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 2.9e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 4: Adjust your expectations accordingly!
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Chain 1:
Chain 1: Gradient evaluation took 3.9e-05 seconds
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Chain 1:
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Chain 2:
Chain 2: Gradient evaluation took 4.1e-05 seconds
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Chain 3:
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Chain 4:
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds.
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Chain 2:
Chain 2: Gradient evaluation took 4.9e-05 seconds
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Chain 3:
Chain 3: Gradient evaluation took 3.8e-05 seconds
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3.6e-05 seconds
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00027 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.7 seconds.
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Chain 2:
Chain 2: Gradient evaluation took 0.000152 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.52 seconds.
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Chain 3:
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Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.54 seconds.
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Chain 4:
Chain 4: Gradient evaluation took 0.000178 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.78 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.52 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:
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Chain 2: Gradient evaluation took 4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
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Chain 2:
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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:
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Chain 3: Gradient evaluation took 6.3e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.63 seconds.
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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
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Chain 4:
Chain 4: Gradient evaluation took 3.8e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds.
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Chain 4:
Chain 4:
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Chain 4: three stages of adaptation as currently configured.
Chain 4: Reducing each adaptation stage to 15%/75%/10% of
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.7 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:
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Chain 2:
Chain 2: Gradient evaluation took 8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.8 seconds.
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Chain 2:
Chain 2:
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Chain 2: three stages of adaptation as currently configured.
Chain 2: Reducing each adaptation stage to 15%/75%/10% of
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Chain 3: Gradient evaluation took 5e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.5 seconds.
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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
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Chain 4:
Chain 4: Gradient evaluation took 5.3e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.53 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
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Chain 4: three stages of adaptation as currently configured.
Chain 4: Reducing each adaptation stage to 15%/75%/10% of
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Chain 4:
Chain 4: Elapsed Time: 0.25117 seconds (Warm-up)
Chain 4: 0.340878 seconds (Sampling)
Chain 4: 0.592048 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'continuous' 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!
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Chain 1:
Chain 1: Elapsed Time: 0.215176 seconds (Warm-up)
Chain 1: 0.202295 seconds (Sampling)
Chain 1: 0.417471 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.208382 seconds (Warm-up)
Chain 2: 0.208226 seconds (Sampling)
Chain 2: 0.416608 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.2e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
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Chain 3:
Chain 3: Elapsed Time: 0.216948 seconds (Warm-up)
Chain 3: 0.218026 seconds (Sampling)
Chain 3: 0.434974 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3.8e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds.
Chain 4: Adjust your expectations accordingly!
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Chain 4:
Chain 4: Elapsed Time: 0.205281 seconds (Warm-up)
Chain 4: 0.191579 seconds (Sampling)
Chain 4: 0.39686 seconds (Total)
Chain 4:
.0%
.33%
.67%
.100%
1
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 5.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.58 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
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Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -403.800 1.000 1.000
Chain 1: 200 -199.756 1.011 1.021
Chain 1: 300 -195.131 0.682 1.000
Chain 1: 400 -195.234 0.511 1.000
Chain 1: 500 -194.906 0.409 0.024
Chain 1: 600 -195.149 0.341 0.024
Chain 1: 700 -195.587 0.293 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
══ testthat results ═══════════════════════════════════════════════════════════
OK: 182 SKIPPED: 0 FAILED: 1
1. Failure: If it works. (@test-analyze.stanreg.R#89)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.3.7
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 4.4Mb
Flavor: r-patched-solaris-x86
Version: 0.3.7
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Flavors: r-patched-solaris-x86, r-release-osx-x86_64
Version: 0.3.7
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp
rstanarm (Version 2.18.2, packaged: 2018-11-08 22:19:38 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- Plotting theme set to bayesplot::theme_default().
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Warning in ypredloo - y :
longer object length is not a multiple of shorter object length
Warning: There were 9 divergent transitions after warmup. Increasing adapt_delta above 0.95 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems
Warning: Markov chains did not converge! Do not analyze results!
Warning: There were 2 divergent transitions after warmup. Increasing adapt_delta above 0.95 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
Quitting from lines 512-540 (bayesian.Rmd)
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [101s/110s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(psycho)
>
> test_check("psycho")
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.56 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 3.33761 seconds (Warm-up)
Chain 1: 2.81119 seconds (Sampling)
Chain 1: 6.1488 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' 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: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 2.1106 seconds (Warm-up)
Chain 1: 1.92162 seconds (Sampling)
Chain 1: 4.03222 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.47 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.110426 seconds (Warm-up)
Chain 1: 0.109068 seconds (Sampling)
Chain 1: 0.219494 seconds (Total)
Chain 1:
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 5.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.59 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -403.800 1.000 1.000
Chain 1: 200 -199.756 1.011 1.021
Chain 1: 300 -195.131 0.682 1.000
Chain 1: 400 -195.234 0.511 1.000
Chain 1: 500 -194.906 0.409 0.024
Chain 1: 600 -195.149 0.341 0.024
Chain 1: 700 -195.587 0.293 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
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: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -93424.409 1.000 1.000
Chain 1: 200 -590.743 79.074 157.147
Chain 1: 300 -522.796 52.759 1.000
Chain 1: 400 -197.216 39.982 1.651
Chain 1: 500 -200.744 31.989 1.000
Chain 1: 600 -197.522 26.660 1.000
Chain 1: 700 -200.282 22.854 0.130
Chain 1: 800 -197.453 19.999 0.130
Chain 1: 900 -195.347 17.778 0.018
Chain 1: 1000 -196.061 16.000 0.018
Chain 1: 1100 -198.630 15.902 0.016 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1200 -195.774 0.188 0.015
Chain 1: 1300 -196.035 0.176 0.014
Chain 1: 1400 -195.408 0.011 0.014
Chain 1: 1500 -196.486 0.010 0.013 MEAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
── 1. Failure: If it works. (@test-analyze.stanreg.R#89) ──────────────────────
round(values$effects$Sepal.Width$median, 2) not equal to -0.12.
1/1 mismatches
[1] -0.33 - -0.12 == -0.21
The Crawford-Howell (1998) t-test suggests no dissociation between test X and test Y (t(5) = 2.10, p = 0.09<b0>). The patient's score on test X is not significantly altered compared to its score on test Y.
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000157 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.57 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.775952 seconds (Warm-up)
Chain 1: 0.797436 seconds (Sampling)
Chain 1: 1.57339 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000101 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.01 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 2000 [ 0%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.780466 seconds (Warm-up)
Chain 2: 0.970999 seconds (Sampling)
Chain 2: 1.75147 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000112 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.12 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
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Chain 3:
Chain 3: Elapsed Time: 0.774445 seconds (Warm-up)
Chain 3: 0.813341 seconds (Sampling)
Chain 3: 1.58779 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000105 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.05 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
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Chain 4:
Chain 4: Elapsed Time: 0.753427 seconds (Warm-up)
Chain 4: 0.822218 seconds (Sampling)
Chain 4: 1.57564 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'continuous' 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:
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Chain 1:
Chain 1: Elapsed Time: 0.222129 seconds (Warm-up)
Chain 1: 0.105145 seconds (Sampling)
Chain 1: 0.327274 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.202118 seconds (Warm-up)
Chain 2: 0.11626 seconds (Sampling)
Chain 2: 0.318378 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 2.3e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
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Chain 3:
Chain 3: Elapsed Time: 0.247769 seconds (Warm-up)
Chain 3: 0.233445 seconds (Sampling)
Chain 3: 0.481214 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.3 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
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SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
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Chain 1:
SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4e-05 seconds
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SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 3e-05 seconds
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SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 2.8e-05 seconds
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.43 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 1.7e-05 seconds
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 2.7e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds.
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SAMPLING FOR MODEL 'continuous' 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.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.1e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 5.2e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.52 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000159 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.59 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000144 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.44 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000169 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.69 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000189 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.89 seconds.
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.47 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:
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Chain 2:
Chain 2: Gradient evaluation took 3.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.33 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:
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.8e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
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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:
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Chain 4:
Chain 4: Gradient evaluation took 3.9e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.39 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
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SAMPLING FOR MODEL 'continuous' 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:
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.55 seconds.
Chain 2: Adjust your expectations accordingly!
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Chain 2: WARNING: There aren't enough warmup iterations to fit the
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.2e-05 seconds
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.7e-05 seconds
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
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SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
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.0%
.33%
.67%
.100%
1
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 7.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.75 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
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Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -403.800 1.000 1.000
Chain 1: 200 -199.756 1.011 1.021
Chain 1: 300 -195.131 0.682 1.000
Chain 1: 400 -195.234 0.511 1.000
Chain 1: 500 -194.906 0.409 0.024
Chain 1: 600 -195.149 0.341 0.024
Chain 1: 700 -195.587 0.293 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
══ testthat results ═══════════════════════════════════════════════════════════
OK: 182 SKIPPED: 0 FAILED: 1
1. Failure: If it works. (@test-analyze.stanreg.R#89)
Error: testthat unit tests failed
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.3.7
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
The following object is masked from 'package:ggplot2':
last_plot
The following objects are masked from 'package:rstanarm':
get_x, get_y
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
path[1]="./webshot6d9639cf936a.png": No such file or directory
Warning in file(con, "rb") :
cannot open file './webshot6d9639cf936a.png': No such file or directory
Quitting from lines 512-540 (bayesian.Rmd)
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Flavor: r-release-osx-x86_64
Version: 0.3.6
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
simulate_data_regression: possible error in diag(x = 1, nrow = n_var +
1, ncol = n_var + 1, names = TRUE): unused argument (names = TRUE)
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.3.6
Flags: --no-vignettes
Check: for unstated dependencies in examples
Result: WARN
Warning in parse(file = files, n = -1L) :
invalid input found on input connection 'psycho-Ex.R'
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.3.6
Flags: --no-vignettes
Check: examples
Result: ERROR
Running examples in 'psycho-Ex.R' failed
The error most likely occurred in:
> ### Name: simulate_data_regression
> ### Title: Simulates data for single or multiple regression.
> ### Aliases: simulate_data_regression
>
> ### ** Examples
>
> library(psycho)
>
> data <- simulate_data_regression(coefs=c(0.1, 0.8), sample=50, error=0)
Error in diag(x = 1, nrow = n_var + 1, ncol = n_var + 1, names = TRUE) :
unused argument (names = TRUE)
Calls: simulate_data_regression
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.3.7
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-osx-x86_64