Last updated on 2025-07-19 01:49:43 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| morse | 13 | ||
| morseDR | 13 | ||
| morseTKTD | 3 | 10 | |
| rbioacc | 2 | 3 | 8 |
| rPBK | 5 | 8 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 3, OK: 10
Version: 0.1.3
Check: installed package size
Result: NOTE
installed size is 86.8Mb
sub-directories of 1Mb or more:
doc 1.0Mb
libs 85.2Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.1.3
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
Current CRAN status: ERROR: 2, NOTE: 3, OK: 8
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [55s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.92 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: 0.005 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.47 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 / 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: 0.006 seconds (Sampling)
Chain 2: 0.007 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000306 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.06 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: 0.018 seconds (Warm-up)
Chain 1: 0.011 seconds (Sampling)
Chain 1: 0.029 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000221 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.21 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 / 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: 0.01 seconds (Warm-up)
Chain 2: 0.01 seconds (Sampling)
Chain 2: 0.02 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.98 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: 0.008 seconds (Warm-up)
Chain 1: 0.009 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.9 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: 0.008 seconds (Warm-up)
Chain 2: 0.009 seconds (Sampling)
Chain 2: 0.017 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' 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: 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: 0.01 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.015 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.52 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: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000312 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.12 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 / 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: 0.009 seconds (Warm-up)
Chain 1: 0.008 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.00017 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.7 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: 0.007 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' 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: 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: 0.006 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.011 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.42 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: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000241 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.41 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: 0.008 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.011 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000162 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.62 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: 0.007 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.015 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' 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 / 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: 0.004 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.53 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: 0.003 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.6e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.46 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: 0.003 seconds (Warm-up)
Chain 3: 0.001 seconds (Sampling)
Chain 3: 0.004 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 4.8e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.48 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: 0.007 seconds (Warm-up)
Chain 4: 0.004 seconds (Sampling)
Chain 4: 0.011 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.00021 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.1 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: 0.008 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.022 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000182 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.82 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: 0.009 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.017 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3:
Chain 3: Gradient evaluation took 0.000188 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.88 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: 0.008 seconds (Warm-up)
Chain 3: 0.008 seconds (Sampling)
Chain 3: 0.016 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000184 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.84 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: 0.009 seconds (Warm-up)
Chain 4: 0.008 seconds (Sampling)
Chain 4: 0.017 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000102 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.02 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: 0.008 seconds (Warm-up)
Chain 1: 0.009 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' 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: 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: 0.009 seconds (Warm-up)
Chain 2: 0.009 seconds (Sampling)
Chain 2: 0.018 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 9.5e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.95 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: 0.007 seconds (Warm-up)
Chain 3: 0.009 seconds (Sampling)
Chain 3: 0.016 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' 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!
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: 0.007 seconds (Warm-up)
Chain 4: 0.009 seconds (Sampling)
Chain 4: 0.016 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.6 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: 0.005 seconds (Warm-up)
Chain 1: 0.007 seconds (Sampling)
Chain 1: 0.012 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.5 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: 0.005 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000262 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.62 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 / 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: 0.006 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000192 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.92 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: 0.006 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.014 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' 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: 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: 0.002 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.54 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: 0.005 seconds (Warm-up)
Chain 2: 0.007 seconds (Sampling)
Chain 2: 0.012 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000198 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.98 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: 0.007 seconds (Warm-up)
Chain 1: 0.008 seconds (Sampling)
Chain 1: 0.015 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000222 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.22 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: 0.007 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' 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.
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 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.49 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 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000219 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.19 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 / 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: 0.007 seconds (Warm-up)
Chain 1: 0.008 seconds (Sampling)
Chain 1: 0.015 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000174 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.74 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: 0.007 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.015 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 88 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 88 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' 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: 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: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.16 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 / 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 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000178 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.78 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: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000123 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.23 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: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.84 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: 0.005 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.01 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.56 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: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.33 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: 0.002 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.15 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: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000171 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.71 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 / 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: 0.004 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000109 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.09 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 / 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: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
Loading required namespace: coda
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.37 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: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.14 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 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.001 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000179 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.79 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: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
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: 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: 0.005 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 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: 0.002 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.15 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: 0.002 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 1.5e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.15 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: 0.002 seconds (Warm-up)
Chain 3: 0.003 seconds (Sampling)
Chain 3: 0.005 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 1.5e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.15 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: 0.002 seconds (Warm-up)
Chain 4: 0.001 seconds (Sampling)
Chain 4: 0.003 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000131 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.31 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 / 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: 0.005 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.007 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000118 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.18 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: 0.004 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3:
Chain 3: Gradient evaluation took 0.00012 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.2 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: 0.004 seconds (Warm-up)
Chain 3: 0.002 seconds (Sampling)
Chain 3: 0.006 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4:
Chain 4: Gradient evaluation took 0.000107 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.07 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: 0.006 seconds (Warm-up)
Chain 4: 0.005 seconds (Sampling)
Chain 4: 0.011 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' 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 / 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: 0.003 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.47 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 / 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: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.6e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.46 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: 0.004 seconds (Warm-up)
Chain 3: 0.005 seconds (Sampling)
Chain 3: 0.009 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 4.5e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.45 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: 0.004 seconds (Warm-up)
Chain 4: 0.005 seconds (Sampling)
Chain 4: 0.009 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.3 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: 0.002 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.17 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: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000164 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.64 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: 0.003 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000103 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.03 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: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 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 seconds (Sampling)
Chain 1: 0.001 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.15 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 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00013 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.3 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: 0.003 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000104 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.04 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: 0.004 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.28 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: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.16 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 / 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: 0.003 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000133 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.33 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: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000104 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.04 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: 0.003 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 87 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 87 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.1
Check: installed package size
Result: NOTE
installed size is 66.1Mb
sub-directories of 1Mb or more:
libs 65.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-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
Current CRAN status: NOTE: 5, OK: 8
Version: 0.2.5
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘rstantools’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.2.5
Check: installed package size
Result: NOTE
installed size is 88.8Mb
sub-directories of 1Mb or more:
libs 87.7Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.2.5
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